diff --git a/doc/GPL b/doc/GPL deleted file mode 100644 --- a/doc/GPL +++ /dev/null @@ -1,75 +0,0 @@ -GNU GENERAL PUBLIC LICENSE Version 2, June 1991 - -Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. - -Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. - - When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. - - To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. - - For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. - - We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. - - Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. - - Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. - -The precise terms and conditions for copying, distribution and modification follow. - -GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION - - 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". - -Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. - - 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. - -You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. - - 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: - - a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. - - b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. - - c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. - -Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. - -In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. - - 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: - - a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) - -The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. - -If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. - - 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. - - 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. - - 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. - -If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. - -It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. - -This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. - - 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. - -Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. - - 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. - -NO WARRANTY - - 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - - 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. - -END OF TERMS AND CONDITIONS diff --git a/doc/gpl3.txt b/doc/gpl3.txt new file mode 100644 --- /dev/null +++ b/doc/gpl3.txt @@ -0,0 +1,243 @@ +GNU GENERAL PUBLIC LICENSE +Version 3, 29 June 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. + +Preamble + +The GNU General Public License is a free, copyleft license for software and other kinds of works. + + The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. + + When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions. + + Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free. + +The precise terms and conditions for copying, distribution and modification follow. + +TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this License. Each licensee is addressed as "you". "Licensees" and "recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a "modified version" of the earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based on the Program. + + To "propagate" a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work for making modifications to it. "Object code" means any non-source form of a work. + + A "Standard Interface" means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A "Major Component", in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work. + + The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source. + +The Corresponding Source for a work in source code form is that same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures. + + When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to "keep intact all notices". + + c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so. + + A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an "aggregate" if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways: + + a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. + + If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM). + + The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or authors of the material; or + + e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. + + All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). + + However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. + + Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. + + If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. + + A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. + + Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. + + Copyright (C) + + This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: + + Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . + + The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . diff --git a/doc/installation.pdf b/doc/installation.pdf new file mode 100644 --- /dev/null +++ b/doc/installation.pdf @@ -0,0 +1,436 @@ +%PDF-1.3 +%“Œ‹ž ReportLab Generated PDF document http://www.reportlab.com +% 'BasicFonts': class PDFDictionary +1 0 obj +% The standard fonts dictionary +<< /F1 2 0 R + /F2 3 0 R + /F3 5 0 R >> +endobj +% 'F1': class PDFType1Font +2 0 obj +% Font Helvetica +<< /BaseFont /Helvetica + /Encoding /WinAnsiEncoding + /Name /F1 + /Subtype /Type1 + /Type /Font >> +endobj +% 'F2': class PDFType1Font +3 0 obj +% Font Helvetica-Bold +<< /BaseFont /Helvetica-Bold + /Encoding /WinAnsiEncoding + /Name /F2 + /Subtype /Type1 + /Type /Font >> +endobj +% 'Annot.NUMBER1': class PDFDictionary +4 0 obj +<< /A << /S /URI + /Type /Action + /URI (http://qt.nokia.com/downloads/downloads#lgpl/) >> + /Border [ 0 + 0 + 0 ] + /Rect [ 332.4149 + 657.5936 + 411.372 + 669.5936 ] + /Subtype /Link + /Type /Annot >> +endobj +% 'F3': class PDFType1Font +5 0 obj +% Font Courier +<< /BaseFont /Courier + /Encoding /WinAnsiEncoding + /Name /F3 + /Subtype /Type1 + /Type /Font >> +endobj +% 'Page1': class PDFPage +6 0 obj +% Page dictionary +<< /Annots [ 4 0 R ] + /Contents 17 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 16 0 R + /Resources << /Font 1 0 R + /ProcSet [ /PDF + /Text + /ImageB + /ImageC + /ImageI ] >> + /Rotate 0 + /Trans << >> + /Type /Page >> +endobj +% 'Page2': class PDFPage +7 0 obj +% Page dictionary +<< /Contents 18 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 16 0 R + /Resources << /Font 1 0 R + /ProcSet [ /PDF + /Text + /ImageB + /ImageC + /ImageI ] >> + /Rotate 0 + /Trans << >> + /Type /Page >> +endobj +% 'R8': class PDFCatalog +8 0 obj +% Document Root +<< /Outlines 10 0 R + /PageLabels 19 0 R + /PageMode /UseNone + /Pages 16 0 R + /Type /Catalog >> +endobj +% 'R9': class PDFInfo +9 0 obj +<< /Author () + /CreationDate (D:20100622164642-01'00') + /Keywords () + /Producer (ReportLab http://www.reportlab.com) + /Subject (\(unspecified\)) + /Title (Installation Instructions) >> +endobj +% 'R10': class PDFOutlines +10 0 obj +<< /Count 5 + /First 11 0 R + /Last 15 0 R + /Type /Outlines >> +endobj +% 'Outline.0': class OutlineEntryObject +11 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 717.0236 + 0 ] + /Next 12 0 R + /Parent 10 0 R + /Title (Requirements) >> +endobj +% 'Outline.1': class OutlineEntryObject +12 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 618.0236 + 0 ] + /Next 13 0 R + /Parent 10 0 R + /Prev 11 0 R + /Title (All Platforms) >> +endobj +% 'Outline.2': class OutlineEntryObject +13 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 507.0236 + 0 ] + /Next 14 0 R + /Parent 10 0 R + /Prev 12 0 R + /Title (Linux) >> +endobj +% 'Outline.3': class OutlineEntryObject +14 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 260.4236 + 0 ] + /Next 15 0 R + /Parent 10 0 R + /Prev 13 0 R + /Title (Windows) >> +endobj +% 'Outline.4': class OutlineEntryObject +15 0 obj +<< /Dest [ 7 0 R + /XYZ + 62.69291 + 753.0236 + 0 ] + /Parent 10 0 R + /Prev 14 0 R + /Title (MacOS) >> +endobj +% 'R16': class PDFPages +16 0 obj +% page tree +<< /Count 2 + /Kids [ 6 0 R + 7 0 R ] + /Type /Pages >> +endobj +% 'R17': class PDFStream +17 0 obj +% page stream +<< /Length 5681 >> +stream +1 0 0 1 0 0 cm BT /F1 12 Tf 14.4 TL ET +q +1 0 0 1 62.69291 729.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 9.64 Tm /F2 20 Tf 24 TL 122.1449 0 Td (Installation Instructions) Tj T* -122.1449 0 Td ET +Q +Q +q +1 0 0 1 62.69291 696.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Requirements) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 630.0236 cm +q +BT 1 0 0 1 0 52.82 Tm .076098 Tw 12 TL /F1 10 Tf 0 0 0 rg (The Virtual Leaf is written with the QT Cross platform application and UI framework, and can run on Linux,) Tj T* 0 Tw 1.85686 Tw (Apple Macintosh and Windows machines. To compile the Virtual Leaf you will need to install the QT) Tj T* 0 Tw .573555 Tw (software development kit which you can download from the ) Tj 0 0 .501961 rg (QT download site) Tj 0 0 0 rg (. Whether installed globally) Tj T* 0 Tw .669986 Tw (by a system administrator our locally in your own user space, make sure the QT bin directory containing) Tj T* 0 Tw (qmake is in your execution path.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 597.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (All Platforms) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 519.0236 cm +q +BT 1 0 0 1 0 64.82 Tm 4.093984 Tw 12 TL /F1 10 Tf 0 0 0 rg (Compilation is effected with make, either the native ) Tj /F3 10 Tf (make ) Tj /F1 10 Tf (on UNIX and MAC systems or the) Tj T* 0 Tw .268735 Tw /F3 10 Tf (mingw32-make ) Tj /F1 10 Tf (distributed with the windows version of QT. In the Virtual Leaf ) Tj /F3 10 Tf (src ) Tj /F1 10 Tf (directory you will find) Tj T* 0 Tw 1.243516 Tw (a ) Tj /F3 10 Tf (Makefile) Tj /F1 10 Tf (, the root of a hierarchy of makefiles, that will guide the compilation and installation of the) Tj T* 0 Tw 4.280814 Tw (VirtualLeaf executable, its default plugins and the tutorial examples. To facilitate cross platform) Tj T* 0 Tw .276651 Tw (compatibility, the makefiles expect an environment variable named ) Tj /F3 10 Tf (MAKE ) Tj /F1 10 Tf (to name the make utility to use.) Tj T* 0 Tw (The fallback default is 'make.' Platform specific instructions follow.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 486.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Linux) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 468.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Prepend the QT bin directory to your path, for example:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 434.8236 cm +q +q +1 0 0 1 0 0 cm +q +1 0 0 1 6.6 6.6 cm +q +.662745 .662745 .662745 RG +.5 w +.960784 .960784 .862745 rg +n -6 -6 468.6898 24 re B* +Q +q +BT 1 0 0 1 0 5.71 Tm 12 TL /F3 10 Tf 0 0 0 rg (>) Tj ( PATH=/opt/QT/qt/bin:$PATH) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 402.8236 cm +q +BT 1 0 0 1 0 16.82 Tm .87686 Tw 12 TL /F1 10 Tf 0 0 0 rg (If you wish to use some other make utility than make, instantiate an environment variable named ) Tj /F3 10 Tf (MAKE) Tj /F1 10 Tf (,) Tj T* 0 Tw (for example:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 369.6236 cm +q +q +1 0 0 1 0 0 cm +q +1 0 0 1 6.6 6.6 cm +q +.662745 .662745 .662745 RG +.5 w +.960784 .960784 .862745 rg +n -6 -6 468.6898 24 re B* +Q +q +BT 1 0 0 1 0 5.71 Tm 12 TL /F3 10 Tf 0 0 0 rg (>) Tj ( export MAKE=gmake.) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 349.6236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Go to the ) Tj /F3 10 Tf (src ) Tj /F1 10 Tf (directory and invoke make, for example:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 304.4236 cm +q +q +1 0 0 1 0 0 cm +q +1 0 0 1 6.6 6.6 cm +q +.662745 .662745 .662745 RG +.5 w +.960784 .960784 .862745 rg +n -6 -6 468.6898 36 re B* +Q +q +BT 1 0 0 1 0 17.71 Tm 12 TL /F3 10 Tf 0 0 0 rg (>) Tj ( cd /home/michael/VirtualLeaf/v1.0/src) Tj T* (>) Tj ( make) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 272.4236 cm +q +BT 1 0 0 1 0 16.82 Tm 6.059213 Tw 12 TL /F1 10 Tf 0 0 0 rg (When complete, you will find the ) Tj /F3 10 Tf (VirtualLeaf ) Tj /F1 10 Tf (binary in ) Tj /F3 10 Tf (v1.0/bin ) Tj /F1 10 Tf (and the plugins in) Tj T* 0 Tw /F3 10 Tf (v1.0/bin/models) Tj /F1 10 Tf (.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 239.4236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Windows) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 185.4236 cm +q +BT 1 0 0 1 0 40.82 Tm 2.017984 Tw 12 TL /F1 10 Tf 0 0 0 rg (For convenience sake the libiconv, libxml2 and libz header files and libraries are distributed with the) Tj T* 0 Tw .669986 Tw (Virtual Leaf code, and Virtual Leaf will compile correctly with them. If, however, you wish to compile with) Tj T* 0 Tw 3.246136 Tw (other versions of these libraries, you will need to reassign the ) Tj /F3 10 Tf (LIBZML2DIR) Tj /F1 10 Tf (, ) Tj /F3 10 Tf (LIBICONVDIR ) Tj /F1 10 Tf (and) Tj T* 0 Tw /F3 10 Tf (LIBZDIR ) Tj /F1 10 Tf (variables in all the project files.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 143.4236 cm +q +0 0 0 rg +BT 1 0 0 1 0 28.82 Tm /F1 10 Tf 12 TL .878876 Tw (After installing QT you should be able to invoke a QT command window from the start menu. This shell) Tj T* 0 Tw .456412 Tw (automatically includes the necessary QT folder in your execution PATH. Within this command window go) Tj T* 0 Tw (to the Virtual Leaf's src directory. The) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 113.4236 cm +q +0 0 0 rg +BT 1 0 0 1 0 16.82 Tm /F1 10 Tf 12 TL 1.927765 Tw (In the start menu, right click on My Computer and choose properties from the drop down list. In the) Tj T* 0 Tw (advanced tab click on environment variables. Append the QT) Tj T* ET +Q +Q +q +1 0 0 1 56.69291 773.1969 cm +q +BT 1 0 0 1 0 4.82 Tm 160.0749 0 Td 12 TL /F1 10 Tf 0 0 0 rg (Installation Instructions - 2010-06-22) Tj T* -160.0749 0 Td ET +Q +Q +q +1 0 0 1 56.69291 56.69291 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 238.1649 0 Td (1) Tj T* -238.1649 0 Td ET +Q +Q + +endstream + +endobj +% 'R18': class PDFStream +18 0 obj +% page stream +<< /Length 452 >> +stream +1 0 0 1 0 0 cm BT /F1 12 Tf 14.4 TL ET +q +1 0 0 1 62.69291 732.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (MacOS) Tj T* ET +Q +Q +q +1 0 0 1 56.69291 773.1969 cm +q +BT 1 0 0 1 0 4.82 Tm 160.0749 0 Td 12 TL /F1 10 Tf 0 0 0 rg (Installation Instructions - 2010-06-22) Tj T* -160.0749 0 Td ET +Q +Q +q +1 0 0 1 56.69291 56.69291 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 238.1649 0 Td (2) Tj T* -238.1649 0 Td ET +Q +Q + +endstream + +endobj +% 'R19': class PDFPageLabels +19 0 obj +% Document Root +<< /Nums [ 0 + 20 0 R + 1 + 21 0 R ] >> +endobj +% 'R20': class PDFPageLabel +20 0 obj +% None +<< /S /D + /St 1 >> +endobj +% 'R21': class PDFPageLabel +21 0 obj +% None +<< /S /D + /St 2 >> +endobj +xref +0 22 +0000000000 65535 f +0000000113 00000 n +0000000233 00000 n +0000000398 00000 n +0000000585 00000 n +0000000835 00000 n +0000000994 00000 n +0000001293 00000 n +0000001572 00000 n +0000001729 00000 n +0000001965 00000 n +0000002090 00000 n +0000002262 00000 n +0000002450 00000 n +0000002630 00000 n +0000002812 00000 n +0000002961 00000 n +0000003076 00000 n +0000008858 00000 n +0000009414 00000 n +0000009520 00000 n +0000009597 00000 n +trailer +<< /ID + % ReportLab generated PDF document -- digest (http://www.reportlab.com) + [(>z\325b\242\314%\325\301\315\254\356\270\004a\252) (>z\325b\242\314%\325\301\315\254\356\270\004a\252)] + + /Info 9 0 R + /Root 8 0 R + /Size 22 >> +startxref +9644 +%%EOF diff --git a/doc/installation.rst b/doc/installation.rst new file mode 100644 --- /dev/null +++ b/doc/installation.rst @@ -0,0 +1,88 @@ +.. $Id$ + +.. |date| date:: +.. |time| date:: %H:%M + +.. header:: + ###Title### - |date| + +.. footer:: + ###Page### + + +Installation Instructions +========================= + +Requirements +------------ + +The Virtual Leaf is written with the QT Cross platform application and +UI framework, and can run on Linux, Apple Macintosh and Windows +machines. To compile the Virtual Leaf you will need to install the QT +software development kit which you can download from the `QT download +site `_. Whether +installed globally by a system administrator our locally in your own +user space, make sure the QT bin directory containing qmake is in your +execution path. + + +All Platforms +------------- + +Compilation is effected with make, either the native ``make`` on UNIX +and MAC systems or the ``mingw32-make`` distributed with the windows +version of QT. In the Virtual Leaf ``src`` directory you will find a +``Makefile``, the root of a hierarchy of makefiles, that will guide +the compilation and installation of the VirtualLeaf executable, its +default plugins and the tutorial examples. To facilitate cross +platform compatibility, the makefiles expect an environment variable +named ``MAKE`` to name the make utility to use. The fallback default +is 'make.' Platform specific instructions follow. + + +Linux +----- + +Prepend the QT bin directory to your path, for example:: + + > PATH=/opt/QT/qt/bin:$PATH + +If you wish to use some other make utility than make, instantiate an +environment variable named ``MAKE``, for example:: + + > export MAKE=gmake. + +Go to the ``src`` directory and invoke make, for example:: + + > cd /home/michael/VirtualLeaf/v1.0/src + > make + +When complete, you will find the ``VirtualLeaf`` binary in +``v1.0/bin`` and the plugins in ``v1.0/bin/models``. + + +Windows +------- + +For convenience sake the libiconv, libxml2 and libz header files and +libraries are distributed with the Virtual Leaf code, and Virtual Leaf +will compile correctly with them. If, however, you wish to compile +with other versions of these libraries, you will need to reassign the +``LIBZML2DIR``, ``LIBICONVDIR`` and ``LIBZDIR`` variables in all the +project files. + +After installing QT you should be able to invoke a QT command window +from the start menu. This shell automatically includes the necessary +QT folder in your execution PATH. Within this command window, go to the +Virtual Leaf's src directory, + +In the start menu, right click on My Computer and choose properties +from the drop down list. In the advanced tab click on environment +variables. Append the QT + + +MacOS +----- + + + diff --git a/src/ChangeLog b/src/ChangeLog --- a/src/ChangeLog +++ b/src/ChangeLog @@ -1,3 +1,13 @@ +2010-06-22 + + * Makefile (tutorials): Add tutorials target. + +2010-06-21 + + * parameter.cpp: Added particular reassignment of datadir. + + * canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists. + 2010-06-18 * canvas.cpp (gpl): Added gpl slot to display GPL license. diff --git a/src/Makefile b/src/Makefile --- a/src/Makefile +++ b/src/Makefile @@ -2,10 +2,15 @@ QMAKE = $(HOME)/Trolltech/Qt-4.4.1/bin/qmake -# Set $(MAKE) to the name of the make command on your machine, e.g. 'make' on Linux and 'mingw32-make' on windows. -MAKE = make # mingw32-make +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. -all: VirtualLeaf libplugin plugins +ifeq ($(MAKE),) + MAKE=make +endif + +all: VirtualLeaf libplugin plugins tutorials VirtualLeaf: Makefile.VirtualLeaf $(MAKE) -f Makefile.VirtualLeaf @@ -22,13 +27,21 @@ Makefile.libplugin: libplugin.pro plugins: $(MAKE) -C build_models +tutorials: + $(MAKE) -C build_models + $(MAKE) -C TutorialCode + clean: $(MAKE) -f Makefile.libplugin clean $(MAKE) -f Makefile.VirtualLeaf clean $(MAKE) -C build_models clean + $(MAKE) -C TutorialCode clean ifeq ($(MAKE),make) touch VirtualLeaf.pro touch libplugin.pro +else + copy /b VirtualLeaf.pro +,, + copy /b libplugin.pro +,, endif #finis diff --git a/src/TutorialCode/Makefile b/src/TutorialCode/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Makefile @@ -0,0 +1,51 @@ +# $Id$ + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial_0 tutorial_1A tutorial_1B tutorial_1C tutorial_1D tutorial_2 tutorial_3 tutorial_4 tutorial_5 + +tutorial_0: + $(MAKE) -C Tutorial0 + +tutorial_1A: + $(MAKE) -C Tutorial1A + +tutorial_1B: + $(MAKE) -C Tutorial1B + +tutorial_1C: + $(MAKE) -C Tutorial1C + +tutorial_1D: + $(MAKE) -C Tutorial1D + +tutorial_2: + $(MAKE) -C Tutorial2 + +tutorial_3: + $(MAKE) -C Tutorial3 + +tutorial_4: + $(MAKE) -C Tutorial4 + +tutorial_5: + $(MAKE) -C Tutorial5 + +clean: + $(MAKE) -C Tutorial0 clean + $(MAKE) -C Tutorial1A clean + $(MAKE) -C Tutorial1B clean + $(MAKE) -C Tutorial1C clean + $(MAKE) -C Tutorial1D clean + $(MAKE) -C Tutorial2 clean + $(MAKE) -C Tutorial3 clean + $(MAKE) -C Tutorial4 clean + $(MAKE) -C Tutorial5 clean + +# finis diff --git a/src/TutorialCode/Tutorial0/Makefile b/src/TutorialCode/Tutorial0/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial0/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial0 + +tutorial0: Makefile.tutorial0 + $(MAKE) -f Makefile.tutorial0 + +Makefile.tutorial0: tutorial0.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial0 clean +ifeq ($(MAKE),make) + touch tutorial0.pro +else + copy /b tutorial0.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial0/mymodel.cpp b/src/TutorialCode/Tutorial0/tutorial0.cpp rename from src/TutorialCode/Tutorial0/mymodel.cpp rename to src/TutorialCode/Tutorial0/tutorial0.cpp --- a/src/TutorialCode/Tutorial0/mymodel.cpp +++ b/src/TutorialCode/Tutorial0/tutorial0.cpp @@ -28,42 +28,42 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial0.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial0::ModelID(void) { // specify the name of your model here return QString( "My first model in VirtualLeaf" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial0::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial0::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial0::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial0::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial0::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial0::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial0::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial0, Tutorial0) diff --git a/src/TutorialCode/Tutorial0/mymodel.h b/src/TutorialCode/Tutorial0/tutorial0.h rename from src/TutorialCode/Tutorial0/mymodel.h rename to src/TutorialCode/Tutorial0/tutorial0.h --- a/src/TutorialCode/Tutorial0/mymodel.h +++ b/src/TutorialCode/Tutorial0/tutorial0.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial0 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial0/mymodel.pro b/src/TutorialCode/Tutorial0/tutorial0.pro rename from src/TutorialCode/Tutorial0/mymodel.pro rename to src/TutorialCode/Tutorial0/tutorial0.pro --- a/src/TutorialCode/Tutorial0/mymodel.pro +++ b/src/TutorialCode/Tutorial0/tutorial0.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial0 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1/mymodel.cpp b/src/TutorialCode/Tutorial1/mymodel.cpp deleted file mode 100644 --- a/src/TutorialCode/Tutorial1/mymodel.cpp +++ /dev/null @@ -1,70 +0,0 @@ -/* - * - * This file is part of the Virtual Leaf. - * - * The Virtual Leaf is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * The Virtual Leaf is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with the Virtual Leaf. If not, see . - * - * Copyright 2010 Roeland Merks. - * - */ - -#include -#include - -#include "simplugin.h" - -#include "parameter.h" - -#include "wallbase.h" -#include "cellbase.h" -#include "mymodel.h" - -static const std::string _module_id("$Id$"); - -QString MyModel::ModelID(void) { - // specify the name of your model here - return QString( "Cell growth" ); -} - -// return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } - -// To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { - // rules to be executed after cell division go here - // (e.g., cell differentiation rules) -} - -void MyModel::SetCellColor(CellBase *c, QColor *color) { - // add cell coloring rules here - -} - -void MyModel::CellHouseKeeping(CellBase *c) { - // add cell behavioral rules here - c->EnlargeTargetArea(par->cell_expansion_rate); -} - -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { - // add biochemical transport rules here -} -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { - // add biochemical networks for reactions occuring at walls here -} -void MyModel::CellDynamics(CellBase *c, double *dchem) { - // add biochemical networks for intracellular reactions here -} - - -Q_EXPORT_PLUGIN2(mymodel, MyModel) diff --git a/src/TutorialCode/Tutorial1/mymodel.h b/src/TutorialCode/Tutorial1/mymodel.h deleted file mode 100644 --- a/src/TutorialCode/Tutorial1/mymodel.h +++ /dev/null @@ -1,60 +0,0 @@ -/* - * $Id$ - * - * This file is part of the Virtual Leaf. - * - * The Virtual Leaf is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * The Virtual Leaf is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with the Virtual Leaf. If not, see . - * - * Copyright 2010 Roeland Merks. - * - */ - - -#include -#include -#include -#include "simplugin.h" - - -class MyModel : public QObject, SimPluginInterface { - Q_OBJECT - Q_INTERFACES(SimPluginInterface); - -public: - virtual QString ModelID(void); - - // Executed after the cellular mechanics steps have equillibrized - virtual void CellHouseKeeping (CellBase *c); - // Differential equations describing transport of chemicals from cell to cell - virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2); - - // Differential equations describing chemical reactions taking place at or near the cell walls - // (e.g. PIN accumulation) - virtual void WallDynamics(Wall *w, double *dw1, double *dw2); - - // Differential equations describing chemical reactions inside the cells - virtual void CellDynamics(CellBase *c, double *dchem); - - // to be executed after a cell division - virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2); - - // to be executed for coloring a cell - virtual void SetCellColor(CellBase *c, QColor *color); - // return number of chemicals - virtual int NChem(void); -}; - - - - diff --git a/src/TutorialCode/Tutorial1/mymodel.pro b/src/TutorialCode/Tutorial1/mymodel.pro deleted file mode 100644 --- a/src/TutorialCode/Tutorial1/mymodel.pro +++ /dev/null @@ -1,61 +0,0 @@ -# -# $Id$ -# -# This file is part of the Virtual Leaf. -# -# The Virtual Leaf is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# The Virtual Leaf is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with the Virtual Leaf. If not, see . -# -# Copyright 2010 Roeland Merks. -# - - -TARGET = mymodel -VLEAFHOME = ../../.. - -CONFIG += release -CONFIG -= debug -CONFIG += plugin - -BINDIR = $${VLEAFHOME}/bin -LIBDIR = $${VLEAFHOME}/lib -INCDIR = $${VLEAFHOME}/src -DEFINES = QTGRAPHICS # VLEAFPLUGIN -DESTDIR = $${BINDIR}/models -HEADERS = $${TARGET}.h -INCLUDEPATH += $${INCDIR} - -QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR} -QMAKE_CXXFLAGS_DEBUG += -g3 -QMAKE_CXXFLAGS_DEBUG += -DQDEBUG -QT += qt3support -SOURCES = $${TARGET}.cpp -TEMPLATE = lib - -unix { - LIBS += -L$${LIBDIR} -lvleaf - QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2 - QMAKE_LFLAGS += -fPIC -} - -win32 { - LIBXML2DIR = C:\libxml2 - LIBICONVDIR = C:\libiconv - LIBZDIR = C:\libz - LIBS += -L$${LIBDIR} -lvleaf - QMAKE_CXXFLAGS += -DLIBXML_STATIC - QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include - -} - -# finish diff --git a/src/TutorialCode/Tutorial1A/Makefile b/src/TutorialCode/Tutorial1A/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1A/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1A + +tutorial1A: Makefile.tutorial1A + $(MAKE) -f Makefile.tutorial1A + +Makefile.tutorial1A: tutorial1A.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1A clean +ifeq ($(MAKE),make) + touch tutorial1A.pro +else + copy /b tutorial1A.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1A/mymodel.cpp b/src/TutorialCode/Tutorial1A/tutorial1A.cpp rename from src/TutorialCode/Tutorial1A/mymodel.cpp rename to src/TutorialCode/Tutorial1A/tutorial1A.cpp --- a/src/TutorialCode/Tutorial1A/mymodel.cpp +++ b/src/TutorialCode/Tutorial1A/tutorial1A.cpp @@ -28,43 +28,43 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1A.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1A::ModelID(void) { // specify the name of your model here - return QString( "Cell growth" ); + return QString( "1A: Cell growth" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1A::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1A::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1A::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1A::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1A::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1A::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1A::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1A, Tutorial1A) diff --git a/src/TutorialCode/Tutorial1A/mymodel.h b/src/TutorialCode/Tutorial1A/tutorial1A.h rename from src/TutorialCode/Tutorial1A/mymodel.h rename to src/TutorialCode/Tutorial1A/tutorial1A.h --- a/src/TutorialCode/Tutorial1A/mymodel.h +++ b/src/TutorialCode/Tutorial1A/tutorial1A.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1A : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1A/mymodel.pro b/src/TutorialCode/Tutorial1A/tutorial1A.pro rename from src/TutorialCode/Tutorial1A/mymodel.pro rename to src/TutorialCode/Tutorial1A/tutorial1A.pro --- a/src/TutorialCode/Tutorial1A/mymodel.pro +++ b/src/TutorialCode/Tutorial1A/tutorial1A.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1A VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1B/Makefile b/src/TutorialCode/Tutorial1B/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1B/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1B + +tutorial1B: Makefile.tutorial1B + $(MAKE) -f Makefile.tutorial1B + +Makefile.tutorial1B: tutorial1B.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1B clean +ifeq ($(MAKE),make) + touch tutorial1B.pro +else + copy /b tutorial1B.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1B/mymodel.cpp b/src/TutorialCode/Tutorial1B/tutorial1B.cpp rename from src/TutorialCode/Tutorial1B/mymodel.cpp rename to src/TutorialCode/Tutorial1B/tutorial1B.cpp --- a/src/TutorialCode/Tutorial1B/mymodel.cpp +++ b/src/TutorialCode/Tutorial1B/tutorial1B.cpp @@ -28,30 +28,30 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1B.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1B::ModelID(void) { // specify the name of your model here - return QString( "Cell growth and cell division" ); + return QString( "1B: Cell growth and cell division" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1B::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1B::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1B::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1B::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { @@ -59,15 +59,15 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1B::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1B::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1B::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1B, Tutorial1B) diff --git a/src/TutorialCode/Tutorial1B/mymodel.h b/src/TutorialCode/Tutorial1B/tutorial1B.h rename from src/TutorialCode/Tutorial1B/mymodel.h rename to src/TutorialCode/Tutorial1B/tutorial1B.h --- a/src/TutorialCode/Tutorial1B/mymodel.h +++ b/src/TutorialCode/Tutorial1B/tutorial1B.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1B : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1B/mymodel.pro b/src/TutorialCode/Tutorial1B/tutorial1B.pro rename from src/TutorialCode/Tutorial1B/mymodel.pro rename to src/TutorialCode/Tutorial1B/tutorial1B.pro --- a/src/TutorialCode/Tutorial1B/mymodel.pro +++ b/src/TutorialCode/Tutorial1B/tutorial1B.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1B VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1C/Makefile b/src/TutorialCode/Tutorial1C/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1C/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1C + +tutorial1C: Makefile.tutorial1C + $(MAKE) -f Makefile.tutorial1C + +Makefile.tutorial1C: tutorial1C.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1C clean +ifeq ($(MAKE),make) + touch tutorial1C.pro +else + copy /b tutorial1C.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1C/mymodel.cpp b/src/TutorialCode/Tutorial1C/tutorial1C.cpp rename from src/TutorialCode/Tutorial1C/mymodel.cpp rename to src/TutorialCode/Tutorial1C/tutorial1C.cpp --- a/src/TutorialCode/Tutorial1C/mymodel.cpp +++ b/src/TutorialCode/Tutorial1C/tutorial1C.cpp @@ -28,29 +28,29 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1C.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1C::ModelID(void) { // specify the name of your model here - return QString( "Cell growth and cell division" ); + return QString( "1C: Vertical cell division" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1C::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1C::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1C::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1C::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { @@ -58,15 +58,15 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1C::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1C::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1C::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1C, Tutorial1C) diff --git a/src/TutorialCode/Tutorial1C/mymodel.h b/src/TutorialCode/Tutorial1C/tutorial1C.h rename from src/TutorialCode/Tutorial1C/mymodel.h rename to src/TutorialCode/Tutorial1C/tutorial1C.h --- a/src/TutorialCode/Tutorial1C/mymodel.h +++ b/src/TutorialCode/Tutorial1C/tutorial1C.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1C : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1C/mymodel.pro b/src/TutorialCode/Tutorial1C/tutorial1C.pro rename from src/TutorialCode/Tutorial1C/mymodel.pro rename to src/TutorialCode/Tutorial1C/tutorial1C.pro --- a/src/TutorialCode/Tutorial1C/mymodel.pro +++ b/src/TutorialCode/Tutorial1C/tutorial1C.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1C VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial1D/Makefile b/src/TutorialCode/Tutorial1D/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial1D/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial1D + +tutorial1D: Makefile.tutorial1D + $(MAKE) -f Makefile.tutorial1D + +Makefile.tutorial1D: tutorial1D.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial1D clean +ifeq ($(MAKE),make) + touch tutorial1D.pro +else + copy /b tutorial1D.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial1D/mymodel.cpp b/src/TutorialCode/Tutorial1D/tutorial1D.cpp rename from src/TutorialCode/Tutorial1D/mymodel.cpp rename to src/TutorialCode/Tutorial1D/tutorial1D.cpp --- a/src/TutorialCode/Tutorial1D/mymodel.cpp +++ b/src/TutorialCode/Tutorial1D/tutorial1D.cpp @@ -28,32 +28,32 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial1D.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial1D::ModelID(void) { // specify the name of your model here - return QString( "Growth, division, coloring" ); + return QString( "1D: Growth, division, coloring" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 0; } +int Tutorial1D::NChem(void) { return 0; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial1D::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial1D::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here if (c->Area()/c->BaseArea()>1.8) { color->setNamedColor("blue"); } else { color->setNamedColor("green"); } } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial1D::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(par->cell_expansion_rate); if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { @@ -61,15 +61,15 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial1D::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial1D::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial1D::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial1D, Tutorial1D) diff --git a/src/TutorialCode/Tutorial1D/mymodel.h b/src/TutorialCode/Tutorial1D/tutorial1D.h rename from src/TutorialCode/Tutorial1D/mymodel.h rename to src/TutorialCode/Tutorial1D/tutorial1D.h --- a/src/TutorialCode/Tutorial1D/mymodel.h +++ b/src/TutorialCode/Tutorial1D/tutorial1D.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial1D : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial1D/mymodel.pro b/src/TutorialCode/Tutorial1D/tutorial1D.pro rename from src/TutorialCode/Tutorial1D/mymodel.pro rename to src/TutorialCode/Tutorial1D/tutorial1D.pro --- a/src/TutorialCode/Tutorial1D/mymodel.pro +++ b/src/TutorialCode/Tutorial1D/tutorial1D.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial1D VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial2/Makefile b/src/TutorialCode/Tutorial2/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial2/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial2 + +tutorial2: Makefile.tutorial2 + $(MAKE) -f Makefile.tutorial2 + +Makefile.tutorial2: tutorial2.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial2 clean +ifeq ($(MAKE),make) + touch tutorial2.pro +else + copy /b tutorial2.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial2/mymodel.cpp b/src/TutorialCode/Tutorial2/tutorial2.cpp rename from src/TutorialCode/Tutorial2/mymodel.cpp rename to src/TutorialCode/Tutorial2/tutorial2.cpp --- a/src/TutorialCode/Tutorial2/mymodel.cpp +++ b/src/TutorialCode/Tutorial2/tutorial2.cpp @@ -28,20 +28,20 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial2.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial2::ModelID(void) { // specify the name of your model here - return QString( "Growth hormones" ); + return QString( "2: Growth hormones" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 1; } +int Tutorial2::NChem(void) { return 1; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial2::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) @@ -78,7 +78,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial2::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // white: high concentration of growth hormone, black low concentration @@ -86,7 +86,7 @@ void MyModel::SetCellColor(CellBase *c, color->setRgbF(val, val, val); } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial2::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here if (CellBase::NCells()==1) // first cell expands unconditionally @@ -99,17 +99,17 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial2::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; dchem_c2[0]-=phi; } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial2::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial2::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here if (c->CellType()==1) { dchem[0] = par->leaf_tip_source; @@ -117,4 +117,4 @@ void MyModel::CellDynamics(CellBase *c, } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial2, Tutorial2) diff --git a/src/TutorialCode/Tutorial2/mymodel.h b/src/TutorialCode/Tutorial2/tutorial2.h rename from src/TutorialCode/Tutorial2/mymodel.h rename to src/TutorialCode/Tutorial2/tutorial2.h --- a/src/TutorialCode/Tutorial2/mymodel.h +++ b/src/TutorialCode/Tutorial2/tutorial2.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial2 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial2/mymodel.pro b/src/TutorialCode/Tutorial2/tutorial2.pro rename from src/TutorialCode/Tutorial2/mymodel.pro rename to src/TutorialCode/Tutorial2/tutorial2.pro --- a/src/TutorialCode/Tutorial2/mymodel.pro +++ b/src/TutorialCode/Tutorial2/tutorial2.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial2 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial3/Makefile b/src/TutorialCode/Tutorial3/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial3/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial3 + +tutorial3: Makefile.tutorial3 + $(MAKE) -f Makefile.tutorial3 + +Makefile.tutorial3: tutorial3.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial3 clean +ifeq ($(MAKE),make) + touch tutorial3.pro +else + copy /b tutorial3.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial3/mymodel.cpp b/src/TutorialCode/Tutorial3/tutorial3.cpp rename from src/TutorialCode/Tutorial3/mymodel.cpp rename to src/TutorialCode/Tutorial3/tutorial3.cpp --- a/src/TutorialCode/Tutorial3/mymodel.cpp +++ b/src/TutorialCode/Tutorial3/tutorial3.cpp @@ -28,20 +28,20 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial3.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial3::ModelID(void) { // specify the name of your model here - return QString( "Growth hormones" ); + return QString( "3: Directed phytohormone transport" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } +int Tutorial3::NChem(void) { return 2; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial3::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // rules to be executed after cell division go here // (e.g., cell differentiation rules) @@ -78,7 +78,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial3::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // white: high concentration of growth hormone, black low concentration @@ -86,7 +86,7 @@ void MyModel::SetCellColor(CellBase *c, color->setRgbF(val, val, val); } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial3::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here if (CellBase::NCells()==1) // first cell expands unconditionally @@ -99,7 +99,7 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial3::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; @@ -119,10 +119,10 @@ void MyModel::CelltoCellTransport(Wall * } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial3::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial3::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here if (c->CellType()==1) { dchem[0] = par->leaf_tip_source; @@ -130,4 +130,4 @@ void MyModel::CellDynamics(CellBase *c, } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial3, Tutorial3) diff --git a/src/TutorialCode/Tutorial3/mymodel.h b/src/TutorialCode/Tutorial3/tutorial3.h rename from src/TutorialCode/Tutorial3/mymodel.h rename to src/TutorialCode/Tutorial3/tutorial3.h --- a/src/TutorialCode/Tutorial3/mymodel.h +++ b/src/TutorialCode/Tutorial3/tutorial3.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial3 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial3/mymodel.pro b/src/TutorialCode/Tutorial3/tutorial3.pro rename from src/TutorialCode/Tutorial3/mymodel.pro rename to src/TutorialCode/Tutorial3/tutorial3.pro --- a/src/TutorialCode/Tutorial3/mymodel.pro +++ b/src/TutorialCode/Tutorial3/tutorial3.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial3 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial4/Makefile b/src/TutorialCode/Tutorial4/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial4/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial4 + +tutorial4: Makefile.tutorial4 + $(MAKE) -f Makefile.tutorial4 + +Makefile.tutorial4: tutorial4.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial4 clean +ifeq ($(MAKE),make) + touch tutorial4.pro +else + copy /b tutorial4.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial4/mymodel b/src/TutorialCode/Tutorial4/mymodel deleted file mode 100644 --- a/src/TutorialCode/Tutorial4/mymodel +++ /dev/null @@ -1,147 +0,0 @@ -/* - * - * This file is part of the Virtual Leaf. - * - * The Virtual Leaf is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * The Virtual Leaf is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with the Virtual Leaf. If not, see . - * - * Copyright 2010 Roeland Merks. - * - */ - -#include -#include -#include -#include "simplugin.h" - -#include "parameter.h" - -#include "wallbase.h" -#include "cellbase.h" -#include "mymodel.h" -#include "flux_function.h" - -static const std::string _module_id("$Id$"); - -QString MyModel::ModelID(void) { - // specify the name of your model here - return QString( "new auxin transport 2" ); -} - -// return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } - -// To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { - - // After divisions, parent and daughter cells get a standard stock of PINs. - daughter1->SetChemical(1, par->initval[1]); - daughter2->SetChemical(1, par->initval[1]); - - -} - -void MyModel::SetCellColor(CellBase *c, QColor *color) { - // add cell coloring rules here - // Red: PIN1 - // Green: Auxin - color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.), 0); - -} - -void MyModel::CellHouseKeeping(CellBase *c) { - // add cell behavioral rules here - - c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); - - if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { - c->Divide(); - } -} - -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { - // add biochemical transport rules here - double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); - dchem_c1[0]+=phi; - dchem_c2[0]-=phi; - - // Active fluxes (PIN1 mediated transport) - - // (Transporters measured in moles, here) - // efflux from cell 1 to cell 2 - double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) ); - - // efflux from cell 2 to cell 1 - double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) ); - - dchem_c1[0] += trans21 - trans12; - dchem_c2[0] += trans12 - trans21; - - // Influx at leaf "AuxinSource" (as specified in initial condition) - if (w->AuxinSource()) { - double aux_flux = par->leaf_tip_source * w->Length(); - dchem_c1[0] += aux_flux; - dchem_c2[0] += aux_flux; - } -} - -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { - // PIN1 localization at wall - // Note: chemical 0 is Auxin (intracellular storage only) - // PIN1 is Chemical 1 (both in walls and intracellular storage) - //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$ - // Note that Pij is measured in term of concentration (mol/L) - // Pi in terms of quantity (mol) - - // Equations as in Merks et al., Trends in Plant Science 2007 - - // calculate PIN translocation rate from cell to membrane - double adj_auxin = adjacent_cell->Chemical(0); - double receptor_level = adj_auxin * par->r / (par->kr + adj_auxin); - double pin_atwall; // pick the correct side of the Wall - - if (w->C1() == this_cell) pin_atwall = w->Transporters1(1); - else pin_atwall=w->Transporters2(1); - - // note: pin_flux is net flux from endosome to wall - double pin_flux = par->k1 * this_cell->Chemical(1) * receptor_level / ( par->km + this_cell->Chemical(1) ) - par->k2 * pin_atwall; - return pin_flux; - - -} - - -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { - // add biochemical networks for reactions occuring at walls here - dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls - dw1[1] = PINflux(w->C1(),w->C2(),w); - dw2[1] = PINflux(w->C2(),w->C1(),w); - //static ofstream pf("pin_flux.dat"); - //pf << dw1[1] << " " << dw2[1] << " " << w->C1()->Chemical(1) << " " << w->C2()->Chemical(1) << endl; - -} - -void MyModel::CellDynamics(CellBase *c, double *dchem) { - // add biochemical networks for intracellular reactions here - - // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); - - // auxin degradation - dchem[0] = - par->aux_breakdown * c->Chemical(0); - - -} - - -Q_EXPORT_PLUGIN2(mymodel, MyModel) diff --git a/src/TutorialCode/Tutorial4/mymodel.cpp b/src/TutorialCode/Tutorial4/tutorial4.cpp rename from src/TutorialCode/Tutorial4/mymodel.cpp rename to src/TutorialCode/Tutorial4/tutorial4.cpp --- a/src/TutorialCode/Tutorial4/mymodel.cpp +++ b/src/TutorialCode/Tutorial4/tutorial4.cpp @@ -28,21 +28,21 @@ #include "wallbase.h" #include "cellbase.h" -#include "mymodel.h" +#include "tutorial4.h" #include "flux_function.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial4::ModelID(void) { // specify the name of your model here - return QString( "new auxin transport 2" ); + return QString( "4: Dynamic PIN orientation" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } +int Tutorial4::NChem(void) { return 2; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial4::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // After divisions, parent and daughter cells get a standard stock of PINs. daughter1->SetChemical(1, par->initval[1]); @@ -51,7 +51,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial4::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // Red: PIN1 // Green: Auxin @@ -59,7 +59,7 @@ void MyModel::SetCellColor(CellBase *c, } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial4::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); @@ -69,7 +69,7 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial4::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; @@ -95,7 +95,7 @@ void MyModel::CelltoCellTransport(Wall * } } -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { +double Tutorial4::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { // PIN1 localization at wall // Note: chemical 0 is Auxin (intracellular storage only) // PIN1 is Chemical 1 (both in walls and intracellular storage) @@ -121,7 +121,7 @@ double MyModel::PINflux(CellBase *this_c } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial4::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls dw1[1] = PINflux(w->C1(),w->C2(),w); @@ -131,15 +131,15 @@ void MyModel::WallDynamics(Wall *w, doub } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial4::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); + dchem[1] = - SumFluxFromWalls( c, Tutorial4::PINflux ); } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial4, Tutorial4) diff --git a/src/TutorialCode/Tutorial4/mymodel.h b/src/TutorialCode/Tutorial4/tutorial4.h rename from src/TutorialCode/Tutorial4/mymodel.h rename to src/TutorialCode/Tutorial4/tutorial4.h --- a/src/TutorialCode/Tutorial4/mymodel.h +++ b/src/TutorialCode/Tutorial4/tutorial4.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial4 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial4/mymodel.pro b/src/TutorialCode/Tutorial4/tutorial4.pro rename from src/TutorialCode/Tutorial4/mymodel.pro rename to src/TutorialCode/Tutorial4/tutorial4.pro --- a/src/TutorialCode/Tutorial4/mymodel.pro +++ b/src/TutorialCode/Tutorial4/tutorial4.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial4 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/TutorialCode/Tutorial5/Makefile b/src/TutorialCode/Tutorial5/Makefile new file mode 100644 --- /dev/null +++ b/src/TutorialCode/Tutorial5/Makefile @@ -0,0 +1,29 @@ +# $Id$ + +QMAKE = qmake + +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif + +all: tutorial5 + +tutorial5: Makefile.tutorial5 + $(MAKE) -f Makefile.tutorial5 + +Makefile.tutorial5: tutorial5.pro + $(QMAKE) -makefile -o $@ $< + +clean: + $(MAKE) -f Makefile.tutorial5 clean +ifeq ($(MAKE), make) + touch tutorial5.pro +else + copy /b tutorial5.pro +,, +endif + +# finis diff --git a/src/TutorialCode/Tutorial5/mymodel b/src/TutorialCode/Tutorial5/mymodel deleted file mode 100644 --- a/src/TutorialCode/Tutorial5/mymodel +++ /dev/null @@ -1,147 +0,0 @@ -/* - * - * This file is part of the Virtual Leaf. - * - * The Virtual Leaf is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * The Virtual Leaf is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with the Virtual Leaf. If not, see . - * - * Copyright 2010 Roeland Merks. - * - */ - -#include -#include -#include -#include "simplugin.h" - -#include "parameter.h" - -#include "wallbase.h" -#include "cellbase.h" -#include "mymodel.h" -#include "flux_function.h" - -static const std::string _module_id("$Id$"); - -QString MyModel::ModelID(void) { - // specify the name of your model here - return QString( "new auxin transport 2" ); -} - -// return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } - -// To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { - - // After divisions, parent and daughter cells get a standard stock of PINs. - daughter1->SetChemical(1, par->initval[1]); - daughter2->SetChemical(1, par->initval[1]); - - -} - -void MyModel::SetCellColor(CellBase *c, QColor *color) { - // add cell coloring rules here - // Red: PIN1 - // Green: Auxin - color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.), 0); - -} - -void MyModel::CellHouseKeeping(CellBase *c) { - // add cell behavioral rules here - - c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); - - if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) { - c->Divide(); - } -} - -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { - // add biochemical transport rules here - double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); - dchem_c1[0]+=phi; - dchem_c2[0]-=phi; - - // Active fluxes (PIN1 mediated transport) - - // (Transporters measured in moles, here) - // efflux from cell 1 to cell 2 - double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) ); - - // efflux from cell 2 to cell 1 - double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) ); - - dchem_c1[0] += trans21 - trans12; - dchem_c2[0] += trans12 - trans21; - - // Influx at leaf "AuxinSource" (as specified in initial condition) - if (w->AuxinSource()) { - double aux_flux = par->leaf_tip_source * w->Length(); - dchem_c1[0] += aux_flux; - dchem_c2[0] += aux_flux; - } -} - -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { - // PIN1 localization at wall - // Note: chemical 0 is Auxin (intracellular storage only) - // PIN1 is Chemical 1 (both in walls and intracellular storage) - //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$ - // Note that Pij is measured in term of concentration (mol/L) - // Pi in terms of quantity (mol) - - // Equations as in Merks et al., Trends in Plant Science 2007 - - // calculate PIN translocation rate from cell to membrane - double adj_auxin = adjacent_cell->Chemical(0); - double receptor_level = adj_auxin * par->r / (par->kr + adj_auxin); - double pin_atwall; // pick the correct side of the Wall - - if (w->C1() == this_cell) pin_atwall = w->Transporters1(1); - else pin_atwall=w->Transporters2(1); - - // note: pin_flux is net flux from endosome to wall - double pin_flux = par->k1 * this_cell->Chemical(1) * receptor_level / ( par->km + this_cell->Chemical(1) ) - par->k2 * pin_atwall; - return pin_flux; - - -} - - -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { - // add biochemical networks for reactions occuring at walls here - dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls - dw1[1] = PINflux(w->C1(),w->C2(),w); - dw2[1] = PINflux(w->C2(),w->C1(),w); - //static ofstream pf("pin_flux.dat"); - //pf << dw1[1] << " " << dw2[1] << " " << w->C1()->Chemical(1) << " " << w->C2()->Chemical(1) << endl; - -} - -void MyModel::CellDynamics(CellBase *c, double *dchem) { - // add biochemical networks for intracellular reactions here - - // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); - - // auxin degradation - dchem[0] = - par->aux_breakdown * c->Chemical(0); - - -} - - -Q_EXPORT_PLUGIN2(mymodel, MyModel) diff --git a/src/TutorialCode/Tutorial5/mymodel.cpp b/src/TutorialCode/Tutorial5/tutorial5.cpp rename from src/TutorialCode/Tutorial5/mymodel.cpp rename to src/TutorialCode/Tutorial5/tutorial5.cpp --- a/src/TutorialCode/Tutorial5/mymodel.cpp +++ b/src/TutorialCode/Tutorial5/tutorial5.cpp @@ -20,20 +20,20 @@ */ #include "vleafmodel.h" - +#include "tutorial5.h" static const std::string _module_id("$Id$"); -QString MyModel::ModelID(void) { +QString Tutorial5::ModelID(void) { // specify the name of your model here - return QString( "auxin flux and growth" ); + return QString( "5: Auxin-driven growth" ); } // return the number of chemicals your model uses -int MyModel::NChem(void) { return 2; } +int Tutorial5::NChem(void) { return 2; } // To be executed after cell division -void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { +void Tutorial5::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) { // After divisions, parent and daughter cells get a standard stock of PINs. daughter1->SetChemical(1, par->initval[1]); @@ -45,7 +45,7 @@ void MyModel::OnDivide(ParentInfo *paren } -void MyModel::SetCellColor(CellBase *c, QColor *color) { +void Tutorial5::SetCellColor(CellBase *c, QColor *color) { // add cell coloring rules here // Red: PIN1 // Green: Auxin @@ -53,7 +53,7 @@ void MyModel::SetCellColor(CellBase *c, } -void MyModel::CellHouseKeeping(CellBase *c) { +void Tutorial5::CellHouseKeeping(CellBase *c) { // add cell behavioral rules here c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate); @@ -63,7 +63,7 @@ void MyModel::CellHouseKeeping(CellBase } } -void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { +void Tutorial5::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) { // add biochemical transport rules here double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) ); dchem_c1[0]+=phi; @@ -89,7 +89,7 @@ void MyModel::CelltoCellTransport(Wall * } } -double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { +double Tutorial5::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) { // PIN1 localization at wall // Note: chemical 0 is Auxin (intracellular storage only) // PIN1 is Chemical 1 (both in walls and intracellular storage) @@ -115,7 +115,7 @@ double MyModel::PINflux(CellBase *this_c } -void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) { +void Tutorial5::WallDynamics(Wall *w, double *dw1, double *dw2) { // add biochemical networks for reactions occuring at walls here dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls dw1[1] = PINflux(w->C1(),w->C2(),w); @@ -123,11 +123,11 @@ void MyModel::WallDynamics(Wall *w, doub } -void MyModel::CellDynamics(CellBase *c, double *dchem) { +void Tutorial5::CellDynamics(CellBase *c, double *dchem) { // add biochemical networks for intracellular reactions here // sum all incoming fluxes of PINs - dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux ); + dchem[1] = - SumFluxFromWalls( c, Tutorial5::PINflux ); // auxin degradation dchem[0] = - par->aux_breakdown * c->Chemical(0); @@ -136,4 +136,4 @@ void MyModel::CellDynamics(CellBase *c, } -Q_EXPORT_PLUGIN2(mymodel, MyModel) +Q_EXPORT_PLUGIN2(tutorial5, Tutorial5) diff --git a/src/TutorialCode/Tutorial5/mymodel.h b/src/TutorialCode/Tutorial5/tutorial5.h rename from src/TutorialCode/Tutorial5/mymodel.h rename to src/TutorialCode/Tutorial5/tutorial5.h --- a/src/TutorialCode/Tutorial5/mymodel.h +++ b/src/TutorialCode/Tutorial5/tutorial5.h @@ -27,7 +27,7 @@ #include "simplugin.h" -class MyModel : public QObject, SimPluginInterface { +class Tutorial5 : public QObject, SimPluginInterface { Q_OBJECT Q_INTERFACES(SimPluginInterface); diff --git a/src/TutorialCode/Tutorial5/mymodel.pro b/src/TutorialCode/Tutorial5/tutorial5.pro rename from src/TutorialCode/Tutorial5/mymodel.pro rename to src/TutorialCode/Tutorial5/tutorial5.pro --- a/src/TutorialCode/Tutorial5/mymodel.pro +++ b/src/TutorialCode/Tutorial5/tutorial5.pro @@ -20,7 +20,7 @@ # -TARGET = mymodel +TARGET = tutorial5 VLEAFHOME = ../../.. CONFIG += release diff --git a/src/build_models/ChangeLog b/src/build_models/ChangeLog --- a/src/build_models/ChangeLog +++ b/src/build_models/ChangeLog @@ -1,3 +1,8 @@ +2010-06-22 + + * Makefile (clean): Add windows equivalent of UNIX touch. + + 2010-06-18 * plugin_auxingrowth.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories. diff --git a/src/build_models/Makefile b/src/build_models/Makefile --- a/src/build_models/Makefile +++ b/src/build_models/Makefile @@ -2,8 +2,13 @@ QMAKE = $(HOME)/Trolltech/Qt-4.4.1/bin/qmake -# Set $(MAKE) to the name of the make command on your machine, e.g. 'make' on Linux and 'mingw32-make' on windows. -MAKE = make # mingw32-make +# Set an environment varible $(MAKE) to the name of the make command +# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows. +# Fallback default is UNIX make. + +ifeq ($(MAKE),) + MAKE=make +endif all: plugin_auxingrowth plugin_meinhardt plugin_test @@ -33,6 +38,11 @@ ifeq ($(MAKE),make) touch plugin_auxingrowth.pro touch plugin_meinhardt.pro touch plugin_test.pro +else + copy /b plugin_auxingrowth.pro +,, + copy /b plugin_meinhardt.pro +,, + copy /b plugin_test.pro +,, + endif #finis diff --git a/src/canvas.cpp b/src/canvas.cpp --- a/src/canvas.cpp +++ b/src/canvas.cpp @@ -20,6 +20,8 @@ */ #include +#include +#include #include #include #include @@ -41,6 +43,8 @@ #include #include #include +#include + #include #include @@ -558,7 +562,7 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q helpmenu->insertSeparator(); helpmenu->insertItem("&About", this, SLOT(about()) ); //, Key_F1); helpmenu->insertSeparator(); - helpmenu->insertItem("&GPL", this, SLOT(gpl()) ); + helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) ); menu->insertItem("&Help",helpmenu); statusBar(); setCentralWidget(editor); @@ -665,8 +669,6 @@ void Main::readPars() } emit ParsChanged(); - /* if (timer_active) - timer->start( 0 );*/ } @@ -948,30 +950,37 @@ void Main::about() } -#include -#include -#include void Main::gpl() { - static QMessageBox* gpl = new QMessageBox ( "License", "", + static QMessageBox* gpl = new QMessageBox ( "GPL License", "", QMessageBox::Information, 1, 0, 0, this, 0, FALSE ); - std::ifstream t("../doc/GPL"); + QDir docDir(QApplication::applicationDirPath()); + docDir.cd("../doc"); + QString path = docDir.filePath("gpl3.txt"); + + std::ifstream file(path.toStdString().c_str()); std::string str; - t.seekg(0, std::ios::end); - str.reserve(t.tellg()); - t.seekg(0, std::ios::beg); + if (file) { + file.seekg(0, std::ios::end); + str.reserve(file.tellg()); + file.seekg(0, std::ios::beg); + + str.assign((std::istreambuf_iterator(file)), + std::istreambuf_iterator()); - str.assign((std::istreambuf_iterator(t)), - std::istreambuf_iterator()); - gpl->setText(QString("

GNU GENERAL PUBLIC LICENSE

" - "

Version 2, June 1991

" - "

Copyright (C) 1989, 1991 Free Software Foundation, Inc. " - "59 Temple Place, Suite 330, Boston, MA 02111-1307 USA: " - "Everyone is permitted to copy and distribute verbatim copies " - "of this license document, but changing it is not allowed.

")); - gpl->setDetailedText(QString(str.c_str())); + gpl->setDetailedText(QString(str.c_str())); + } + + gpl->setText(QString( "

GNU GENERAL PUBLIC LICENSE

" + "

Version 3, 29 June 2007

" + "

Copyright © 2007 Free Software Foundation, Inc. " + "<http://fsf.org/>

" + "Everyone is permitted to copy and distribute verbatim copies " + "of this license document, but changing it is not allowed.

" + "

GNU GENERAL PUBLIC LICENSE

")); + gpl->setButtonText( 1, "Dismiss" ); gpl->show(); } diff --git a/src/parameter.cpp b/src/parameter.cpp --- a/src/parameter.cpp +++ b/src/parameter.cpp @@ -31,6 +31,8 @@ #include "xmlwrite.h" #include "warning.h" #include +#include +#include using namespace std; @@ -45,7 +47,7 @@ Parameter::Parameter() { node_mag = 1.0; outlinewidth = 1.0; cell_outline_color = strdup("forestgreen"); - resize_stride = 10; + resize_stride = 0; T = 1.0; lambda_length = 100.; lambda_celllength = 0.; @@ -180,14 +182,19 @@ Parameter::Parameter() { b4 = false; dir1 = strdup("."); dir2 = strdup("."); + // reassign datadir outside the loop + QDir dataDir(datadir); + if (dataDir.isRelative()){ + QStringList path; + path << QDir::homePath() << dataDir.dirName(); + datadir = strdup((char *) path.join("/").toStdString().c_str()); + } } Parameter::~Parameter() { - + // destruct parameter object - // free string parameter - CleanUp(); } @@ -216,17 +223,18 @@ void Parameter::CleanUp(void) { free(dir1); if (dir2) free(dir2); + } void Parameter::Read(const char *filename) { - + static bool ReadP=false; if (ReadP) { //throw "Run Time Error in parameter.cpp: Please Read parameter file only once!!"; CleanUp(); - + } else ReadP=true; @@ -241,7 +249,7 @@ void Parameter::Read(const char *filenam node_mag = fgetpar(fp, "node_mag", 1.0, true); outlinewidth = fgetpar(fp, "outlinewidth", 1.0, true); cell_outline_color = sgetpar(fp, "cell_outline_color", "forestgreen", true); - resize_stride = igetpar(fp, "resize_stride", 10, true); + resize_stride = igetpar(fp, "resize_stride", 0, true); T = fgetpar(fp, "T", 1.0, true); lambda_length = fgetpar(fp, "lambda_length", 100., true); lambda_celllength = fgetpar(fp, "lambda_celllength", 0., true); @@ -468,6 +476,7 @@ void Parameter::Write(ostream &os) const if (dir2) os << " dir2 = " << dir2 << endl; } + void Parameter::XMLAdd(xmlNode *root) const { xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL); { @@ -1838,43 +1847,18 @@ void Parameter::AssignValArrayToPar(cons k[i++]=*(v++); } } + // reassign datadir outside the loop + if (!strcmp(namec, "datadir")) { + if (datadir) { free(datadir); } + QDir dataDir(datadir); + if (dataDir.isRelative()){ + QStringList path; + path << QDir::homePath() << dataDir.dirName(); + datadir = strdup((char *) path.join("/").toStdString().c_str()); + } + } } -/* void Parameter::XMLRead(xmlNode *root) { - - xmlNode *cur = root->xmlChildrenNode; - while (cur!=NULL) { - if ((!xmlStrcmp(cur->name, (const xmlChar *)"parameter"))){ - xmlNode *par_node = cur->xmlChildrenNode; - while (par_node!=NULL) { - { - if (!xmlStrcmp(par_node->name, (const xmlChar *)"par")) { - xmlChar *namec = xmlGetProp(par_node, BAD_CAST "name"); - xmlChar *valc = xmlGetProp(par_node, BAD_CAST "val"); - if (valc) { - AssignValToPar((const char*)namec,(const char*)valc); - } else { - // Probably a valarray - xmlNode *sub_par_node = par_node->xmlChildrenNode; - vector valarray; - while (sub_par_node != NULL) { - if (!xmlStrcmp(sub_par_node->name, (const xmlChar *)"valarray")) { - valarray = XMLIO::XMLReadValArray(sub_par_node); - } - sub_par_node = sub_par_node->next; - } - AssignValArrayToPar((const char*)namec, valarray); - } - } - } - par_node = par_node->next; - } - - } - cur=cur->next; - } - }*/ - ostream &operator<<(ostream &os, Parameter &p) { p.Write(os); return os; diff --git a/src/parameter.h b/src/parameter.h --- a/src/parameter.h +++ b/src/parameter.h @@ -30,7 +30,7 @@ #include class Parameter { - + public: Parameter(); ~Parameter(); diff --git a/src/pardialog.cpp b/src/pardialog.cpp --- a/src/pardialog.cpp +++ b/src/pardialog.cpp @@ -137,7 +137,7 @@ ParameterDialog::ParameterDialog(QWidget dir2_edit = new QLineEdit( QString("%1").arg(par.dir2), this, "dir2_edit" ); // make a 1x1 grid; it will auto-expand QGridLayout *grid = new QGridLayout( this, 1, 1 ); - + // add the first four widgets with (row, column) addressing setWindowTitle( QString( " Parameter values for The Virtual Leaf") ); grid->addWidget( new QLabel( "

Parameter values for The Virtual Leaf

",this), 0, 0, 1, -1, Qt::AlignCenter); @@ -463,7 +463,7 @@ ParameterDialog::~ParameterDialog(void) } void ParameterDialog::write(void) { - + extern Parameter par; QString tmpval; par.arrowcolor = strdup((const char *)arrowcolor_edit->text()); @@ -694,6 +694,7 @@ void ParameterDialog::write(void) { par.dir1 = strdup((const char *)dir1_edit->text()); par.dir2 = strdup((const char *)dir2_edit->text()); Reset(); + } void ParameterDialog::Reset(void) { extern Parameter par; @@ -803,5 +804,4 @@ void ParameterDialog::Reset(void) { dir2_edit->setText( QString("%1").arg(par.dir2) ); } - /* finis */ diff --git a/src/pardialog.h b/src/pardialog.h --- a/src/pardialog.h +++ b/src/pardialog.h @@ -1,26 +1,3 @@ -/* - * - * $Id$ - * - * This file is part of the Virtual Leaf. - * - * The Virtual Leaf is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * The Virtual Leaf is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with the Virtual Leaf. If not, see . - * - * Copyright 2010 Roeland Merks. - * - */ - #ifndef PARAMETER_DIALOG_H #define PARAMETER_DIALOG_H #include @@ -31,18 +8,18 @@ #include class ParameterDialog : public QDialog { - Q_OBJECT + Q_OBJECT + + public: + ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0); + virtual ~ParameterDialog(void); + public slots: + void Reset(void); - public: - ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0); - virtual ~ParameterDialog(void); - public slots: - void Reset(void); + private slots: + void write(void); - private slots: - void write(void); - - private: + private: QLineEdit *arrowcolor_edit; QLineEdit *arrowsize_edit; QLineEdit *textcolor_edit; @@ -142,7 +119,4 @@ class ParameterDialog : public QDialog { QLineEdit *dir1_edit; QLineEdit *dir2_edit; }; - #endif - -/* finis */ diff --git a/src/perl/ChangeLog b/src/perl/ChangeLog new file mode 100644 --- /dev/null +++ b/src/perl/ChangeLog @@ -0,0 +1,6 @@ +2010-06-21 + + * make_pardialog_source.pl: Reformatted. If datadir is relative append it to the user's home directory. + * make_parameter_source.pl: Ditto. + * make_xmlwritecode.pl: Ditto. + diff --git a/src/perl/make_parameter_source.pl b/src/perl/make_parameter_source.pl --- a/src/perl/make_parameter_source.pl +++ b/src/perl/make_parameter_source.pl @@ -103,293 +103,273 @@ print cppfile < +#include +#include - using namespace std; - +using namespace std; Parameter::Parameter() { - END_HEADER +END_HEADER - for ($i=0;$i<$lines;$i++) { - if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { - if ($convtype[$i] eq "char *") { - print cppfile " $param[$i] = strdup($value[$i]);\n"; - } else { - if ($convtype[$i] eq "double *") { - #comma separated list expected - @paramlist = split(/,/, $value[$i]); - $length = $#paramlist+1; - print cppfile " $param[$i] = new double\[$length\];\n"; - for ($j=0;$j<=$#paramlist;$j++) { - print cppfile " $param[$i]\[$j\] = $paramlist[$j];\n"; - } - } else { - print cppfile " $param[$i] = $value[$i];\n"; - } +for ($i=0;$i<$lines;$i++) { + if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { + if ($convtype[$i] eq "char *") { + print cppfile " $param[$i] = strdup($value[$i]);\n"; + } else { + if ($convtype[$i] eq "double *") { + #comma separated list expected + @paramlist = split(/,/, $value[$i]); + $length = $#paramlist+1; + print cppfile " $param[$i] = new double\[$length\];\n"; + for ($j=0;$j<=$#paramlist;$j++) { + print cppfile " $param[$i]\[$j\] = $paramlist[$j];\n"; } + } else { + print cppfile " $param[$i] = $value[$i];\n"; } + } } +} - print cppfile < valarray) {\n"; - print cppfile; +print cppfile "void Parameter::AssignValArrayToPar(const char *namec, vector valarray) {\n"; +print cppfile; - for ($i=0;$i<$lines;$i++) { +for ($i=0;$i<$lines;$i++) { - if ($convtype[$i] eq "double *") { - @paramlist = split(/,/,$value[$i]); - print cppfile "if (!strcmp(namec, \"$param[$i]\")) {\n"; - print cppfile " int i=0;\n"; - print cppfile " vector::const_iterator v=valarray.begin();\n"; - print cppfile " while (v!=valarray.end() && i <= $#paramlist ) {\n"; - print cppfile " $param[$i]\[i++\]=*(v++);\n"; - print cppfile " }\n"; - print cppfile "}\n"; - } - } + if ($convtype[$i] eq "double *") { + @paramlist = split(/,/,$value[$i]); + print cppfile "if (!strcmp(namec, \"$param[$i]\")) {\n"; + print cppfile " int i=0;\n"; + print cppfile " vector::const_iterator v=valarray.begin();\n"; + print cppfile " while (v!=valarray.end() && i <= $#paramlist ) {\n"; + print cppfile " $param[$i]\[i++\]=*(v++);\n"; + print cppfile " }\n"; print cppfile "}\n"; - - - print cppfile <xmlChildrenNode; - while (cur!=NULL) { - if ((!xmlStrcmp(cur->name, (const xmlChar *)"parameter"))){ - xmlNode *par_node = cur->xmlChildrenNode; - while (par_node!=NULL) { - { - if (!xmlStrcmp(par_node->name, (const xmlChar *)"par")) { - xmlChar *namec = xmlGetProp(par_node, BAD_CAST "name"); - xmlChar *valc = xmlGetProp(par_node, BAD_CAST "val"); - if (valc) { - AssignValToPar((const char*)namec,(const char*)valc); - } else { - // Probably a valarray - xmlNode *sub_par_node = par_node->xmlChildrenNode; - vector valarray; - while (sub_par_node != NULL) { - if (!xmlStrcmp(sub_par_node->name, (const xmlChar *)"valarray")) { - valarray = XMLIO::XMLReadValArray(sub_par_node); - } - sub_par_node = sub_par_node->next; - } - AssignValArrayToPar((const char*)namec, valarray); - } - } - } - par_node = par_node->next; - } +print cppfile <next; - } - - }*/ +print cppfile "}\n"; + +print cppfile <parameter.h"; - print hfile <parameter.h"; +print hfile < #include - class Parameter { + class Parameter { - public: - Parameter(); - ~Parameter(); - void CleanUp(void); - void Read(const char *filename); - void Write(ostream &os) const; - void XMLAdd(xmlNode *root) const; - void XMLRead(xmlNode *root); - void AssignValToPar(const char *namec, const char *valc); - void AssignValArrayToPar(const char *namec, vector valarray); - END_HEADER2 + public: + Parameter(); + ~Parameter(); + void CleanUp(void); + void Read(const char *filename); + void Write(ostream &os) const; + void XMLAdd(xmlNode *root) const; + void XMLRead(xmlNode *root); + void AssignValToPar(const char *namec, const char *valc); + void AssignValArrayToPar(const char *namec, vector valarray); +END_HEADER2 - for ($i=0;$i<$lines;$i++) { - if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { - print hfile " $convtype[$i] $param[$i];\n"; - } - } + for ($i=0;$i<$lines;$i++) { + if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { + print hfile " $convtype[$i] $param[$i];\n"; + } + } - print hfile <default.par"; +open parfile,">default.par"; - for ($i=0;$i<$lines;$i++) { - if ($type[$i] ne "title" && $type[$i] ne "label") { - $value[$i] =~ s/\"//g; - print parfile " $param[$i] = $value[$i]\n"; - } - } +for ($i=0;$i<$lines;$i++) { + if ($type[$i] ne "title" && $type[$i] ne "label") { + $value[$i] =~ s/\"//g; + print parfile " $param[$i] = $value[$i]\n"; + } +} # finis diff --git a/src/perl/make_pardialog_source.pl b/src/perl/make_pardialog_source.pl --- a/src/perl/make_pardialog_source.pl +++ b/src/perl/make_pardialog_source.pl @@ -98,140 +98,139 @@ print cppfile <addWidget( new QLabel( \"$value[$i]\", this), $row, $col, 1, 2 );\n"; +$numrows = 30; +$c = 0; +for ($i=0;$i<$lines;$i++) { + $col = 2*int($c/($numrows-3)); + $row = $c % ($numrows-3) + $ntitles * 3; + if ($convtype[$i] eq "label") { + print cppfile " grid->addWidget( new QLabel( \"$value[$i]\", this), $row, $col, 1, 2 );\n"; + $c++; + } else { + if ($convtype[$i] eq "title") { + if ($ntitles) { + print stderr "Sorry, only one title allowed. Aborting source construction...\n"; + exit(1); + } + print cppfile " setWindowTitle( QString( \"$value[$i]\") );\n"; + print cppfile " grid->addWidget( new QLabel( \"

$value[$i]

\",this), $row, $col, 1, -1, Qt::AlignCenter);\n"; + print cppfile " grid->addWidget( new QLabel( \"\", this), $row+1, $col, 1, -1);\n"; + $ntitles++; + } else { + print cppfile " grid->addWidget( new QLabel( \"$param[$i]\", this ),$row, $col );\n"; + print cppfile " grid->addWidget( $param[$i]_edit, $row, $col+1 );\n"; $c++; - } else { - if ($convtype[$i] eq "title") { - if ($ntitles) { - print stderr "Sorry, only one title allowed. Aborting source construction...\n"; - exit(1); - } - print cppfile " setWindowTitle( QString( \"$value[$i]\") );\n"; - print cppfile " grid->addWidget( new QLabel( \"

$value[$i]

\",this), $row, $col, 1, -1, Qt::AlignCenter);\n"; - print cppfile " grid->addWidget( new QLabel( \"\", this), $row+1, $col, 1, -1);\n"; - $ntitles++; - } else { - print cppfile " grid->addWidget( new QLabel( \"$param[$i]\", this ),$row, $col );\n"; - print cppfile " grid->addWidget( $param[$i]_edit, $row, $col+1 );\n"; - $c++; - } } } +} - $row = $numrows+1; - $col = 2*int($i/$numrows); +$row = $numrows+1; +$col = 2*int($i/$numrows); - print cppfile <addWidget(pb, $row, $col ); - connect( pb, SIGNAL( clicked() ), this, SLOT( write() ) ); - QPushButton *pb2 = new QPushButton( \"&Close\", this ); - grid->addWidget(pb2,$row, $col+1 ); - connect( pb2, SIGNAL( clicked() ), this, SLOT( close() ) ); - QPushButton *pb3 = new QPushButton( \"&Reset\", this ); - grid->addWidget(pb3, $row, $col+2 ); - connect( pb3, SIGNAL( clicked() ), this, SLOT( Reset() ) ); - show(); +print cppfile <addWidget(pb, $row, $col ); +connect( pb, SIGNAL( clicked() ), this, SLOT( write() ) ); +QPushButton *pb2 = new QPushButton( \"&Close\", this ); +grid->addWidget(pb2,$row, $col+1 ); +connect( pb2, SIGNAL( clicked() ), this, SLOT( close() ) ); +QPushButton *pb3 = new QPushButton( \"&Reset\", this ); +grid->addWidget(pb3, $row, $col+2 ); +connect( pb3, SIGNAL( clicked() ), this, SLOT( Reset() ) ); +show(); }; ParameterDialog::~ParameterDialog(void) { - ANOTHER_LABEL +ANOTHER_LABEL - for ($i=0;$i<$lines;$i++) { - if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { - print cppfile "delete $param[$i]_edit;\n"; - } +for ($i=0;$i<$lines;$i++) { + if ($convtype[$i] ne "label" && $convtype[$i] ne "title") { + print cppfile "delete $param[$i]_edit;\n"; } - - print cppfile <text().section(',', $j, $j);\n"; + print cppfile " par.$param[$i]\[$j\] = tmpval.toDouble();\n"; } - if ($convtype[$i] eq "double *") { - @paramlist = split(/,/,$value[$i]); - for ($j=0;$j<=$#paramlist;$j++) { - print cppfile " tmpval = $param[$i]_edit->text().section(',', $j, $j);\n"; - print cppfile " par.$param[$i]\[$j\] = tmpval.toDouble();\n"; - } + } else { + if ($convtype[$i] eq "bool") { + print cppfile " tmpval = $param[$i]_edit->text().stripWhiteSpace();\n"; + print cppfile " if (tmpval == \"true\" || tmpval == \"yes\" ) par.$param[$i] = true;\n"; + print cppfile " else if (tmpval == \"false\" || tmpval == \"no\") par.$param[$i] = false;\n"; + print cppfile " else {\n"; + print cppfile " if (QMessageBox::question(this, \"Syntax error\", tr(\"Value %1 of parameter %2 is not recognized as Boolean.\\nDo you mean TRUE or FALSE?\").arg(tmpval).arg(\"$param[$i]\"),\"True\",\"False\", QString::null, 0, 1)==0) par.$param[$i]=true;\n"; + print cppfile " else par.$param[$i]=false;\n"; + print cppfile " }\n"; } else { - if ($convtype[$i] eq "bool") { - print cppfile " tmpval = $param[$i]_edit->text().stripWhiteSpace();\n"; - print cppfile " if (tmpval == \"true\" || tmpval == \"yes\" ) par.$param[$i] = true;\n"; - print cppfile " else if (tmpval == \"false\" || tmpval == \"no\") par.$param[$i] = false;\n"; - print cppfile " else {\n"; - print cppfile " if (QMessageBox::question(this, \"Syntax error\", tr(\"Value %1 of parameter %2 is not recognized as Boolean.\\nDo you mean TRUE or FALSE?\").arg(tmpval).arg(\"$param[$i]\"),\"True\",\"False\", QString::null, 0, 1)==0) par.$param[$i]=true;\n"; - print cppfile " else par.$param[$i]=false;\n"; - print cppfile " }\n"; + if ($convtype[$i] eq "char *") { + print cppfile " par.$param[$i] = strdup((const char *)$param[$i]_edit->text());\n"; } else { - if ($convtype[$i] eq "char *") { - print cppfile " par.$param[$i] = strdup((const char *)$param[$i]_edit->text());\n"; - } else { - print cppfile " par.$param[$i] = $param[$i]_edit->text().$funname{$convtype[$i]}();\n"; - } + print cppfile " par.$param[$i] = $param[$i]_edit->text().$funname{$convtype[$i]}();\n"; } } - } + } +} - print cppfile <) { - chomp; - s/\\/\\\\/g; - s/\"/\\\"/g; - s/\&/\&/g; - $str.=$_."\\n"; - } - $str .= "\";\n"; - return $str; - } + open srcfile, "<$fname"; + while () { + chomp; + s/\\/\\\\/g; + s/\"/\\\"/g; + s/\&/\&/g; + $str.=$_."\\n"; + } + $str .= "\";\n"; + return $str; +} - print xmlsrc "xmlChar *sourcecode = (xmlChar *)\"".construct_string_constant_from_file( "$mainsource" ); - print xmlsrc <