# HG changeset patch # User Michael Guravage # Date 2010-10-07 17:16:03 # Node ID b3943d0b8126f31b6a660a4e63704ac73eb99573 # Parent 4cb24b73768381a1632cceec91b5a9ef9e999016 Added a Q3FileDialog in canvas.cpp:Main::exportCellData() inquire where to write the exportCellData. -- user: Michael Guravage branch 'default' added doc/Makefile added doc/stylesheet.json added doc/v1.html added doc/v1.pdf added doc/v1.rst added src/leaficon.png changed src/ChangeLog changed src/canvas.cpp diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,18 @@ +.SUFFIXES : .rst .html .pdf + +.rst.pdf : + rst2pdf -s stylesheet.json $< -o $@ + +.rst.html : + rst2html.py $< $@ + +all: v1.pdf v1.html + +v1.pdf : v1.rst + +v1.html : v1.rst + +clean: + /bin/rm -f v1.pdf v1.html + +#finis \ No newline at end of file diff --git a/doc/stylesheet.json b/doc/stylesheet.json new file mode 100644 --- /dev/null +++ b/doc/stylesheet.json @@ -0,0 +1,557 @@ +{ + "embeddedFonts" : [ ], + "pageSetup" : { + "size": "A4", + "width": null, + "height": null, + "margin-top": "2cm", + "margin-bottom": "2cm", + "margin-left": "2cm", + "margin-right": "2cm", + "margin-gutter": "0cm", + "spacing-header": "5mm", + "spacing-footer": "5mm", + "firstTemplate": "oneColumn" + }, + "pageTemplates" : { + "coverPage": { + "frames": [ + ["0cm", "0cm", "100%", "100%"] + ], + "showHeader" : false, + "showFooter" : false + }, + "oneColumn": { + "frames": [ + ["0cm", "0cm", "100%", "100%"] + ], + "showHeader" : true, + "showFooter" : true + }, + "twoColumn": { + "frames": [ + ["0cm", "0cm", "49%", "100%"], + ["51%", "0cm", "49%", "100%"] + ], + "showHeader" : true, + "showFooter" : true + }, + "threeColumn": { + "frames": [ + ["2%", "0cm", "29.333%", "100%"], + ["35.333%", "0cm", "29.333%", "100%"], + ["68.666%", "0cm", "29.333%", "100%"] + ], + "showHeader" : true, + "showFooter" : true + }, + "cutePage": { + "frames": [ + ["0%", "0%", "100%", "100%"] + ], + "showHeader" : true, + "showFooter" : true, + "defaultFooter" : "###Page###", + "defaultHeader" : "###Section###" + } + }, + "fontsAlias" : { + "stdFont": "Helvetica", + "stdBold": "Helvetica-Bold", + "stdItalic": "Helvetica-Oblique", + "stdBoldItalic": "Helvetica-BoldOblique", + "stdSans": "Helvetica", + "stdSansBold": "Helvetica-Bold", + "stdSansItalic": "Helvetica-Oblique", + "stdSansBoldItalic": "Helvetica-BoldOblique", + "stdMono": "Courier", + "stdMonoItalic": "Courier-Oblique", + "stdMonoBold": "Courier-Bold", + "stdMonoBoldItalic": "Courier-BoldOblique", + "stdSerif": "Times-Roman" + }, + "linkColor" : "navy", + "styles" : [ + [ "base" , { + "parent": null, + "fontName": "stdFont", + "fontSize":10, + "leading":12, + "leftIndent":0, + "rightIndent":0, + "firstLineIndent":0, + "alignment":"TA_LEFT", + "spaceBefore":0, + "spaceAfter":0, + "bulletFontName":"stdFont", + "bulletFontSize":10, + "bulletIndent":0, + "textColor": "black", + "backColor": null, + "wordWrap": null, + "borderWidth": 0, + "borderPadding": 0, + "borderColor": null, + "borderRadius": null, + "allowWidows": false, + "allowOrphans": false, + "hyphenation": false, + "kerning": false + }] , + ["normal" , { + "parent": "base" + }], + ["title_reference" , { + "parent": "normal", + "fontName": "stdItalic" + }], + ["bodytext" , { + "parent": "normal", + "spaceBefore":6, + "alignment": "TA_JUSTIFY", + "hyphenation": true + }], + ["toc" , { + "parent": "normal" + }], + ["blockquote" , { + "parent": "bodytext", + "leftIndent": 20 + }], + ["lineblock" , { + "parent": "bodytext" + }], + ["toc1" , { + "parent": "toc", + "fontName": "stdBold" + }], + ["toc2" , { + "parent": "toc", + "leftIndent": 20 + }], + ["toc3" , { + "parent": "toc", + "leftIndent": 40 + }], + ["toc4" , { + "parent": "toc", + "leftIndent": 60 + }], + ["toc5" , { + "parent": "toc", + "leftIndent": 80 + }], + ["toc6" , { + "parent": "toc", + "leftIndent": 100 + }], + ["toc7" , { + "parent": "toc", + "leftIndent": 100 + }], + 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"bodytext", + "spaceBefore":-3 + }], + ["item_list_item" , { + "parent": "bodytext", + "spaceBefore":-3 + }], + ["enumerated_list" , { + "parent": "bodytext", + "spaceBefore": 0 + }], + ["enumerated_list_item" , { + "parent": "bodytext" + }], + ["definition_list_term" , { + "parent": "normal", + "fontName": "stdBold", + "spaceBefore": 4, + "spaceAfter": 0, + "keepWithNext": true + }], + ["definition_list_classifier" , { + "parent": "normal", + "fontName": "stdItalic" + }], + ["definition" , { + "parent": "bodytext", + "firstLineIndent": 0, + "bulletIndent": 0, + "spaceBefore": 0 + }], + ["fieldname" , { + "parent": "bodytext", + "alignment": "TA_RIGHT", + "fontName": "stdBold" + }], + ["fieldvalue" , { + "parent": "bodytext" + }], + ["rubric" , { + "parent": "bodytext", + "textColor": "darkred", + "alignment": "TA_CENTER" + }], + ["italic" , { + "parent": "bodytext", + "fontName": "stdItalic" + }], + ["heading" , { + "parent": "normal", + "keepWithNext": true, + "spaceBefore": 12, + "spaceAfter": 6 + }], + ["title" , { + "parent": "heading", + "fontName": "stdBold", + "fontSize": "200%", + "alignment": "TA_LEFT", + "keepWithNext": false, + "spaceAfter": 10 + }], + ["subtitle" , { + "parent": "title", + "spaceBefore": 12, + "fontSize": "75%" + }], + ["heading1" , { + "parent": "heading", + "fontName": "stdBold", + "fontSize": "175%" + }], + ["heading2" , { + "parent": "heading", + "fontName": "stdBold", + "fontSize": "150%" + }], + ["heading3" , { + "parent": "heading", + "fontName": "stdBoldItalic", + "fontSize": "125%" + }], + ["heading4" , { + "parent": "heading", + "fontName": "stdBoldItalic" + }], + ["heading5" , { + "parent": "heading", + "fontName": "stdBoldItalic" + }], + ["heading6" , { + "parent": "heading", + "fontName": "stdBoldItalic" + }], + ["topic-title" , { + "parent": "heading3" + }], + ["sidebar-title" , { + "parent": "heading3" + }], + ["sidebar-subtitle" , { + "parent": "heading4" + }], + ["sidebar" , { + "float": "none", + "width": "100%", + "parent": "normal", + "backColor": "beige", + "borderColor": "darkgray", + "borderPadding": 8, + "borderWidth": 0.5 + }], + ["admonition" , { + "parent": "normal", + "spaceBefore": 12, + "spaceAfter": 6, + "borderPadding": [16,16,16,16], + "backColor": "beige", + "borderColor": "darkgray", + "borderWidth": 0.5, + "commands":[ + [ "VALIGN", [ 0, 0 ], [ -1, -1 ], "TOP" ] + ] + }], + ["attention" , { + "parent": "admonition" + }], + ["caution" , { + "parent": "admonition" + }], + ["danger" , { + "parent": "admonition" + }], + ["error" , { + "parent": "admonition" + }], + ["hint" , { + "parent": "admonition" + }], + ["important" , { + "parent": "admonition" + }], + ["note" , { + "parent": "admonition" + }], + ["tip" , { + "parent": "admonition" + }], + ["warning" , { + "parent": "admonition" + }], + ["admonition-title" , { + "parent": "heading3" + }], + ["admonition-heading" , { + "parent": "heading3" + }], + ["attention-heading" , { + "parent": "admonition-heading" + }], + ["caution-heading" , { + "parent": "admonition-heading" + }], + ["danger-heading" , { + "parent": "admonition-heading" + }], + ["error-heading" , { + "parent": "admonition-heading" + }], + ["hint-heading" , { + "parent": "admonition-heading" + }], + ["important-heading" , { + "parent": "admonition-heading" + }], + ["note-heading" , { + "parent": "admonition-heading" + }], + ["tip-heading" , { + "parent": "admonition-heading" + }], + ["warning-heading" , { + "parent": "admonition-heading" + }], + ["literal" , { + "parent": "normal", + "fontName": "stdMono", + "firstLineIndent": 0, + "hyphenation": false + }], + ["aafigure" , { + "parent": "literal" + }], + ["table" , { + "spaceBefore":6, + "spaceAfter":0, + "commands": [ + [ "VALIGN", [ 0, 0 ], [ -1, -1 ], "TOP" ], + [ "INNERGRID", [ 0, 0 ], [ -1, -1 ], 0.25, "black" ], + [ "ROWBACKGROUNDS", [0, 0], [-1, -1], ["white","#E0E0E0"]], + [ "BOX", [ 0, 0 ], [ -1, -1 ], 0.25, "black" ] + ] + }], + ["table-title" , { + "parent" : "heading4", + 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"TOPPADDING", [ 0, 0 ], [ -1, -1 ], 0 ], + [ "BOTTOMPADDING", [ 0, 0 ], [ -1, -1 ], 0 ], + [ "RIGHTPADDING", [ 0, 0 ], [ 1, -1 ], 0 ] + ], + "colWidths": ["3cm",null] + }], + [ "field_list", { + "parent": "bodytext", + "commands": [ + [ "VALIGN", [ 0, 0 ], [ -1, -1 ], "TOP" ], + [ "TOPPADDING", [ 0, 0 ], [ -1, -1 ], 0 ] + ], + "colWidths": ["3cm",null], + "spaceBefore": 6 + }], + [ "option_list", { + "commands": [ + [ "VALIGN", [ 0, 0 ], [ -1, -1 ], "TOP" ], + [ "TOPPADDING", [ 0, 0 ], [ -1, -1 ], 0 ] + ], + "colWidths": [null,null] + }] + ] +} + diff --git a/doc/v1.html b/doc/v1.html new file mode 100644 --- /dev/null +++ b/doc/v1.html @@ -0,0 +1,469 @@ + + + + + + +The Virtual Leaf + + + +
+###Title### +
+
+
+

The Virtual Leaf

+ +
+

Friday 11 June 2010

+

Issues:

+
+
    +

  1. Every class that has an association or composition eventually will +need its own custom view page template, e.g. sed_view. For the moment +I have set the default view for these classes to dev_view ( a copy of +base_view ).

    +
    2. +

  2. An association in UML is cast as a ReferenceField in the resulting +class schema. Open the association and add the widget:label tag to +the class that is being associated.

    +
    3. +

  3. The default description text for a class should be a informative +description of the class, not the instance, derived from the +SED-ML manual.

    +
    4. +

  4. Apply 'searchable' tags to the appropriate class attributes.

    +
    5. +

  5. I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will +this work?

    +
    6. +

  6. What should be added to our implementation of SED-ML to make it +more than merely a mirror image of the SED-ML XML format?

    +
    +
      +
    1. The ability to attach files at various points, e.g. parameter files.
      2. +
    2. Additional output types, e.g. animations.
      3. +
    3. Custom page templates
      4. +
    4. Custom search form
      5. +
    5. Custom catalog indexes
      6. +
    6. Custom portlet(s)
      7. +
    7. Custom viewlet(s)
      8. +
    +
    +
    7. +
+
+
+
+

Friday 24 September 2010

+
+
To Do:
+
    +
  1. Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.
    2. +
  2. Create a vleaf mailing list (Henk).
    3. +
+
+
+

Found an article on SBRML - a markup language for associating systems +biology data with models. At a glance the schema seems bigger than +SED-ML's, but SBRML appears to be SBML specific.

+
+
+

Monday 27 September 2010

+

Spoke with Chris about publishing the Mercurial repositories and +deploying Plone. Both can be accomplished in their own project space +on a server in the DMZ. Chris said he would supply me with login +credentials for both accounts. I will install Plone and Chris (or +Maarten) will help me configure Apache/nginx and Varnish. Chris will +install the required Mercurial packages; after which I can clone the +repositories to their new home.

+
+
+

Tuesday 5 October 20010

+
+

tutorial0.pro

+

Added simplugin.h to list of header files. NB: this is the only +tutorial in which simplugin.h appears.

+
+
+

auxingrowthplugin.h

+

Declared, and defined, a virtual function named DefaultLeafML() +which merely returns a QString naming a LeafML filename sans path.

+
+
+

VirtualLeaf.cpp

+

Moved Cell::SetMagnification() and Cell::SetOffset() from +main() to MainBase::Init().

+
+
+

canvas.h

+

Declare exportCellData().

+
+
+

canvas.cpp

+

Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - Main::exportCellData():

+
+void Main::exportCellData(void) {
+  QFile file("areas.csv");
+  if ( file.open( IO_WriteOnly ) ) {
+    QTextStream stream( &file );
+    mesh.CSVExportCellData(stream);
+    mesh.CSVExportMeshData(stream);
+    file.close();
+  }
+}
+
+
+
+

mesh.h

+

Include <QTextStream>

+

Set the boundary_poloygon pointer to zero in the class constructor, +and delete it, if it exists, in the class destructor.

+

Declare Compactness(), CSVExportCellData() and CSVExportMeshData():

+
+double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0);
+void CSVExportCellData(QTextStream &csv_stream) const;
+void CSVExportMeshData(QTextStream &csv_stream);
+
+
+
+

mesh.cpp

+

In mesh::clear(), delete the boundary_polygon only if the pointer hasn't been assigned:

+
+if (boundary_polygon) {
+   delete boundary_polygon;
+   boundary_polygon=0;
+ }
+
+

Ditto for mesh::clean().

+

Define the code for Compactness(), CSVExportCellData() and CSVExportMeshData().

+
+
+

modelcatalogue.cpp

+

In InstallModel(), find and load the default LeafML file.

+
+
+

simplugin.h

+

Declare DefaultLeafML():

+
+// Default LeafML-file to be read after model startup
+virtual QString DefaultLeafML(void);
+
+
+
+

simplugin.cpp

+

Define DefaultLeafML(). Returns an empty QString:

+
+QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
+
+
+
+

xmlwrite.cpp

+

In Mesh::XMLReadCells() - Delete the boundary_ploygon only if its +pointer has been assigned.

+
+
+
+
+
+###Page### +
+ + diff --git a/doc/v1.pdf b/doc/v1.pdf new file mode 100644 --- /dev/null +++ b/doc/v1.pdf @@ -0,0 +1,1229 @@ +%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 +% 'Page1': class PDFPage +4 0 obj +% Page dictionary +<< /Contents 27 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 26 0 R + /Resources << /Font 1 0 R + /ProcSet [ /PDF + /Text + /ImageB + /ImageC + /ImageI ] >> + /Rotate 0 + /Trans << >> + /Type /Page >> +endobj +% 'F3': class PDFType1Font +5 0 obj +% Font Courier +<< /BaseFont /Courier + /Encoding /WinAnsiEncoding + /Name /F3 + /Subtype /Type1 + /Type /Font >> +endobj +% 'Page2': class PDFPage +6 0 obj +% Page dictionary +<< /Contents 28 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 26 0 R + /Resources << /Font 1 0 R + /ProcSet [ /PDF + /Text + /ImageB + /ImageC + /ImageI ] >> + /Rotate 0 + /Trans << >> + /Type /Page >> +endobj +% 'Page3': class PDFPage +7 0 obj +% Page dictionary +<< /Contents 29 0 R + /MediaBox [ 0 + 0 + 595.2756 + 841.8898 ] + /Parent 26 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 30 0 R + /PageMode /UseNone + /Pages 26 0 R + /Type /Catalog >> +endobj +% 'R9': class PDFInfo +9 0 obj +<< /Author () + /CreationDate (D:20101005155533-01'00') + /Keywords () + /Producer (ReportLab http://www.reportlab.com) + /Subject (\(unspecified\)) + /Title (The Virtual Leaf) >> +endobj +% 'R10': class PDFOutlines +10 0 obj +<< /Count 16 + /First 11 0 R + /Last 14 0 R + /Type /Outlines >> +endobj +% 'Outline.0': class OutlineEntryObject +11 0 obj +<< /Dest [ 4 0 R + /XYZ + 62.69291 + 717.0236 + 0 ] + /Next 12 0 R + /Parent 10 0 R + /Title (Friday 11 June 2010) >> +endobj +% 'Outline.1': class OutlineEntryObject +12 0 obj +<< /Dest [ 4 0 R + /XYZ + 62.69291 + 393.0236 + 0 ] + /Next 13 0 R + /Parent 10 0 R + /Prev 11 0 R + /Title (Friday 24 September 2010) >> +endobj +% 'Outline.2': class OutlineEntryObject +13 0 obj +<< /Dest [ 4 0 R + /XYZ + 62.69291 + 273.0236 + 0 ] + /Next 14 0 R + /Parent 10 0 R + /Prev 12 0 R + /Title (Monday 27 September 2010) >> +endobj +% 'Outline.3': class OutlineEntryObject +14 0 obj +<< /Count 11 + /Dest [ 4 0 R + /XYZ + 62.69291 + 174.0236 + 0 ] + /First 15 0 R + /Last 25 0 R + /Parent 10 0 R + /Prev 13 0 R + /Title (Tuesday 5 October 20010) >> +endobj +% 'Outline.16.0': class OutlineEntryObject +15 0 obj +<< /Dest [ 4 0 R + /XYZ + 62.69291 + 141.0236 + 0 ] + /Next 16 0 R + /Parent 14 0 R + /Title (tutorial0.pro) >> +endobj +% 'Outline.16.1': class OutlineEntryObject +16 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 753.0236 + 0 ] + /Next 17 0 R + /Parent 14 0 R + /Prev 15 0 R + /Title (auxingrowthplugin.h) >> +endobj +% 'Outline.16.2': class OutlineEntryObject +17 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 693.0236 + 0 ] + /Next 18 0 R + /Parent 14 0 R + /Prev 16 0 R + /Title (VirtualLeaf.cpp) >> +endobj +% 'Outline.16.3': class OutlineEntryObject +18 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 633.0236 + 0 ] + /Next 19 0 R + /Parent 14 0 R + /Prev 17 0 R + /Title (canvas.h) >> +endobj +% 'Outline.16.4': class OutlineEntryObject +19 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 585.0236 + 0 ] + /Next 20 0 R + /Parent 14 0 R + /Prev 18 0 R + /Title (canvas.cpp) >> +endobj +% 'Outline.16.5': class OutlineEntryObject +20 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 395.8236 + 0 ] + /Next 21 0 R + /Parent 14 0 R + /Prev 19 0 R + /Title (mesh.h) >> +endobj +% 'Outline.16.6': class OutlineEntryObject +21 0 obj +<< /Dest [ 6 0 R + /XYZ + 62.69291 + 250.4814 + 0 ] + /Next 22 0 R + /Parent 14 0 R + /Prev 20 0 R + /Title (mesh.cpp) >> +endobj +% 'Outline.16.7': class OutlineEntryObject +22 0 obj +<< /Dest [ 7 0 R + /XYZ + 62.69291 + 753.0236 + 0 ] + /Next 23 0 R + /Parent 14 0 R + /Prev 21 0 R + /Title (modelcatalogue.cpp) >> +endobj +% 'Outline.16.8': class OutlineEntryObject +23 0 obj +<< /Dest [ 7 0 R + /XYZ + 62.69291 + 705.0236 + 0 ] + /Next 24 0 R + /Parent 14 0 R + /Prev 22 0 R + /Title (simplugin.h) >> +endobj +% 'Outline.16.9': class OutlineEntryObject +24 0 obj +<< /Dest [ 7 0 R + /XYZ + 62.69291 + 611.8236 + 0 ] + /Next 25 0 R + /Parent 14 0 R + /Prev 23 0 R + /Title (simplugin.cpp) >> +endobj +% 'Outline.16.10': class OutlineEntryObject +25 0 obj +<< /Dest [ 7 0 R + /XYZ + 62.69291 + 530.6236 + 0 ] + /Parent 14 0 R + /Prev 24 0 R + /Title (xmlwrite.cpp) >> +endobj +% 'R26': class PDFPages +26 0 obj +% page tree +<< /Count 3 + /Kids [ 4 0 R + 6 0 R + 7 0 R ] + /Type /Pages >> +endobj +% 'R27': class PDFStream +27 0 obj +% page stream +<< /Length 8892 >> +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 (The Virtual Leaf) Tj T* 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 (Friday 11 June 2010) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 678.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Issues:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 672.0236 cm +Q +q +1 0 0 1 62.69291 405.0236 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +BT 1 0 0 1 0 2 Tm T* ET +q +1 0 0 1 20 267 cm +Q +q +1 0 0 1 20 267 cm +Q +q +1 0 0 1 20 225 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 27 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (1.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 28.82 Tm /F1 10 Tf 12 TL 1.55284 Tw (Every class that has an association or composition eventually will need its own custom view) Tj T* 0 Tw .83436 Tw (page template, e.g. sed_view. For the moment I have set the default view for these classes to) Tj T* 0 Tw (dev_view \( a copy of base_view \).) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 225 cm +Q +q +1 0 0 1 20 228 cm +Q +q +1 0 0 1 20 198 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 15 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (2.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 16.82 Tm /F1 10 Tf 12 TL 1.744651 Tw (An association in UML is cast as a ReferenceField in the resulting class schema. Open the) Tj T* 0 Tw (association and add the widget:label tag to the class that is being associated.) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 198 cm +Q +q +1 0 0 1 20 201 cm +Q +q +1 0 0 1 20 171 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 15 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (3.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 16.82 Tm /F1 10 Tf 12 TL .73061 Tw (The default description text for a class should be a informative description of the class, not the) Tj T* 0 Tw (instance, derived from the SED-ML manual.) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 171 cm +Q +q +1 0 0 1 20 174 cm +Q +q +1 0 0 1 20 156 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (4.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Apply 'searchable' tags to the appropriate class attributes.) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 156 cm +Q +q +1 0 0 1 20 159 cm +Q +q +1 0 0 1 20 141 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (5.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will this work?) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 141 cm +Q +q +1 0 0 1 20 144 cm +Q +q +1 0 0 1 20 0 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 129 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (6.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 117 cm +q +0 0 0 rg +BT 1 0 0 1 0 16.82 Tm /F1 10 Tf 12 TL .76811 Tw (What should be added to our implementation of SED-ML to make it more than merely a mirror) Tj T* 0 Tw (image of the SED-ML XML format?) Tj T* ET +Q +Q +q +1 0 0 1 23 111 cm +Q +q +1 0 0 1 23 3 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +BT 1 0 0 1 0 2 Tm T* ET +q +1 0 0 1 20 108 cm +Q +q +1 0 0 1 20 108 cm +Q +q +1 0 0 1 20 90 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (a.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (The ability to attach files at various points, e.g. parameter files.) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 90 cm +Q +q +1 0 0 1 20 93 cm +Q +q +1 0 0 1 20 75 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (b.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Additional output types, e.g. animations.) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 75 cm +Q +q +1 0 0 1 20 78 cm +Q +q +1 0 0 1 20 60 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 6.22 0 Td (c.) Tj T* -6.22 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Custom page templates) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 60 cm +Q +q +1 0 0 1 20 63 cm +Q +q +1 0 0 1 20 45 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (d.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Custom search form) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 45 cm +Q +q +1 0 0 1 20 48 cm +Q +q +1 0 0 1 20 30 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (e.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Custom catalog indexes) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 30 cm +Q +q +1 0 0 1 20 33 cm +Q +q +1 0 0 1 20 15 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 8.44 0 Td (f.) Tj T* -8.44 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Custom portlet\(s\)) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 15 cm +Q +q +1 0 0 1 20 18 cm +Q +q +1 0 0 1 20 0 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (g.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Custom viewlet\(s\)) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 20 0 cm +Q +q +1 0 0 1 20 0 cm +Q +q +Q +Q +q +1 0 0 1 23 3 cm +Q +q +Q +Q +q +1 0 0 1 20 0 cm +Q +q +1 0 0 1 20 0 cm +Q +q +Q +Q +q +1 0 0 1 62.69291 405.0236 cm +Q +q +1 0 0 1 62.69291 372.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Friday 24 September 2010) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 315.0236 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 0 36 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F2 10 Tf 12 TL (To Do:) Tj T* ET +Q +Q +BT 1 0 0 1 0 23 Tm T* ET +q +1 0 0 1 10 33 cm +Q +q +1 0 0 1 10 33 cm +Q +q +1 0 0 1 10 15 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (1.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Publish our mercurial repositories \(Chris/Martin\). This may mesh with deploying Plone.) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 10 15 cm +Q +q +1 0 0 1 10 18 cm +Q +q +1 0 0 1 10 0 cm +0 0 0 rg +BT /F1 10 Tf 12 TL ET +q +1 0 0 1 6 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL 5.66 0 Td (2.) Tj T* -5.66 0 Td ET +Q +Q +q +1 0 0 1 23 3 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Create a vleaf mailing list \(Henk\).) Tj T* ET +Q +Q +q +Q +Q +q +1 0 0 1 10 0 cm +Q +q +1 0 0 1 10 0 cm +Q +q +Q +Q +q +1 0 0 1 62.69291 285.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 16.82 Tm /F1 10 Tf 12 TL .602927 Tw (Found an article on SBRML - a markup language for associating systems biology data with models. At a) Tj T* 0 Tw (glance the schema seems bigger than SED-ML's, but SBRML appears to be SBML specific.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 252.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Monday 27 September 2010) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 186.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 52.82 Tm /F1 10 Tf 12 TL 3.993828 Tw (Spoke with Chris about publishing the Mercurial repositories and deploying Plone. Both can be) Tj T* 0 Tw .131567 Tw (accomplished in their own project space on a server in the DMZ. Chris said he would supply me with login) Tj T* 0 Tw 3.871984 Tw (credentials for both accounts. I will install Plone and Chris \(or Maarten\) will help me configure) Tj T* 0 Tw .795318 Tw (Apache/nginx and Varnish. Chris will install the required Mercurial packages; after which I can clone the) Tj T* 0 Tw (repositories to their new home.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 153.0236 cm +q +BT 1 0 0 1 0 8.435 Tm 21 TL /F2 17.5 Tf 0 0 0 rg (Tuesday 5 October 20010) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 123.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (tutorial0.pro) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 105.0236 cm +q +0 0 0 rg +BT 1 0 0 1 0 4.82 Tm /F1 10 Tf 12 TL (Added simplugin.h to list of header files. NB: this is the only tutorial in which simplugin.h appears.) 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 205.6499 0 Td 12 TL /F1 10 Tf 0 0 0 rg (The Virtual Leaf) Tj T* -205.6499 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 +% 'R28': class PDFStream +28 0 obj +% page stream +<< /Length 4804 >> +stream +1 0 0 1 0 0 cm BT /F1 12 Tf 14.4 TL ET +q +1 0 0 1 62.69291 735.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (auxingrowthplugin.h) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 705.0236 cm +q +BT 1 0 0 1 0 16.82 Tm 2.02498 Tw 12 TL /F1 10 Tf 0 0 0 rg (Declared, and defined, a virtual function named ) Tj /F3 10 Tf (DefaultLeafML\(\) ) Tj /F1 10 Tf (which merely returns a QString) Tj T* 0 Tw (naming a LeafML filename sans path.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 675.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (VirtualLeaf.cpp) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 645.0236 cm +q +BT 1 0 0 1 0 16.82 Tm 14.41996 Tw 12 TL /F1 10 Tf 0 0 0 rg (Moved ) Tj /F3 10 Tf (Cell::SetMagnification\(\) ) Tj /F1 10 Tf (and ) Tj /F3 10 Tf (Cell::SetOffset\(\) ) Tj /F1 10 Tf (from ) Tj /F3 10 Tf (main\(\) ) Tj /F1 10 Tf (to) Tj T* 0 Tw /F3 10 Tf (MainBase::Init\(\)) Tj /F1 10 Tf (.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 615.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (canvas.h) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 597.0236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Declare ) Tj /F3 10 Tf (exportCellData\(\)) Tj /F1 10 Tf (.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 567.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (canvas.cpp) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 537.0236 cm +q +BT 1 0 0 1 0 16.82 Tm 8.836412 Tw 12 TL /F1 10 Tf 0 0 0 rg (Add an 'Export cell areas' to the file dropdown menu which invokes - surprise -) Tj T* 0 Tw /F3 10 Tf (Main::exportCellData\(\)) Tj /F1 10 Tf (:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 407.8236 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 120 re B* +Q +q +BT 1 0 0 1 0 101.71 Tm 12 TL /F3 10 Tf 0 0 0 rg (void Main::exportCellData\(void\) {) Tj T* ( QFile file\("areas.csv"\);) Tj T* ( if \( file.open\( IO_WriteOnly \) \) {) Tj T* ( QTextStream stream\( ) Tj (&) Tj (file \);) Tj T* ( mesh.CSVExportCellData\(stream\);) Tj T* ( mesh.CSVExportMeshData\(stream\);) Tj T* ( file.close\(\);) Tj T* ( }) Tj T* (}) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 377.8236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (mesh.h) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 359.8236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Include ) Tj /F3 10 Tf (<) Tj (QTextStream) Tj (>) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 329.8236 cm +q +0 0 0 rg +BT 1 0 0 1 0 16.82 Tm /F1 10 Tf 12 TL .752765 Tw (Set the boundary_poloygon pointer to zero in the class constructor, and delete it, if it exists, in the class) Tj T* 0 Tw (destructor.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 311.8236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Declare ) Tj /F3 10 Tf (Compactness\(\)) Tj /F1 10 Tf (, ) Tj /F3 10 Tf (CSVExportCellData\(\) ) Tj /F1 10 Tf (and ) Tj /F3 10 Tf (CSVExportMeshData\(\)) Tj /F1 10 Tf (:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 262.4814 cm +q +q +.840289 0 0 .840289 0 0 cm +q +1 0 0 1 6.6 7.854438 cm +q +.662745 .662745 .662745 RG +.5 w +.960784 .960784 .862745 rg +n -6 -6 558 48 re B* +Q +q +BT 1 0 0 1 0 29.71 Tm 12 TL /F3 10 Tf 0 0 0 rg (double Compactness\(double *res_compactness=0, double *res_area=0, double *res_cell_area=0\);) Tj T* (void CSVExportCellData\(QTextStream ) Tj (&) Tj (csv_stream\) const;) Tj T* (void CSVExportMeshData\(QTextStream ) Tj (&) Tj (csv_stream\);) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 232.4814 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (mesh.cpp) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 214.4814 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (In ) Tj /F3 10 Tf (mesh::clear\(\)) Tj /F1 10 Tf (, delete the boundary_polygon only if the pointer hasn't been assigned:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 145.2814 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 60 re B* +Q +q +0 0 0 rg +BT 1 0 0 1 0 41.71 Tm /F3 10 Tf 12 TL (if \(boundary_polygon\) {) Tj T* ( delete boundary_polygon;) Tj T* ( boundary_polygon=0;) Tj T* ( }) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 125.2814 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Ditto for ) Tj /F3 10 Tf (mesh::clean\(\)) Tj /F1 10 Tf (.) 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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 205.6499 0 Td 12 TL /F1 10 Tf 0 0 0 rg (The Virtual Leaf) Tj T* -205.6499 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 +% 'R29': class PDFStream +29 0 obj +% page stream +<< /Length 2249 >> +stream +1 0 0 1 0 0 cm BT /F1 12 Tf 14.4 TL ET +q +1 0 0 1 62.69291 735.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (modelcatalogue.cpp) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 717.0236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (In ) Tj /F3 10 Tf (InstallModel\(\)) Tj /F1 10 Tf (, find and load the default LeafML file.) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 687.0236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (simplugin.h) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 669.0236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Declare ) Tj /F3 10 Tf (DefaultLeafML\(\)) Tj /F1 10 Tf (:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 623.8236 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 36 re B* +Q +q +0 0 0 rg +BT 1 0 0 1 0 17.71 Tm /F3 10 Tf 12 TL (// Default LeafML-file to be read after model startup) Tj T* (virtual QString DefaultLeafML\(void\);) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 593.8236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (simplugin.cpp) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 575.8236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (Define ) Tj /F3 10 Tf (DefaultLeafML\(\)) Tj /F1 10 Tf (. Returns an empty ) Tj /F3 10 Tf (QString) Tj /F1 10 Tf (:) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 542.6236 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 +0 0 0 rg +BT 1 0 0 1 0 5.71 Tm /F3 10 Tf 12 TL (QString SimPluginInterface::DefaultLeafML\(void\) { return QString\(\); }) Tj T* ET +Q +Q +Q +Q +Q +q +1 0 0 1 62.69291 512.6236 cm +q +BT 1 0 0 1 0 7.23 Tm 18 TL /F2 15 Tf 0 0 0 rg (xmlwrite.cpp) Tj T* ET +Q +Q +q +1 0 0 1 62.69291 494.6236 cm +q +BT 1 0 0 1 0 4.82 Tm 12 TL /F1 10 Tf 0 0 0 rg (In ) Tj /F3 10 Tf (Mesh::XMLReadCells\(\) ) Tj /F1 10 Tf (- Delete the boundary_ploygon only if its pointer has been assigned.) 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Every class that has an association or composition eventually will + need its own custom view page template, e.g. sed_view. For the moment + I have set the default view for these classes to dev_view ( a copy of + base_view ). + + 2. An association in UML is cast as a ReferenceField in the resulting + class schema. Open the association and add the widget:label tag to + the class that is being associated. + + 3. The default description text for a class should be a informative + description of the class, not the instance, derived from the + SED-ML manual. + + 4. Apply 'searchable' tags to the appropriate class attributes. + + 5. I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will + this work? + + 6. What should be added to our implementation of SED-ML to make it + more than merely a mirror image of the SED-ML XML format? + + a. The ability to attach files at various points, e.g. parameter files. + + b. Additional output types, e.g. animations. + + c. Custom page templates + + d. Custom search form + + e. Custom catalog indexes + + f. Custom portlet(s) + + g. Custom viewlet(s) + + +Friday 24 September 2010 +------------------------ + +To Do: + 1. Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone. + + 2. Create a vleaf mailing list (Henk). + +Found an article on SBRML - a markup language for associating systems +biology data with models. At a glance the schema seems bigger than +SED-ML's, but SBRML appears to be SBML specific. + + + +Monday 27 September 2010 +------------------------ + +Spoke with Chris about publishing the Mercurial repositories and +deploying Plone. Both can be accomplished in their own project space +on a server in the DMZ. Chris said he would supply me with login +credentials for both accounts. I will install Plone and Chris (or +Maarten) will help me configure Apache/nginx and Varnish. Chris will +install the required Mercurial packages; after which I can clone the +repositories to their new home. + + + +Tuesday 5 October 20010 +----------------------- + + +tutorial0.pro ++++++++++++++ + +Added simplugin.h to list of header files. NB: this is the only +tutorial in which simplugin.h appears. + + +auxingrowthplugin.h ++++++++++++++++++++ + +Declared, and defined, a virtual function named ``DefaultLeafML()`` +which merely returns a QString naming a LeafML filename sans path. + + + +VirtualLeaf.cpp ++++++++++++++++ + +Moved ``Cell::SetMagnification()`` and ``Cell::SetOffset()`` from +``main()`` to ``MainBase::Init()``. + + +canvas.h +++++++++ + +Declare ``exportCellData()``. + + +canvas.cpp +++++++++++ + +Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - ``Main::exportCellData()``:: + + void Main::exportCellData(void) { + QFile file("areas.csv"); + if ( file.open( IO_WriteOnly ) ) { + QTextStream stream( &file ); + mesh.CSVExportCellData(stream); + mesh.CSVExportMeshData(stream); + file.close(); + } + } + + +mesh.h +++++++ + +Include ```` + +Set the boundary_poloygon pointer to zero in the class constructor, +and delete it, if it exists, in the class destructor. + +Declare ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``:: + + double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0); + void CSVExportCellData(QTextStream &csv_stream) const; + void CSVExportMeshData(QTextStream &csv_stream); + + +mesh.cpp +++++++++ + +In ``mesh::clear()``, delete the boundary_polygon only if the pointer hasn't been assigned:: + + if (boundary_polygon) { + delete boundary_polygon; + boundary_polygon=0; + } + +Ditto for ``mesh::clean()``. + +Define the code for ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``. + + + +modelcatalogue.cpp +++++++++++++++++++ + +In ``InstallModel()``, find and load the default LeafML file. + +simplugin.h ++++++++++++ + +Declare ``DefaultLeafML()``:: + + // Default LeafML-file to be read after model startup + virtual QString DefaultLeafML(void); + + +simplugin.cpp ++++++++++++++ + +Define ``DefaultLeafML()``. Returns an empty ``QString``:: + + QString SimPluginInterface::DefaultLeafML(void) { return QString(); } + + +xmlwrite.cpp +++++++++++++ + +In ``Mesh::XMLReadCells()`` - Delete the boundary_ploygon only if its +pointer has been assigned. + + + +Wednesday 6 October 2010 +------------------------ + +Wrote Simon van Mourik about his missing libiconv-2.dll. + + +Thursday 7 October 2010 +----------------------- + +Added a Q3FileDialog in ``canvas.cpp:Main::exportCellData(void)`` to +choose where to write the exported cell data. diff --git a/src/ChangeLog b/src/ChangeLog --- a/src/ChangeLog +++ b/src/ChangeLog @@ -1,3 +1,8 @@ +2010-10-07 + + * canvas.cpp (exportCellData): Added a Q3FileDialog to inquire + where to write the exportCellData. + 2010-06-28 diff --git a/src/canvas.cpp b/src/canvas.cpp --- a/src/canvas.cpp +++ b/src/canvas.cpp @@ -1367,17 +1367,32 @@ xmlNode *Main::XMLSettingsTree(void) } void Main::exportCellData(void) { + Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE ); + QString fileName; + + stopSimulation(); + fd->setMode( Q3FileDialog::AnyFile ); + + if ( fd->exec() == QDialog::Accepted ) { + fileName = fd->selectedFile(); + +#ifdef QDEBUG + qDebug() << "exportCellData filename: " << fileName << endl; +#endif // perhaps make this more general: a popup window were user selects data he wants to export // can go to "settings" section of XML file as well so this can also be measured off-line // mesh.CSVExport would take an QMap or so to record all options // first line gives legenda - QFile file("areas.csv"); - if ( file.open( IO_WriteOnly ) ) { - QTextStream stream( &file ); - mesh.CSVExportCellData(stream); - mesh.CSVExportMeshData(stream); - file.close(); + + QFile file(fileName); + if ( file.open( IO_WriteOnly ) ) { + QTextStream stream( &file ); + mesh.CSVExportCellData(stream); + mesh.CSVExportMeshData(stream); + file.close(); + } } } + /* finis */ diff --git a/src/leaficon.png b/src/leaficon.png new file mode 100644 index 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