}\r
catch (Exception ex)\r
{\r
+ ex.printStackTrace();\r
}\r
}\r
\r
object.setVamsasModel(new VamsasModel());\r
\r
object.setCreationDate(new java.util.Date(timeStamp));\r
- object.setVersion(jalview.bin.Cache.VERSION);\r
+ object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
\r
jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
\r
///////////////////////////////////\r
if (af.viewport.currentTree != null)\r
{\r
- // FIND ANY ASSOCIATED TREES\r
+ // FIND ANY ASSOCIATED TREES\r
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
+ if (Desktop.desktop != null)\r
+ {\r
JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
\r
for (int t = 0; t < frames.length; t++)\r
{\r
- if (frames[t] instanceof TreePanel)\r
- {\r
- TreePanel tp = (TreePanel) frames[t];\r
+ if (frames[t] instanceof TreePanel)\r
+ {\r
+ TreePanel tp = (TreePanel) frames[t];\r
\r
- if (tp.treeCanvas.av.alignment == jal)\r
- {\r
- Tree tree = new Tree();\r
- tree.setTitle(tp.getTitle());\r
- tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));\r
- tree.setNewick(tp.getTree().toString());\r
- tree.setThreshold(tp.treeCanvas.threshold);\r
-\r
- tree.setFitToWindow(tp.fitToWindow.getState());\r
- tree.setFontSize(tp.treeCanvas.fontSize);\r
- tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
- tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
- tree.setShowDistances(tp.distanceMenu.getState());\r
-\r
- tree.setHeight(tp.getHeight());\r
- tree.setWidth(tp.getWidth());\r
- tree.setXpos(tp.getX());\r
- tree.setYpos(tp.getY());\r
-\r
- jms.addTree(tree);\r
- }\r
+ if (tp.treeCanvas.av.alignment == jal)\r
+ {\r
+ Tree tree = new Tree();\r
+ tree.setTitle(tp.getTitle());\r
+ tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
+ tree.setNewick(tp.getTree().toString());\r
+ tree.setThreshold(tp.treeCanvas.threshold);\r
+\r
+ tree.setFitToWindow(tp.fitToWindow.getState());\r
+ tree.setFontSize(tp.treeCanvas.fontSize);\r
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
+ tree.setShowDistances(tp.distanceMenu.getState());\r
+\r
+ tree.setHeight(tp.getHeight());\r
+ tree.setWidth(tp.getWidth());\r
+ tree.setXpos(tp.getX());\r
+ tree.setYpos(tp.getY());\r
+\r
+ jms.addTree(tree);\r
}\r
+ }\r
}\r
+ }\r
}\r
\r
//SAVE ANNOTATIONS\r
groups[i].setEnd(sg.getEndRes());\r
groups[i].setName(sg.getName());\r
\r
- if (sg.cs instanceof ConservationColourScheme)\r
+ if (sg.cs.conservationApplied())\r
{\r
- groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);\r
- }\r
+ groups[i].setConsThreshold(sg.cs.getConservationInc());\r
\r
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold());\r
+ if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ {\r
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
+ jms));\r
+ }\r
+ else\r
+ {\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));\r
+ }\r
}\r
\r
- if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
{\r
groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
jms));\r
}\r
else\r
{\r
- groups[i].setColour(ColourSchemeProperty.getColourName(\r
- sg.cs));\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(\r
+ sg.cs));\r
}\r
\r
+\r
+ groups[i].setPidThreshold( sg.cs.getThreshold() );\r
+\r
groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
groups[i].setDisplayText(sg.getDisplayText());\r
\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
- if (cs instanceof ConservationColourScheme)\r
+ if (cs.conservationApplied())\r
{\r
- view.setConsThreshold(((ConservationColourScheme) cs).inc);\r
+ view.setConsThreshold(cs.getConservationInc());\r
+ if(cs instanceof jalview.schemes.UserColourScheme)\r
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
}\r
\r
if (cs instanceof ResidueColourScheme)\r
{\r
- view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- view.setPidThreshold(((ScoreColourScheme) cs).getThreshold());\r
+ view.setPidThreshold( cs.getThreshold() );\r
}\r
\r
view.setConservationSelected(av.getConservationSelected());\r
view.setPidSelected(av.getAbovePIDThreshold());\r
- view.setFontName(av.font.getFontName());\r
+ view.setFontName(av.font.getName());\r
view.setFontSize(av.font.getSize());\r
view.setFontStyle(av.font.getStyle());\r
view.setRenderGaps(av.renderGaps);\r
}\r
catch (Exception ex)\r
{\r
+ ex.printStackTrace();\r
System.err.println("Exception whilst loading jalview XML file : " +\r
ex + "\n");\r
JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
groups[i].getColour());\r
}\r
\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
- }\r
+ cs.setThreshold(groups[i].getPidThreshold(), true);\r
}\r
\r
Vector seqs = new Vector();\r
sg.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, 25);\r
- cs = new ConservationColourScheme(c, cs);\r
- sg.cs = cs;\r
+ sg.cs.setConservation(c);\r
}\r
\r
al.addGroup(sg);\r
cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
}\r
\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- ((ConservationColourScheme) cs).inc = view.getConsThreshold();\r
- }\r
+ cs.setThreshold(view.getPidThreshold(), true);\r
\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
- }\r
+ if(cs!=null)\r
+ cs.setConsensus(af.viewport.vconsensus);\r
}\r
\r
+ af.setColourSelected(view.getBgColour());\r
af.viewport.setGlobalColourScheme(cs);\r
-\r
af.viewport.setColourAppliesToAllGroups(false);\r
af.changeColour(af.viewport.getGlobalColourScheme());\r
+ if (view.getConservationSelected())\r
+ {\r
+ af.viewport.getGlobalColourScheme().setConservationInc(view.getConsThreshold());\r
+ }\r
+\r
af.viewport.setColourAppliesToAllGroups(true);\r
\r
if (view.getShowSequenceFeatures())\r
git://source.jalview.org / jalview.git / blobdiff