-\r
- al.addGroup(sg);\r
- }\r
- }\r
-\r
- Desktop.addInternalFrame(af, view.getTitle(),\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
- view.getHeight());\r
- af.viewport.setStartRes(view.getStartRes());\r
- af.viewport.setStartSeq(view.getStartSeq());\r
- af.viewport.showConservation = view.getShowConservation();\r
- af.viewport.showQuality = view.getShowQuality();\r
- af.viewport.showIdentity = view.getShowIdentity();\r
- af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
- af.viewport.setColourText(view.getShowColourText());\r
- af.viewport.setConservationSelected(view.getConservationSelected());\r
- af.viewport.setShowFullId(view.getShowFullId());\r
- af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(), view.getFontSize()));\r
- af.alignPanel.fontChanged();\r
-\r
- af.sequenceFeatures_actionPerformed(null);\r
- af.viewport.setRenderGaps(view.getRenderGaps());\r
-\r
- af.viewport.setWrapAlignment(view.getWrapAlignment());\r
-\r
- if (view.getWrapAlignment())\r
- {\r
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
- }\r
- else\r
- {\r
- af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
- }\r
-\r
- af.viewport.setShowBoxes(view.getShowBoxes());\r
- af.viewport.setShowText(view.getShowText());\r
-\r
- ColourSchemeI cs = null;\r
-\r
- if (view.getBgColour() != null)\r
- {\r
- if (view.getBgColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, view.getBgColour());\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
- }\r
-\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
- }\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
- }\r
-\r
- af.viewport.setGlobalColourScheme(cs);\r
-\r
- af.viewport.setColourAppliesToAllGroups(false);\r
- af.changeColour(af.viewport.getGlobalColourScheme());\r
- af.viewport.setColourAppliesToAllGroups(true);\r
-\r
- if (view.getShowSequenceFeatures())\r
- {\r
- af.viewport.showSequenceFeatures = true;\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,\r
- af.alignPanel);\r
- al.featuresAdded = true;\r
- }\r
-\r
- //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
- if (object.getVamsasModel().getTreeCount() > 0)\r
- {\r
- try\r
- {\r
- af.ShowNewickTree(new jalview.io.NewickFile(\r
- (String) object.getVamsasModel().getTree(0)), "Tree");\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r