+ al.addGroup(sg);\r
+ }\r
+ }\r
+\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.setShowAnnotation(view.getShowAnnotation());\r
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
+ af.viewport.setColourText(view.getShowColourText());\r
+ af.viewport.setConservationSelected(view.getConservationSelected());\r
+ af.viewport.setShowJVSuffix(view.getShowFullId());\r
+ af.viewport.setFont(new java.awt.Font(view.getFontName(), view\r
+ .getFontStyle(), view.getFontSize()));\r
+ af.alignPanel.fontChanged();\r
+\r
+ af.viewport.setRenderGaps(view.getRenderGaps());\r
+ af.viewport.setWrapAlignment(view.getWrapAlignment());\r
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
+ af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\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 != null)\r
+ {\r
+ cs.setThreshold(view.getPidThreshold(), true);\r
+ cs.setConsensus(af.viewport.hconsensus);\r
+ }\r
+ }\r
+\r
+ af.viewport.setGlobalColourScheme(cs);\r
+ af.viewport.setColourAppliesToAllGroups(false);\r
+ af.changeColour(cs);\r
+ if (view.getConservationSelected() && cs != null)\r
+ {\r
+ cs.setConservationInc(view.getConsThreshold());\r
+ }\r
+\r
+ af.viewport.setColourAppliesToAllGroups(true);\r
+ af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
+\r
+ if (jms.getFeatureSettings() != null)\r
+ {\r
+ af.viewport.featuresDisplayed = new Hashtable();\r
+ String[] renderOrder = new String[jms.getFeatureSettings()\r
+ .getSettingCount()];\r
+ for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)\r
+ {\r
+ Setting setting = jms.getFeatureSettings().getSetting(fs);\r
+\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(\r
+ setting.getType(), new java.awt.Color(setting.getColour()));\r
+\r
+ renderOrder[fs] = setting.getType();\r
+\r
+ if (setting.getDisplay())\r