+ if (sg.cs instanceof ZappoColourScheme)\r
+ {\r
+ zappoColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof TaylorColourScheme)\r
+ {\r
+ taylorColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof PIDColourScheme)\r
+ {\r
+ PIDColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof Blosum62ColourScheme)\r
+ {\r
+ BLOSUM62Colour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof UserColourScheme)\r
+ {\r
+ userDefinedColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof HydrophobicColourScheme)\r
+ {\r
+ hydrophobicityColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof HelixColourScheme)\r
+ {\r
+ helixColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof StrandColourScheme)\r
+ {\r
+ strandColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof TurnColourScheme)\r
+ {\r
+ turnColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof BuriedColourScheme)\r
+ {\r
+ buriedColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ clustalColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)\r
+ {\r
+ purinePyrimidineColour.setSelected(true);\r
+ }\r
+ /*\r
+ * else if (sg.cs instanceof CovariationColourScheme) {\r
+ * covariationColour.setSelected(true); }\r
+ */\r
+ else\r
+ {\r
+ noColourmenuItem.setSelected(true);\r
+ }\r
+\r
+ if (sg.cs != null && sg.cs.conservationApplied())\r
+ {\r
+ conservationMenuItem.setSelected(true);\r
+ }\r
+ displayNonconserved.setSelected(sg.getShowNonconserved());\r
+ showText.setSelected(sg.getDisplayText());\r
+ showColourText.setSelected(sg.getColourText());\r
+ showBoxes.setSelected(sg.getDisplayBoxes());\r
+ // add any groupURLs to the groupURL submenu and make it visible\r
+ if (groupLinks != null && groupLinks.size() > 0)\r
+ {\r
+ buildGroupURLMenu(sg, groupLinks);\r
+ }\r
+ // Add a 'show all structures' for the current selection\r
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();\r
+ SequenceI sqass = null;\r
+ for (SequenceI sq : ap.av.getSequenceSelection())\r
+ {\r
+ Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()\r
+ .getPDBId();\r
+ if (pes != null)\r
+ {\r
+ for (PDBEntry pe : pes)\r
+ {\r
+ pdbe.put(pe.getId(), pe);\r
+ if (sqass == null)\r
+ {\r
+ sqass = sq;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (pdbe.size() > 0)\r
+ {\r
+ final PDBEntry[] pe = pdbe.values().toArray(\r
+ new PDBEntry[pdbe.size()]);\r
+ final JMenuItem gpdbview;\r
+ if (pdbe.size() == 1)\r
+ {\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
+ }\r
+ else\r
+ {\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r