+ if (seq != null && links!=null)\r
+ {\r
+ Menu linkMenu = new Menu("Link");\r
+ MenuItem item;\r
+ String link;\r
+ for(int i=0; i<links.size(); i++)\r
+ {\r
+ link = links.elementAt(i).toString();\r
+ final String target = link.substring(0, link.indexOf("|"));\r
+ item = new MenuItem(target);\r
+ String id = seq.getName();\r
+ if(id.indexOf("|")>-1)\r
+ id = id.substring(id.lastIndexOf("|")+1);\r
+\r
+ final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+ });\r
+ linkMenu.add(item);\r
+ }\r
+ add(linkMenu);\r
+\r
+ item = new MenuItem("Show PDB Structure");\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addPDB(seq);\r
+ }\r
+ });\r
+\r
+ add(item);\r
+\r
+\r
+ }\r
+ }\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==abovePIDColour)\r
+ abovePIDColour_itemStateChanged();\r
+ else if(evt.getSource()==showColourText)\r
+ showColourText_itemStateChanged();\r
+ else if(evt.getSource()==showText)\r
+ showText_itemStateChanged();\r
+ else if(evt.getSource()==showBoxes)\r
+ showBoxes_itemStateChanged() ;\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+ if(source==clustalColour)\r
+ clustalColour_actionPerformed();\r
+ else if(source==zappoColour)\r
+ zappoColour_actionPerformed();\r
+ else if(source==taylorColour)\r
+ taylorColour_actionPerformed();\r
+ else if(source==hydrophobicityColour)\r
+ hydrophobicityColour_actionPerformed();\r
+ else if(source==helixColour)\r
+ helixColour_actionPerformed();\r
+ else if(source==strandColour)\r
+ strandColour_actionPerformed();\r
+ else if(source==clustalColour)\r
+ turnColour_actionPerformed();\r
+ else if(source==buriedColour)\r
+ buriedColour_actionPerformed();\r
+ else if(source==nucleotideMenuItem)\r
+ nucleotideMenuItem_actionPerformed();\r
+\r
+ else if(source==userDefinedColour)\r
+ userDefinedColour_actionPerformed();\r
+ else if(source==PIDColour)\r
+ PIDColour_actionPerformed();\r
+ else if(source==BLOSUM62Colour)\r
+ BLOSUM62Colour_actionPerformed();\r
+ else if(source==noColourmenuItem)\r
+ noColourmenuItem_actionPerformed();\r
+ else if(source==conservationMenuItem)\r
+ conservationMenuItem_itemStateChanged();\r
+ else if(source==unGroupMenuItem)\r
+ unGroupMenuItem_actionPerformed();\r
+\r
+ else if(source==copy)\r
+ ap.alignFrame.copy_actionPerformed();\r
+ else if(source==cut)\r
+ ap.alignFrame.cut_actionPerformed();\r
+ else if(source==toUpper || source==toLower || source==toggleCase)\r