/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
e.printStackTrace();\r
}\r
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
{\r
- MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
- elementAt(\r
- i));\r
+ MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
item.addActionListener(this);\r
outputmenu.add(item);\r
}\r
else\r
url = link.substring(link.lastIndexOf("|")+1);\r
\r
- System.out.println("add "+url +" "+target);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
helixColour_actionPerformed();\r
else if(source==strandColour)\r
strandColour_actionPerformed();\r
- else if(source==clustalColour)\r
+ else if(source==turnColour)\r
turnColour_actionPerformed();\r
else if(source==buriedColour)\r
buriedColour_actionPerformed();\r
else if(source == revealAll)\r
{\r
ap.av.showAllHiddenSeqs();\r
- ap.repaint();\r
}\r
\r
else if(source==copy)\r
else if(source==cut)\r
ap.alignFrame.cut_actionPerformed();\r
else if(source==toUpper || source==toLower || source==toggleCase)\r
- {\r
+ {/*\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
if (sg != null)\r
{\r
for (int g = 0; g < sg.getSize(true); g++)\r
{\r
- if (source == toggleCase)\r
- ((SequenceI) sg.getSequences(true).elementAt(g))\r
- .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
- else\r
- ((SequenceI) sg.getSequences(true).elementAt(g))\r
- .changeCase(source == toUpper, sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ end = sg.getEndRes() + 1;\r
+ if (end > sg.getEndRes())\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+\r
+ if (source == toggleCase)\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(start, end);\r
+ else\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == toUpper, start, end);\r
+\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(end);\r
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ }\r
+\r
+ }\r
+ while (end < sg.getEndRes());\r
}\r
ap.seqPanel.seqCanvas.repaint();\r
- }\r
+ }*/\r
}\r
else\r
outputText(evt);\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
if(sg==null || sg.getSize(false)<1)\r
{\r
- ap.av.hideSequence(seq);\r
+ ap.av.hideSequence(new SequenceI[]{seq});\r
return;\r
}\r
\r
+ int gsize = sg.getSize(false);\r
+ SequenceI [] hseqs;\r
+\r
+ hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+\r
int index = 0;\r
- while(index < sg.getSize(false))\r
+ for(int i=0; i<gsize; i++)\r
{\r
- if(representGroup && sg.getSequenceAt(index)!=seq)\r
+ if(representGroup && sg.getSequenceAt(i)!=seq)\r
{\r
- seq.addHiddenSequence(sg.getSequenceAt(index));\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
+ seq.addHiddenSequence(sg.getSequenceAt(i));\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
}\r
else if(!representGroup)\r
{\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
}\r
- index ++;\r
- }\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
\r
ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
- refresh();\r
}\r
\r
}\r