add(menuItem);\r
\r
if(ap.av.getSelectionGroup() !=null\r
- && ap.av.getSelectionGroup().getSize(false)>1)\r
+ && ap.av.getSelectionGroup().getSize()>1)\r
{\r
menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
ap.av.alignment.getWidth());\r
refresh();\r
}\r
if (abovePIDColour.isSelected())\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(true), sg.getStartRes(),\r
+ sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
sg.getEndRes() + 1));\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
sg.getStartRes(),\r
sg.getEndRes() + 1));\r
refresh();\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
sg.getStartRes(),\r
sg.getEndRes() + 1));\r
\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true),\r
+ sg.getSequences(ap.av.hiddenRepSequences),\r
sg.getStartRes(),\r
sg.getEndRes() + 1);\r
\r
void hideSequences(boolean representGroup)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize(false)<1)\r
+ if(sg==null || sg.getSize()<1)\r
{\r
ap.av.hideSequence(new SequenceI[]{sequence});\r
return;\r
}\r
\r
- int gsize = sg.getSize(false);\r
- SequenceI [] hseqs;\r
+ ap.av.setSelectionGroup(null);\r
\r
- hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(sequence, sg);\r
\r
- int index = 0;\r
- for(int i=0; i<gsize; i++)\r
- {\r
- if(representGroup && sg.getSequenceAt(i)!=sequence)\r
- {\r
- sequence.addHiddenSequence(sg.getSequenceAt(i));\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
- else if(!representGroup)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
- }\r
+ return;\r
+ }\r
\r
- ap.av.hideSequence(hseqs);\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
\r
- ap.av.setSelectionGroup(null);\r
+ hseqs = new SequenceI[gsize];\r
+\r
+ int index = 0;\r
+ for (int i = 0; i < gsize; i++)\r
+ {\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
}\r
\r
public void copy_actionPerformed(ActionEvent e)\r
}\r
\r
ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
- description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+ description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
+ startEnd, caseChange\r
);\r
\r
ap.alignFrame.addHistoryItem(caseCommand);\r
if(sg==null)\r
return;\r
\r
- int gSize= sg.getSize(false);\r
+ int gSize= sg.getSize();\r
SequenceI [] seqs = new SequenceI[gSize];\r
SequenceFeature [] features = new SequenceFeature[gSize];\r
\r