\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
- if (sg != null && sg.getSize(false)>0)\r
+ if (sg != null && sg.getSize()>0)\r
{\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
}\r
\r
ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
- description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+ description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange\r
);\r
\r
ap.alignFrame.addHistoryItem(caseCommand);\r
protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
+ ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
\r
if (abovePIDColour.getState())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
\r
refresh();\r
\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
+ sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\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[]{seq});\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(seq, sg);\r
\r
- int index = 0;\r
- for(int i=0; i<gsize; i++)\r
- {\r
- if(representGroup && sg.getSequenceAt(i)!=seq)\r
- {\r
- seq.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
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
\r
- ap.av.hideSequence(hseqs);\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.setSelectionGroup(null);\r
+ ap.av.hideSequence(hseqs);\r
}\r
\r
}\r