\r
if(toggleSeqs)\r
{\r
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
{\r
hide = true;\r
viewport.hideAllSelectedSeqs();\r
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(false).contains(seq))\r
+ if (!sg.getSequences(null).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.getSequences(false).contains(temp))\r
+ if (sg.getSequences(null).contains(temp))\r
{\r
continue;\r
}\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(true).contains(seq))\r
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.getSequences(true).contains(temp))\r
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
{\r
continue;\r
}\r
SequenceGroup sg = viewport.getSelectionGroup();\r
copiedSequences = new StringBuffer();\r
Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
copiedHiddenColumns = null;\r
\r
\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
SequenceI seq = null;\r
\r
\r
Vector seqs = new Vector();\r
SequenceI seq;\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
seq = sg.getSequenceAt(i);\r
seqs.addElement(seq);\r
\r
\r
// If the cut affects all sequences, remove highlighted columns\r
- if (sg.getSize(false) == viewport.alignment.getHeight())\r
+ if (sg.getSize() == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
sg.getEndRes() + 1);\r
\r
SequenceI [] seqs;\r
if(viewport.getSelectionGroup()!=null)\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
else\r
seqs = viewport.alignment.getSequencesArray();\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
}\r
else\r
{\r
|| cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
}\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
if (viewport.getSelectionGroup()!=null\r
- && viewport.getSelectionGroup().getSize(false) > 1)\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) < 4 &&\r
- viewport.getSelectionGroup().getSize(false) > 0)\r
+ viewport.getSelectionGroup().getSize() < 4 &&\r
+ viewport.getSelectionGroup().getSize() > 0)\r
|| viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) > 1)\r
+ viewport.getSelectionGroup().getSize() > 1)\r
|| (viewport.getSelectionGroup() == null\r
&& viewport.alignment.getHeight() > 1))\r
{\r