\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
- if (sg != null && sg.getSize()>0)\r
+ if (sg != null && sg.getSize(false)>0)\r
{\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
if (sg != null)\r
{\r
- for (int g = 0; g < sg.getSize(); g++)\r
+ for (int g = 0; g < sg.getSize(true); g++)\r
{\r
if (source == toggleCase)\r
- sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+ ((SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
else\r
- sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),\r
+ ((SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == toUpper, sg.getStartRes(),\r
sg.getEndRes() + 1);\r
}\r
ap.seqPanel.seqCanvas.repaint();\r
protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
\r
if (abovePIDColour.getState())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 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.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
ap.av.alignment.getWidth()));\r
\r
refresh();\r
\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(true), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r