}\r
}\r
\r
+\r
}\r
\r
public void inputText_actionPerformed(ActionEvent e)\r
orderedSeqs.put(index + "", seq);\r
}\r
\r
- int index = 0;\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
- SequenceI seq = null;\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
{\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
}\r
- else\r
+\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
{\r
- index++;\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if(endRes>0)\r
+ {\r
+ endRes += seq.getStart() -1;\r
}\r
- }\r
\r
- copiedSequences.append(seq.getName() + "\t" +\r
- seq.findPosition(sg.getStartRes()) + "\t"\r
- + seq.findPosition(sg.getEndRes()) + "\t"\r
- +\r
- sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ copiedSequences.append(seq.getName() + "\t" +\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
}\r
\r
int start=0, end = viewport.alignment.getWidth();\r
\r
- if(viewport.getSelectionGroup()!=null\r
- || viewport.getSelectionGroup().sequences.size()<1)\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size()>0)\r
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
\r
if (cs instanceof ResidueColourScheme)\r
{\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
}\r
\r
viewport.setGlobalColourScheme(cs);\r
}\r
else if (cs instanceof ResidueColourScheme)\r
{\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
+ ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
}\r
\r
if (viewport.getConservationSelected())\r
{\r
if (sg.cs instanceof ResidueColourScheme)\r
{\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
}\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
}\r
}\r
\r
+ updateCSConsensus();\r
+\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
alignPanel.repaint();\r
}\r
\r
+ public void updateCSConsensus()\r
+ {\r
+ //Colour schemes must have their consensus updated\r
+\r
+ }\r
+\r
protected void modifyPID_actionPerformed(ActionEvent e)\r
{\r
if (viewport.getAbovePIDThreshold())\r
//are the sequences aligned?\r
if (!viewport.alignment.isAligned())\r
{\r
- return;\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
+\r
}\r
\r
final TreePanel tp;\r
int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("JalView - Release 2.01", 200, y += fh);\r
+ g.drawString("JalView - Release 2.02", 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
x, y += fh * 2);\r