seq.findPosition(sg.getStartRes()) + "\t"\r
+ seq.findPosition(sg.getEndRes()) + "\t"\r
+\r
- sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+ seq.getSequence(sg.getStartRes(),\r
sg.getEndRes() + 1) + "\n");\r
}\r
\r
return;\r
}\r
\r
+\r
SequenceGroup sg = viewport.getSelectionGroup();\r
+ boolean allSequences = false;\r
+ if(sg.sequences.size()==viewport.alignment.getHeight())\r
+ allSequences = true;\r
+\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (allSequences)\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+\r
if (seq.getSequence().length() < 1)\r
{\r
viewport.getAlignment().deleteSequence(seq);\r
SequenceGroup sg = new SequenceGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
sg.setEndRes(viewport.alignment.getWidth());\r
viewport.setSelectionGroup(sg);\r
SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
\r
PaintRefresher.Refresh(null);\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Remove Gaps",\r
- viewport.alignment,\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
+\r
SequenceI current;\r
int jSize;\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+\r
+ Vector seqs=null;\r
+\r
+ int start=0, end = viewport.alignment.getWidth();\r
+\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
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ seqs = viewport.alignment.getSequences();\r
+\r
+ for (int i = 0; i <seqs.size(); i++)\r
{\r
- current = viewport.getAlignment().getSequenceAt(i);\r
+ current = (SequenceI)seqs.elementAt(i);\r
jSize = current.getLength();\r
- for (int j = 0; j < jSize; j++)\r
+\r
+ int j = start;\r
+ do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
j--;\r
jSize--;\r
}\r
+ j++;\r
}\r
+ while(j < end && j < jSize) ;\r
}\r
+\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
alignPanel.repaint();\r
}\r
\r
+\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
Finder finder = new Finder(alignPanel);\r
{\r
( (ResidueColourScheme) cs).setThreshold(threshold);\r
}\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
- }\r
\r
viewport.setGlobalColourScheme(cs);\r
}\r
{\r
( (ResidueColourScheme) cs).setThreshold(0);\r
}\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
- }\r
\r
if (viewport.getConservationSelected())\r
{\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
+ if(cs==null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
+ cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
+ sg.cs = cxs;\r
}\r
else\r
{\r
{\r
( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
}\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
}\r
addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.repaint();\r
+\r
}\r
\r
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
\r
protected void documentation_actionPerformed(ActionEvent e)\r
{\r
-\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
-\r
+ jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
}\r
\r
protected void about_actionPerformed(ActionEvent e)\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 2.0", 200, y += fh);\r
+ g.drawString("JalView - Release 2.01", 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