alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
alignPanel.repaint();\r
}\r
- else\r
- {\r
- System.out.println("No Features found for " +\r
- evt.getDasSource().getNickname());\r
- }\r
}\r
\r
Hashtable progressBars;\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).contains(temp))\r
{\r
continue;\r
}\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).contains(temp))\r
{\r
continue;\r
}\r
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
\r
Hashtable orderedSeqs = new Hashtable();\r
- SequenceI[] seqs = new SequenceI[sg.getSize()];\r
+ SequenceI[] seqs = new SequenceI[sg.getSize(false)];\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
int index = 0, startRes, endRes;\r
char ch;\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = null;\r
\r
HistoryItem.HIDE));\r
\r
\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ for (int i = 0; i < sg.getSize(false); 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 (sg.sequences.size() == viewport.alignment.getHeight())\r
+ if (sg.getSize(false) == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
sg.getEndRes() + 1);\r
viewport.setSelectionGroup(null);\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
int end = viewport.alignment.getWidth();\r
\r
if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size() > 0)\r
+ && viewport.getSelectionGroup().getSequences(true) != null\r
+ && viewport.getSelectionGroup().getSize(true) > 0)\r
{\r
- seqs = viewport.getSelectionGroup().sequences;\r
+ seqs = viewport.getSelectionGroup().getSequences(true);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+ sg.getSequences(true), sg.getWidth());\r
}\r
sg.recalcConservation();\r
}\r
new DBRefFetcher(viewport.alignment, this);\r
}\r
\r
- public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+ public void defaultDASSource_actionPerformed(ActionEvent e)\r
{\r
- new DasSequenceFeatureFetcher(viewport.alignment,\r
- this);\r
- viewport.setShowSequenceFeatures(true);\r
- showSeqFeatures.setSelected(true);\r
+ new DasSequenceFeatureFetcher(viewport.alignment, this);\r
+ viewport.setShowSequenceFeatures(true);\r
+ showSeqFeatures.setSelected(true);\r
+ }\r
+\r
+ public void modifyDASSource_actionPerformed(ActionEvent e)\r
+ {\r
+ DasSourceBrowser dsb = new DasSourceBrowser();\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(dsb);\r
+ Desktop.addInternalFrame(frame, "Modify DAS Source",\r
+ 600,370);\r
}\r
\r
\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(true), sg.getWidth());\r
}\r
else if (cs instanceof UserColourScheme)\r
{\r
sg.cs.setThreshold(threshold,\r
viewport.getIgnoreGapsConsensus());\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
- }\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), 0,\r
+ sg.getWidth()));\r
+ }\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(true), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
if ( (viewport.getSelectionGroup() == null) ||\r
- (viewport.getSelectionGroup().getSize() < 2))\r
+ (viewport.getSelectionGroup().getSize(false) < 2))\r
{\r
JOptionPane.showInternalMessageDialog(this,\r
"You must select at least 2 sequences.",\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
if ( ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() < 4) &&\r
- (viewport.getSelectionGroup().getSize() > 0)) ||\r
+ (viewport.getSelectionGroup().getSize(false) < 4) &&\r
+ (viewport.getSelectionGroup().getSize(false) > 0)) ||\r
(viewport.getAlignment().getHeight() < 4))\r
{\r
JOptionPane.showInternalMessageDialog(this,\r
TreePanel tp;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 3))\r
+ (viewport.getSelectionGroup().getSize(false) > 3))\r
{\r
int s = 0;\r
SequenceGroup sg = viewport.getSelectionGroup();\r
\r
/* Decide if the selection is a column region */\r
- while (s < sg.sequences.size())\r
+ while (s < sg.getSize(false))\r
{\r
- if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
+ if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <\r
sg.getEndRes())\r
{\r
JOptionPane.showMessageDialog(Desktop.desktop,\r
\r
title = title + " on region";\r
tp = new TreePanel(viewport,\r
- viewport.getSelectionGroup().sequences, type, pwType,\r
+ viewport.getSelectionGroup().getSequences(false),\r
+ type, pwType,\r
sg.getStartRes(), sg.getEndRes());\r
}\r
else\r
SequenceI[] msa = null;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
+ (viewport.getSelectionGroup().getSize(false) > 1))\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
SequenceGroup seqs = viewport.getSelectionGroup();\r
int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
+ msa = new SequenceI[sz = seqs.getSize(false)];\r
\r
for (int i = 0; i < sz; i++)\r
{\r
SequenceI[] msa = null;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 0))\r
+ (viewport.getSelectionGroup().getSize(false) > 0))\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
SequenceGroup seqs = viewport.getSelectionGroup();\r
\r
- if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
+ if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned())\r
{\r
seq = (SequenceI) seqs.getSequenceAt(0);\r
}\r
else\r
{\r
int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
+ msa = new SequenceI[sz = seqs.getSize(false)];\r
\r
for (int i = 0; i < sz; i++)\r
{\r
git://source.jalview.org / jalview.git / blobdiff