import java.awt.event.*;\r
import java.awt.print.*;\r
import javax.swing.*;\r
-import javax.swing.event.*;\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
\r
/** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_HEIGHT = 500;\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
+ AlignmentPanel alignPanel;\r
+ AlignViewport viewport;\r
+\r
+ Vector viewports = new Vector();\r
+ Vector alignPanels = new Vector();\r
\r
/** DOCUMENT ME!! */\r
public String currentFileFormat = null;\r
public AlignFrame(AlignmentI al)\r
{\r
viewport = new AlignViewport(al);\r
+ viewports.add(viewport);\r
+\r
+\r
+ if(viewport.vconsensus==null)\r
+ {\r
+ //Out of memory calculating consensus.\r
+ BLOSUM62Colour.setEnabled(false);\r
+ PIDColour.setEnabled(false);\r
+ conservationMenuItem.setEnabled(false);\r
+ modifyConservation.setEnabled(false);\r
+ abovePIDThreshold.setEnabled(false);\r
+ modifyPID.setEnabled(false);\r
+ }\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.\r
- annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.\r
- getPreferredSize());\r
- alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
+ alignPanels.add(alignPanel);\r
+\r
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+ if(sortby.equals("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if(sortby.equals("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
\r
- addInternalFrameListener(new InternalFrameAdapter()\r
+ tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ if(al.getDataset()==null)\r
{\r
- public void internalFrameActivated(InternalFrameEvent evt)\r
- {\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- alignPanel.requestFocus();\r
- }\r
- });\r
- }\r
- });\r
+ al.setDataset(null);\r
+ }\r
+\r
+ AlignViewport ds = new AlignViewport(al.getDataset());\r
+ ds.setDataset(true);\r
+ AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ tabbedPane.add("Dataset", dap);\r
+ viewports.add(ds);\r
+ alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+ viewport.addPropertyChangeListener(new PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
+\r
+\r
+ if(Desktop.desktop!=null)\r
addServiceListeners();\r
}\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
private void addServiceListeners()\r
{\r
-\r
- final AlignFrame thisFrame = this;\r
final java.beans.PropertyChangeListener thisListener;\r
// Do this once to get current state\r
- thisFrame.BuildWebServiceMenu();\r
+ BuildWebServiceMenu();\r
Desktop.discoverer.addPropertyChangeListener(\r
thisListener = new java.beans.PropertyChangeListener()\r
{\r
if (evt.getPropertyName().equals("services"))\r
{\r
// System.out.println("Rebuilding web service menu");\r
- thisFrame.BuildWebServiceMenu();\r
+ BuildWebServiceMenu();\r
}\r
}\r
});\r
{\r
// System.out.println("deregistering discoverer listener");\r
Desktop.discoverer.removePropertyChangeListener(thisListener);\r
+ closeMenuItem_actionPerformed(null);\r
}\r
;\r
});\r
{\r
BufferedReader in = new BufferedReader(new FileReader(file));\r
SequenceI seq = null;\r
- String line, text, token;\r
- UserColourScheme ucs;\r
+ String line, type, desc, token;\r
+\r
int index, start, end;\r
StringTokenizer st;\r
- SequenceGroup sg;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
while ( (line = in.readLine()) != null)\r
{\r
+ lineNo++;\r
st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() != 6)\r
+ if (st.countTokens() == 2)\r
{\r
- System.out.println("Groups file " + file +\r
- " is invalid. Read help file.");\r
- System.exit(1);\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
}\r
\r
while (st.hasMoreElements())\r
{\r
- text = st.nextToken();\r
+ desc = st.nextToken();\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\r
{\r
\r
start = Integer.parseInt(st.nextToken());\r
end = Integer.parseInt(st.nextToken());\r
- ucs = new UserColourScheme(st.nextToken());\r
\r
seq = viewport.alignment.getSequenceAt(index);\r
start = seq.findIndex(start) - 1;\r
end = seq.findIndex(end) - 1;\r
\r
- sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
- sg.addSequence(seq, true);\r
+ type = st.nextToken();\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+ System.out.println(sf.getType()+" "+sf.getBegin());\r
+\r
+ // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ // sg.addSequence(seq, false);\r
+\r
+ // viewport.alignment.addGroup(sg);\r
\r
- viewport.alignment.addGroup(sg);\r
}\r
}\r
\r
+ viewport.showSequenceFeatures = true;\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+\r
+ alignPanel.repaint();\r
+\r
}\r
catch (Exception ex)\r
{\r
\r
if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- currentFileFormat = chooser.getSelectedFormat();\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+\r
+ if (currentFileFormat == null)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "You must select a file format before saving!",\r
+ "File format not specified",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ value = chooser.showSaveDialog(this);\r
+ return;\r
+ }\r
+\r
jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
currentFileFormat);\r
\r
}\r
else\r
{\r
- String output = FormatAdapter.formatSequences(format,\r
+ String output = new FormatAdapter().formatSequences(format,\r
viewport.getAlignment().\r
getSequences());\r
if (output == null)\r
{\r
java.io.PrintWriter out = new java.io.PrintWriter(\r
new java.io.FileWriter(file));\r
- out.println(output);\r
+\r
+ out.print(output);\r
out.close();\r
return true;\r
}\r
Desktop.addInternalFrame(cap,\r
"Alignment output - " + e.getActionCommand(), 600,\r
500);\r
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
viewport.getAlignment().\r
getSequences()));\r
}\r
{\r
try\r
{\r
+ PaintRefresher.components.remove(viewport.alignment);\r
this.setClosed(true);\r
}\r
catch (Exception ex)\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
/**\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
// used by undo and redo\r
\r
updateEditMenuBar();\r
\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
viewport.firePropertyChange("alignment", null,\r
viewport.getAlignment().getSequences());\r
}\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
+ System.out.println("null here");\r
return;\r
}\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
\r
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- StringBuffer buffer = new StringBuffer();\r
\r
Hashtable orderedSeqs = new Hashtable();\r
+ SequenceI [] seqs = new SequenceI[sg.getSize()];\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
index++;\r
}\r
}\r
+\r
+\r
//FIND START RES\r
//Returns residue following index if gap\r
startRes = seq.findPosition(sg.getStartRes());\r
endRes += seq.getStart() - 1;\r
}\r
\r
- buffer.append(seq.getName() + "\t" +\r
- startRes + "\t" +\r
- endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),\r
+ startRes,\r
+ endRes);\r
}\r
\r
- c.setContents(new StringSelection(buffer.toString()), null);\r
+ c.setContents(new StringSelection(new FastaFile().print(seqs)), null);\r
}\r
\r
/**\r
}\r
\r
String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- StringTokenizer st = new StringTokenizer(str);\r
- ArrayList seqs = new ArrayList();\r
+ if(str.length()<1)\r
+ return;\r
\r
- while (st.hasMoreElements())\r
- {\r
- String name = st.nextToken();\r
- int start = Integer.parseInt(st.nextToken());\r
- int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name, st.nextToken(), start,\r
- end);\r
+ String format = IdentifyFile.Identify(str, "Paste");\r
+ SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);\r
\r
- if (!newAlignment)\r
- {\r
- viewport.alignment.addSequence(sequence);\r
- }\r
- else\r
- {\r
- seqs.add(sequence);\r
- }\r
- }\r
\r
if (newAlignment)\r
{\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- seqs.toArray(newSeqs);\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
+ Alignment alignment = new Alignment(sequences);\r
+ alignment.setDataset( viewport.alignment.getDataset() );\r
+ AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
if (title.startsWith("Copied sequences"))\r
}\r
else\r
{\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ //!newAlignment\r
+ for (int i = 0; i < sequences.length; i++)\r
+ viewport.alignment.addSequence(sequences[i]);\r
+\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
catch (Exception ex)\r
{\r
+ // could be anything being pasted in here\r
}\r
\r
- // could be anything being pasted in here\r
+\r
}\r
\r
/**\r
*/\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
- boolean seqsdeleted = false;\r
\r
if (viewport.getSelectionGroup() == null)\r
{\r
\r
if (seq.getSequence().length() < 1)\r
{\r
- seqsdeleted = true;\r
viewport.getAlignment().deleteSequence(seq);\r
}\r
else\r
viewport.setSelectionGroup(null);\r
viewport.alignment.deleteGroup(sg);\r
\r
- if (seqsdeleted)\r
- {\r
- viewport.firePropertyChange("alignment", null,\r
+ viewport.firePropertyChange("alignment", null,\r
viewport.getAlignment().getSequences());\r
- }\r
\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
+\r
\r
if (viewport.getAlignment().getHeight() < 1)\r
{\r
{\r
}\r
}\r
-\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
}\r
\r
/**\r
}\r
}\r
\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
}\r
}\r
\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
viewport.alignment, HistoryItem.HIDE));\r
\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
viewport.getAlignment().removeGaps();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
/**\r
addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+\r
SequenceI current;\r
int jSize;\r
\r
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
else\r
{\r
current = (SequenceI) seqs.elementAt(i);\r
jSize = current.getLength();\r
\r
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
\r
do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
+ }\r
+ else\r
+ {\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
}\r
- j++;\r
}\r
while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ }\r
}\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void alignmentChanged()\r
+ {\r
+ if(viewport.vconsensus!=null)\r
+ {\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ }\r
+ resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+ Provenance prov = viewport.alignment.getProvenance();\r
+ if(prov == null)\r
+ {\r
+ prov = new Provenance();\r
+ viewport.alignment.setProvenance(prov);\r
+ }\r
+\r
+ prov.addEntry("Me",\r
+ "Edited in Jalview", new java.util.Date(), "myID");\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
+ int s, sSize = viewport.alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\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
+ }\r
+ sg.recalcConservation();\r
+ }\r
}\r
\r
/**\r
}\r
}\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ alignmentChanged();\r
}\r
\r
/**\r
*/\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- FontChooser fc = new FontChooser(alignPanel);\r
+ new FontChooser(alignPanel);\r
}\r
\r
/**\r
if (viewport.showSequenceFeatures &&\r
! ( (Alignment) viewport.alignment).featuresAdded)\r
{\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
+ new SequenceFeatureFetcher(viewport.\r
alignment,\r
alignPanel);\r
- ( (Alignment) viewport.alignment).featuresAdded = true;\r
}\r
\r
+ featureSettings.setEnabled(true);\r
+\r
alignPanel.repaint();\r
}\r
\r
*/\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if (annotationPanelMenuItem.isSelected() &&\r
- viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setSelected(false);\r
-\r
- return;\r
- }\r
-\r
viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
}\r
conservationMenuItem.setSelected(false);\r
viewport.setConservationSelected(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
changeColour(viewport.getGlobalColourScheme());\r
\r
modifyPID_actionPerformed(null);\r
return;\r
}\r
\r
- try\r
- {\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(pcaPanel);\r
- Desktop.addInternalFrame(frame, "Principal component analysis",\r
- 400, 400);\r
- }\r
- catch (java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this,\r
- "Too many sequences selected\nfor Principal Component Analysis!!",\r
- "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
+ new PCAPanel(viewport);\r
}\r
\r
/**\r
}\r
;\r
});\r
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
- {\r
- public void propertyChange(PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
- treePanel.repaint();\r
- }\r
- }\r
- });\r
}\r
\r
/**\r
*/\r
public void BuildWebServiceMenu()\r
{\r
- if ( (Desktop.discoverer.services != null)\r
- && (Desktop.discoverer.services.size() > 0))\r
+ if ( (Discoverer.services != null)\r
+ && (Discoverer.services.size() > 0))\r
{\r
- Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");\r
- Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");\r
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");\r
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");\r
Vector wsmenu = new Vector();\r
if (msaws != null)\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
- MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+ new jalview.ws.MsaWSClient(sh, title, msa,\r
false, true);\r
\r
}\r
public void actionPerformed(ActionEvent e)\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
- MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+ new jalview.ws.MsaWSClient(sh, title, msa,\r
true, true);\r
\r
}\r
if (msa.length == 1)\r
{\r
// Single Sequence prediction\r
- jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
- title, msa[0]);\r
+ new jalview.ws.JPredClient(sh,title, msa[0]);\r
}\r
else\r
{\r
// TODO: group services by location as well as function.\r
}\r
\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Export to Vamsas file");\r
+ chooser.setToolTipText("Export");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+ vs.store(chooser.getSelectedFile().getAbsolutePath()\r
+ );\r
+ }\r
+ }\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+\r
+\r
+public void showTranslation_actionPerformed(ActionEvent e)\r
+{\r
+\r
+ if(!viewport.alignment.isNucleotide())\r
+ return;\r
+\r
+ viewport.showTranslation(showTranslation.isSelected());\r
+\r
+ if(!viewport.alignment.isNucleotide())\r
+ return;\r
+\r
+ int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] newSeq = new SequenceI[sSize];\r
+\r
+ int res, resSize;\r
+ StringBuffer protein;\r
+ SequenceI seq;\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ protein = new StringBuffer();\r
+ seq = (SequenceI)viewport.alignment.getSequenceAt(s);\r
+ resSize = seq.getLength();\r
+ for(res = 0; res < resSize; res+=3)\r
+ {\r
+ String codon = seq.getSequence(res, res+3);\r
+ codon = codon.replace('U', 'T');\r
+ String aa = ResidueProperties.codonTranslate(codon);\r
+ if(aa==null)\r
+ protein.append(viewport.getGapCharacter());\r
+ else if(aa.equals("STOP"))\r
+ protein.append("X");\r
+ else\r
+ protein.append( aa );\r
+ }\r
+ newSeq[s] = new Sequence(seq.getName(), protein.toString());\r
+ }\r
+\r
+\r
+ AlignmentI al = new Alignment(newSeq);\r
+ al.setDataset(null);\r
+\r
+\r
+ ////////////////////////////////\r
+ // Copy annotations across\r
+ jalview.datamodel.AlignmentAnnotation[] annotations\r
+ = viewport.alignment.getAlignmentAnnotation();\r
+ int a, aSize;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ aSize = viewport.alignment.getWidth()/3;\r
+ jalview.datamodel.Annotation [] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
+\r
+ for(a=0; a<viewport.alignment.getWidth(); a++)\r
+ {\r
+ if( annotations[i].annotations[a]==null\r
+ || annotations[i].annotations[a]==null)\r
+ continue;\r
+\r
+ anots[a/3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
+ annotations[i].description, anots );\r
+ al.addAnnotation(aa);\r
+ }\r
+\r
+\r
+ // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ // NEW_WINDOW_WIDTH,\r
+ // NEW_WINDOW_HEIGHT);\r
+\r
+ AlignViewport newViewport = new AlignViewport(al);\r
+ AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ tabbedPane.add("Protein", ap);\r
+ viewports.add(newViewport);\r
+ alignPanels.add(ap);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ AlignViewport ds = new AlignViewport(al.getDataset());\r
+ ds.setDataset(true);\r
+ AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ tabbedPane.add("Dataset", dap);\r
+ viewports.add(ds);\r
+ alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+}\r
+\r
+public void tabSelected()\r
+{\r
+ int index = tabbedPane.getSelectedIndex();\r
+ viewport = (AlignViewport)viewports.elementAt(index);\r
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
+}\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff