\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 caluclating consensus.\r
+ //Out of memory calculating consensus.\r
BLOSUM62Colour.setEnabled(false);\r
PIDColour.setEnabled(false);\r
conservationMenuItem.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
else if(sortby.equals("Pairwise Identity"))\r
sortPairwiseMenuItem_actionPerformed(null);\r
\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+ tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ if(al.getDataset()==null)\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
}\r
});\r
\r
+\r
if(Desktop.desktop!=null)\r
addServiceListeners();\r
}\r
{\r
BufferedReader in = new BufferedReader(new FileReader(file));\r
SequenceI seq = null;\r
- String line, text, token;\r
+ String line, type, desc, token;\r
UserColourScheme ucs;\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() != 7)\r
{\r
System.out.println("Groups file " + file +\r
- " is invalid. Read help file.");\r
- System.exit(1);\r
+ " is invalid. Read help file.\nLine: \n"\r
+ +lineNo +": "+line);\r
+ break;\r
}\r
\r
while (st.hasMoreElements())\r
{\r
- text = st.nextToken();\r
+ type = st.nextToken();\r
+ desc = st.nextToken();\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\r
{\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
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+ fr.setColour(type, ucs.findColour("A"));\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
endRes);\r
}\r
\r
- c.setContents(new StringSelection(FastaFile.print(seqs)), 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
+ if(str.length()<1)\r
+ return;\r
\r
String format = IdentifyFile.Identify(str, "Paste");\r
SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);\r
\r
if (newAlignment)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\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
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
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
// 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