import jalview.jbgui.*;\r
import jalview.schemes.*;\r
import jalview.ws.*;\r
+import javax.swing.event.AncestorEvent;\r
\r
/**\r
* DOCUMENT ME!\r
* @version $Revision$\r
*/\r
public class AlignFrame\r
- extends GAlignFrame\r
+ extends GAlignFrame implements ClipboardOwner\r
{\r
/** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_WIDTH = 700;\r
Stack redoList = new Stack();\r
private int treeCount = 0;\r
\r
+\r
/**\r
* Creates a new AlignFrame object.\r
*\r
else if(sortby.equals("Pairwise Identity"))\r
sortPairwiseMenuItem_actionPerformed(null);\r
\r
- tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+ // remove(tabbedPane);\r
+ getContentPane().add(alignPanel, BorderLayout.CENTER);\r
+\r
+\r
+\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
+ // AlignViewport ds = new AlignViewport(al.getDataset(), 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
\r
- if(Desktop.desktop!=null)\r
+ if (Desktop.desktop != null)\r
+ {\r
addServiceListeners();\r
+ setGUINucleotide(al.isNucleotide());\r
+ }\r
}\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
\r
}\r
\r
+ public void setGUINucleotide(boolean nucleotide)\r
+ {\r
+ showTranslation.setVisible( nucleotide );\r
+ sequenceFeatures.setVisible(!nucleotide );\r
+ featureSettings.setVisible( !nucleotide );\r
+ conservationMenuItem.setVisible( !nucleotide );\r
+ modifyConservation.setVisible( !nucleotide );\r
+\r
+ //Deal with separators\r
+ //Remember AlignFrame always starts as protein\r
+ if(nucleotide)\r
+ {\r
+ viewMenu.remove(viewMenu.getItemCount()-2);\r
+ }\r
+ else\r
+ {\r
+ calculateMenu.remove(calculateMenu.getItemCount()-2);\r
+ }\r
+ }\r
+\r
+\r
+ /*\r
+ Added so Castor Mapping file can obtain Jalview Version\r
+ */\r
+ public String getVersion()\r
+ {\r
+ return jalview.bin.Cache.getProperty("VERSION");\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
type = st.nextToken();\r
\r
+ if (fr.getColour(type) == null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
+\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
\r
viewport.showSequenceFeatures = true;\r
- ((Alignment)viewport.alignment).featuresAdded = true;\r
\r
alignPanel.repaint();\r
\r
}\r
}\r
\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(this);\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
- new HTMLOutput(viewport);\r
+ new HTMLOutput(viewport,\r
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
}\r
\r
public void createImageMap(File file, String image)\r
alignPanel.repaint();\r
}\r
\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
- System.out.println("null here");\r
return;\r
}\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()];\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
}\r
}\r
\r
-\r
//FIND START RES\r
//Returns residue following index if gap\r
startRes = seq.findPosition(sg.getStartRes());\r
}\r
\r
seqs[i] = new Sequence(seq.getName(),\r
- seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),\r
+ seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),\r
startRes,\r
endRes);\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
}\r
\r
- c.setContents(new StringSelection(new FastaFile().print(seqs)), null);\r
+ FastaFile ff = new FastaFile();\r
+ ff.addJVSuffix( viewport.showJVSuffix );\r
+ c.setContents(new StringSelection( ff.print(seqs)), this);\r
+ Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
}\r
\r
/**\r
return;\r
\r
String format = IdentifyFile.Identify(str, "Paste");\r
- SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ SequenceI[] sequences;\r
\r
+ if(Desktop.jalviewClipboard!=null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the sequences\r
+ // And dataset from the copied alignment\r
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];\r
+ }\r
+ else\r
+ {\r
+ sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ }\r
\r
if (newAlignment)\r
{\r
+\r
Alignment alignment = new Alignment(sequences);\r
- alignment.setDataset( viewport.alignment.getDataset() );\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
+ else\r
+ alignment.setDataset( null );\r
+\r
+\r
AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
{\r
//!newAlignment\r
for (int i = 0; i < sequences.length; i++)\r
+ {\r
viewport.alignment.addSequence(sequences[i]);\r
+ if(sequences[i].getDatasetSequence()==null)\r
+ {\r
+ ////////////////////////////\r
+ //Datset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ sequences[i].setDatasetSequence(ds);\r
+ viewport.alignment.getDataset().addSequence(ds);\r
+\r
\r
+ }\r
+\r
+ }\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowFullId(fullSeqId.isSelected());\r
+ viewport.setShowJVSuffix(seqLimits.isSelected());\r
\r
alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
alignPanel.repaint();\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
\r
- if (viewport.showSequenceFeatures &&\r
- ! ( (Alignment) viewport.alignment).featuresAdded)\r
+ /* if (viewport.showSequenceFeatures &&\r
+ ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)\r
{\r
+ System.out.println("new fetcher");\r
new SequenceFeatureFetcher(viewport.\r
- alignment,\r
+ alignment,\r
alignPanel);\r
}\r
-\r
+*/\r
featureSettings.setEnabled(true);\r
\r
alignPanel.repaint();\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- false, true);\r
+ false, true, viewport.getAlignment().getDataset());\r
\r
}\r
\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- true, true);\r
+ true, true, viewport.getAlignment().getDataset());\r
\r
}\r
\r
// TODO: group services by location as well as function.\r
}\r
\r
- public void vamsasStore_actionPerformed(ActionEvent e)\r
+ /* public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
getProperty("LAST_DIRECTORY"));\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
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );\r
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
}\r
- }\r
+ }*/\r
\r
public void featureSettings_actionPerformed(ActionEvent e)\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
+ String 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
+ seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ resSize = seq.length();\r
for(res = 0; res < resSize; res+=3)\r
{\r
- String codon = seq.getSequence(res, res+3);\r
+ String codon = seq.substring(res, res+3);\r
codon = codon.replace('U', 'T');\r
String aa = ResidueProperties.codonTranslate(codon);\r
if(aa==null)\r
else\r
protein.append( aa );\r
}\r
- newSeq[s] = new Sequence(seq.getName(), protein.toString());\r
+ newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
}\r
\r
\r
}\r
\r
\r
- // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
- // NEW_WINDOW_WIDTH,\r
- // NEW_WINDOW_HEIGHT);\r
+ AlignFrame af = new AlignFrame(al);\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
+ // 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
+ // 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
+/*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
}\r
git://source.jalview.org / jalview.git / blobdiff