* @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
al.setDataset(null);\r
}\r
\r
- AlignViewport ds = new AlignViewport(al.getDataset());\r
- ds.setDataset(true);\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
\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
BufferedReader in = new BufferedReader(new FileReader(file));\r
SequenceI seq = null;\r
String line, type, desc, token;\r
- UserColourScheme ucs;\r
+\r
int index, start, end;\r
StringTokenizer st;\r
SequenceFeature sf;\r
{\r
lineNo++;\r
st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() != 7)\r
+ if (st.countTokens() == 2)\r
{\r
- System.out.println("Groups file " + file +\r
- " is invalid. Read help file.\nLine: \n"\r
- +lineNo +": "+line);\r
- break;\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
- type = st.nextToken();\r
desc = st.nextToken();\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\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
+ 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
- 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
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.addDBPrefix( viewport.showDBPrefix );\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.setShowJVSuffix(seqLimits.isSelected());\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void seqDBRef_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowFullId(fullSeqId.isSelected());\r
+ viewport.setShowDBPrefix(seqDBRef.isSelected());\r
\r
alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
alignPanel.repaint();\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
\r
if (viewport.showSequenceFeatures &&\r
- ! ( (Alignment) viewport.alignment).featuresAdded)\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
addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
HistoryItem.SORT));\r
- AlignmentSorter.sortByID(viewport.getAlignment());\r
+ AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
alignPanel.repaint();\r
}\r
\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
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
git://source.jalview.org / jalview.git / blobdiff