X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=575746a25cb64ee8d36ceff1ff1c490015cfbfa1;hb=ff5f2b888385f85e9fd99a226c9da098a06016d8;hp=f2d0b697cb8e050835c5ff8d862d53b94377bf25;hpb=ba86f4f86b87511a9852e60088dd5327adf547eb;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f2d0b69..575746a 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -34,6 +34,7 @@ import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; +import javax.swing.event.AncestorEvent; /** * DOCUMENT ME! @@ -42,7 +43,7 @@ import jalview.ws.*; * @version $Revision$ */ public class AlignFrame - extends GAlignFrame + extends GAlignFrame implements ClipboardOwner { /** DOCUMENT ME!! */ public static final int NEW_WINDOW_WIDTH = 700; @@ -61,6 +62,7 @@ public class AlignFrame Stack redoList = new Stack(); private int treeCount = 0; + /** * Creates a new AlignFrame object. * @@ -93,22 +95,24 @@ public class AlignFrame else if(sortby.equals("Pairwise Identity")) sortPairwiseMenuItem_actionPerformed(null); - tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); + // remove(tabbedPane); + getContentPane().add(alignPanel, BorderLayout.CENTER); + + + + // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); ///Dataset tab ///////////////////////// - if(al.getDataset()==null) { al.setDataset(null); } - - AlignViewport ds = new AlignViewport(al.getDataset()); - ds.setDataset(true); - AlignmentPanel dap = new AlignmentPanel(this, ds); - tabbedPane.add("Dataset", dap); - viewports.add(ds); - alignPanels.add(dap); + // AlignViewport ds = new AlignViewport(al.getDataset(), true); + // AlignmentPanel dap = new AlignmentPanel(this, ds); + // tabbedPane.add("Dataset", dap); + // viewports.add(ds); + // alignPanels.add(dap); ///////////////////////// @@ -124,8 +128,11 @@ public class AlignFrame }); - if(Desktop.desktop!=null) + if (Desktop.desktop != null) + { addServiceListeners(); + setGUINucleotide(al.isNucleotide()); + } } /* Set up intrinsic listeners for dynamically generated GUI bits. */ @@ -162,6 +169,36 @@ public class AlignFrame } + public void setGUINucleotide(boolean nucleotide) + { + showTranslation.setVisible( nucleotide ); + sequenceFeatures.setVisible(!nucleotide ); + featureSettings.setVisible( !nucleotide ); + conservationMenuItem.setVisible( !nucleotide ); + modifyConservation.setVisible( !nucleotide ); + + //Deal with separators + //Remember AlignFrame always starts as protein + if(nucleotide) + { + viewMenu.remove(viewMenu.getItemCount()-2); + } + else + { + calculateMenu.remove(calculateMenu.getItemCount()-2); + } + } + + + /* + Added so Castor Mapping file can obtain Jalview Version + */ + public String getVersion() + { + return jalview.bin.Cache.getProperty("VERSION"); + } + + /** * DOCUMENT ME! * @@ -217,11 +254,18 @@ public class AlignFrame type = st.nextToken(); + if (fr.getColour(type) == null) + { + // Probably the old style groups file + UserColourScheme ucs = new UserColourScheme(type); + fr.setColour(type, ucs.findColour("A")); + } + + sf = new SequenceFeature(type, desc, "", start, end); seq.addSequenceFeature(sf); - System.out.println(sf.getType()+" "+sf.getBegin()); // sg = new SequenceGroup(text, ucs, true, true, false, start, end); // sg.addSequence(seq, false); @@ -232,7 +276,6 @@ public class AlignFrame } viewport.showSequenceFeatures = true; - ((Alignment)viewport.alignment).featuresAdded = true; alignPanel.repaint(); @@ -243,6 +286,12 @@ public class AlignFrame } } + public void fetchSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(this); + } + + /** * DOCUMENT ME! * @@ -361,7 +410,9 @@ public class AlignFrame */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(viewport); + new HTMLOutput(viewport, + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) @@ -596,6 +647,12 @@ public class AlignFrame alignPanel.repaint(); } + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + Desktop.jalviewClipboard = null; + } + + /** * DOCUMENT ME! * @@ -605,7 +662,6 @@ public class AlignFrame { if (viewport.getSelectionGroup() == null) { - System.out.println("null here"); return; } @@ -614,7 +670,7 @@ public class AlignFrame Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); Hashtable orderedSeqs = new Hashtable(); - SequenceI [] seqs = new SequenceI[sg.getSize()]; + SequenceI[] seqs = new SequenceI[sg.getSize()]; for (int i = 0; i < sg.getSize(); i++) { @@ -645,7 +701,6 @@ public class AlignFrame } } - //FIND START RES //Returns residue following index if gap startRes = seq.findPosition(sg.getStartRes()); @@ -669,12 +724,20 @@ public class AlignFrame } seqs[i] = new Sequence(seq.getName(), - seq.getSequence(sg.getStartRes(), sg.getEndRes()+1), + seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1), startRes, endRes); + seqs[i].setDescription(seq.getDescription()); + seqs[i].setDBRef(seq.getDBRef()); + seqs[i].setSequenceFeatures(seq.getSequenceFeatures()); + seqs[i].setDatasetSequence(seq.getDatasetSequence()); + } - c.setContents(new StringSelection(new FastaFile().print(seqs)), null); + FastaFile ff = new FastaFile(); + ff.addJVSuffix( viewport.showJVSuffix ); + c.setContents(new StringSelection( ff.print(seqs)), this); + Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()}; } /** @@ -721,13 +784,30 @@ public class AlignFrame return; String format = IdentifyFile.Identify(str, "Paste"); - SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format); + SequenceI[] sequences; + if(Desktop.jalviewClipboard!=null) + { + // The clipboard was filled from within Jalview, we must use the sequences + // And dataset from the copied alignment + sequences = (SequenceI[])Desktop.jalviewClipboard[0]; + } + else + { + sequences = new FormatAdapter().readFile(str, "Paste", format); + } if (newAlignment) { + Alignment alignment = new Alignment(sequences); - alignment.setDataset( viewport.alignment.getDataset() ); + + if(Desktop.jalviewClipboard!=null) + alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] ); + else + alignment.setDataset( null ); + + AlignFrame af = new AlignFrame(alignment); String newtitle = new String("Copied sequences"); @@ -747,8 +827,24 @@ public class AlignFrame { //!newAlignment for (int i = 0; i < sequences.length; i++) + { viewport.alignment.addSequence(sequences[i]); + if(sequences[i].getDatasetSequence()==null) + { + //////////////////////////// + //Datset needs extension; + ///////////////////////////// + Sequence ds = new Sequence(sequences[i].getName(), + AlignSeq.extractGaps("-. ", sequences[i].getSequence()), + sequences[i].getStart(), + sequences[i].getEnd()); + sequences[i].setDatasetSequence(ds); + viewport.alignment.getDataset().addSequence(ds); + + } + + } viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -1216,14 +1312,15 @@ public class AlignFrame * * @param e DOCUMENT ME! */ - protected void fullSeqId_actionPerformed(ActionEvent e) + protected void seqLimit_actionPerformed(ActionEvent e) { - viewport.setShowFullId(fullSeqId.isSelected()); + viewport.setShowJVSuffix(seqLimits.isSelected()); alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth()); alignPanel.repaint(); } + /** * DOCUMENT ME! * @@ -1325,14 +1422,15 @@ public class AlignFrame { viewport.showSequenceFeatures(sequenceFeatures.isSelected()); - if (viewport.showSequenceFeatures && - ! ( (Alignment) viewport.alignment).featuresAdded) + /* if (viewport.showSequenceFeatures && + ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded) { + System.out.println("new fetcher"); new SequenceFeatureFetcher(viewport. - alignment, + alignment, alignPanel); } - +*/ featureSettings.setEnabled(true); alignPanel.repaint(); @@ -2310,7 +2408,7 @@ public class AlignFrame { SequenceI[] msa = gatherSequencesForAlignment(); new jalview.ws.MsaWSClient(sh, title, msa, - false, true); + false, true, viewport.getAlignment().getDataset()); } @@ -2327,7 +2425,7 @@ public class AlignFrame { SequenceI[] msa = gatherSequencesForAlignment(); new jalview.ws.MsaWSClient(sh, title, msa, - true, true); + true, true, viewport.getAlignment().getDataset()); } @@ -2388,7 +2486,7 @@ public class AlignFrame // TODO: group services by location as well as function. } - public void vamsasStore_actionPerformed(ActionEvent e) + /* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. getProperty("LAST_DIRECTORY")); @@ -2402,10 +2500,10 @@ public class AlignFrame if (value == JalviewFileChooser.APPROVE_OPTION) { jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - vs.store(chooser.getSelectedFile().getAbsolutePath() - ); + //vs.store(chooser.getSelectedFile().getAbsolutePath() ); + vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); } - } + }*/ public void featureSettings_actionPerformed(ActionEvent e) { @@ -2416,29 +2514,20 @@ public class AlignFrame public void showTranslation_actionPerformed(ActionEvent e) { - - if(!viewport.alignment.isNucleotide()) - return; - - viewport.showTranslation(showTranslation.isSelected()); - - if(!viewport.alignment.isNucleotide()) - return; - int s, sSize = viewport.alignment.getHeight(); SequenceI [] newSeq = new SequenceI[sSize]; int res, resSize; StringBuffer protein; - SequenceI seq; + String seq; for(s=0; s