X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=81e55644b6b34e941aa0fc24f6970fd085d1dc30;hb=966e2e639242c252f4ed9e5f0e3e91b0389bd2de;hp=da4f93b033f8bf1c06fc222ccac899a4011eecdf;hpb=d7b15f85f8a1f1440e011116b5aa0d31306c217c;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index da4f93b..81e5564 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -27,7 +27,6 @@ import java.awt.datatransfer.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; -import javax.swing.event.*; import jalview.analysis.*; import jalview.datamodel.*; @@ -35,6 +34,7 @@ import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; +import javax.swing.event.AncestorEvent; /** * DOCUMENT ME! @@ -43,15 +43,18 @@ import jalview.ws.*; * @version $Revision$ */ public class AlignFrame - extends GAlignFrame + extends GAlignFrame implements ClipboardOwner { /** DOCUMENT ME!! */ public static final int NEW_WINDOW_WIDTH = 700; /** DOCUMENT ME!! */ public static final int NEW_WINDOW_HEIGHT = 500; - final AlignmentPanel alignPanel; - final AlignViewport viewport; + AlignmentPanel alignPanel; + AlignViewport viewport; + + Vector viewports = new Vector(); + Vector alignPanels = new Vector(); /** DOCUMENT ME!! */ public String currentFileFormat = null; @@ -59,6 +62,7 @@ public class AlignFrame Stack redoList = new Stack(); private int treeCount = 0; + /** * Creates a new AlignFrame object. * @@ -67,10 +71,12 @@ public class AlignFrame public AlignFrame(AlignmentI al) { viewport = new AlignViewport(al); + viewports.add(viewport); + if(viewport.vconsensus==null) { - //Out of memory caluclating consensus. + //Out of memory calculating consensus. BLOSUM62Colour.setEnabled(false); PIDColour.setEnabled(false); conservationMenuItem.setEnabled(false); @@ -80,12 +86,7 @@ public class AlignFrame } alignPanel = new AlignmentPanel(this, viewport); - alignPanel.annotationPanel.adjustPanelHeight(); - alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel. - annotationPanel.getPreferredSize()); - alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel. - getPreferredSize()); - alignPanel.setAnnotationVisible(viewport.getShowAnnotation()); + alignPanels.add(alignPanel); String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); @@ -94,7 +95,26 @@ public class AlignFrame else if(sortby.equals("Pairwise Identity")) sortPairwiseMenuItem_actionPerformed(null); - getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); + // 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(), true); + // AlignmentPanel dap = new AlignmentPanel(this, ds); + // tabbedPane.add("Dataset", dap); + // viewports.add(ds); + // alignPanels.add(dap); + ///////////////////////// + viewport.addPropertyChangeListener(new PropertyChangeListener() { @@ -108,7 +128,11 @@ public class AlignFrame }); + if (Desktop.desktop != null) + { addServiceListeners(); + setGUINucleotide(al.isNucleotide()); + } } /* Set up intrinsic listeners for dynamically generated GUI bits. */ @@ -145,6 +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! * @@ -157,24 +211,28 @@ public class AlignFrame { BufferedReader in = new BufferedReader(new FileReader(file)); SequenceI seq = null; - String line, text, token; - UserColourScheme ucs; + String line, type, desc, token; + int index, start, end; StringTokenizer st; - SequenceGroup sg; + SequenceFeature sf; + FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + int lineNo = 0; while ( (line = in.readLine()) != null) { + lineNo++; st = new StringTokenizer(line, "\t"); - if (st.countTokens() != 6) + if (st.countTokens() == 2) { - System.out.println("Groups file " + file + - " is invalid. Read help file."); - System.exit(1); + type = st.nextToken(); + UserColourScheme ucs = new UserColourScheme(st.nextToken()); + fr.setColour(type, ucs.findColour("A")); + continue; } while (st.hasMoreElements()) { - text = st.nextToken(); + desc = st.nextToken(); token = st.nextToken(); if (!token.equals("ID_NOT_SPECIFIED")) { @@ -189,19 +247,38 @@ public class AlignFrame start = Integer.parseInt(st.nextToken()); end = Integer.parseInt(st.nextToken()); - ucs = new UserColourScheme(st.nextToken()); seq = viewport.alignment.getSequenceAt(index); start = seq.findIndex(start) - 1; end = seq.findIndex(end) - 1; - sg = new SequenceGroup(text, ucs, true, true, false, start, end); - sg.addSequence(seq, true); + 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); + + + // sg = new SequenceGroup(text, ucs, true, true, false, start, end); + // sg.addSequence(seq, false); + + // viewport.alignment.addGroup(sg); - viewport.alignment.addGroup(sg); } } + viewport.showSequenceFeatures = true; + + alignPanel.repaint(); + } catch (Exception ex) { @@ -209,6 +286,12 @@ public class AlignFrame } } + public void fetchSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(this); + } + + /** * DOCUMENT ME! * @@ -238,7 +321,18 @@ public class AlignFrame if (value == JalviewFileChooser.APPROVE_OPTION) { - currentFileFormat = chooser.getSelectedFormat(); + currentFileFormat = chooser.getSelectedFormat(); + + if (currentFileFormat == null) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "You must select a file format before saving!", + "File format not specified", + JOptionPane.WARNING_MESSAGE); + value = chooser.showSaveDialog(this); + return; + } + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat); @@ -268,7 +362,7 @@ public class AlignFrame } else { - String output = FormatAdapter.formatSequences(format, + String output = new FormatAdapter().formatSequences(format, viewport.getAlignment(). getSequences()); if (output == null) @@ -304,7 +398,7 @@ public class AlignFrame Desktop.addInternalFrame(cap, "Alignment output - " + e.getActionCommand(), 600, 500); - cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), viewport.getAlignment(). getSequences())); } @@ -316,7 +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) @@ -551,6 +647,12 @@ public class AlignFrame alignPanel.repaint(); } + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + Desktop.jalviewClipboard = null; + } + + /** * DOCUMENT ME! * @@ -566,9 +668,9 @@ public class AlignFrame SequenceGroup sg = viewport.getSelectionGroup(); Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - StringBuffer buffer = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); + SequenceI[] seqs = new SequenceI[sg.getSize()]; for (int i = 0; i < sg.getSize(); i++) { @@ -598,6 +700,7 @@ public class AlignFrame index++; } } + //FIND START RES //Returns residue following index if gap startRes = seq.findPosition(sg.getStartRes()); @@ -620,14 +723,21 @@ public class AlignFrame endRes += seq.getStart() - 1; } - buffer.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + seqs[i] = new Sequence(seq.getName(), + 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(buffer.toString()), 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()}; } /** @@ -670,33 +780,35 @@ public class AlignFrame } String str = (String) contents.getTransferData(DataFlavor.stringFlavor); - StringTokenizer st = new StringTokenizer(str); - ArrayList seqs = new ArrayList(); + if(str.length()<1) + return; - while (st.hasMoreElements()) - { - String name = st.nextToken(); - int start = Integer.parseInt(st.nextToken()); - int end = Integer.parseInt(st.nextToken()); - Sequence sequence = new Sequence(name, st.nextToken(), start, - end); + String format = IdentifyFile.Identify(str, "Paste"); + SequenceI[] sequences; - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.add(sequence); - } - } + 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) { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - seqs.toArray(newSeqs); - AlignFrame af = new AlignFrame(new Alignment(newSeqs)); + Alignment alignment = new Alignment(sequences); + + 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"); if (title.startsWith("Copied sequences")) @@ -713,6 +825,27 @@ public class AlignFrame } else { + //!newAlignment + for (int i = 0; i < sequences.length; i++) + { + Sequence newseq = new Sequence(sequences[i].getName(), + sequences[i].getSequence(), sequences[i].getStart(), + sequences[i].getEnd()); + viewport.alignment.addSequence(newseq); + 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()); + newseq.setDatasetSequence(ds); + viewport.alignment.getDataset().addSequence(ds); + } + + } viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -744,7 +877,6 @@ public class AlignFrame */ protected void delete_actionPerformed(ActionEvent e) { - boolean seqsdeleted = false; if (viewport.getSelectionGroup() == null) { @@ -776,7 +908,6 @@ public class AlignFrame if (seq.getSequence().length() < 1) { - seqsdeleted = true; viewport.getAlignment().deleteSequence(seq); } else @@ -847,6 +978,7 @@ public class AlignFrame viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.annotationPanel.activeRes = null; PaintRefresher.Refresh(null, viewport.alignment); } @@ -1005,7 +1137,7 @@ public class AlignFrame { seqs = viewport.getSelectionGroup().sequences; start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); + end = viewport.getSelectionGroup().getEndRes()+1; } else { @@ -1017,19 +1149,45 @@ public class AlignFrame current = (SequenceI) seqs.elementAt(i); jSize = current.getLength(); + // Removing a range is much quicker than removing gaps + // one by one for long sequences int j = start; + int rangeStart=-1, rangeEnd=-1; do { if (jalview.util.Comparison.isGap(current.getCharAt(j))) { - current.deleteCharAt(j); - j--; - jSize--; + if(rangeStart==-1) + { + rangeStart = j; + rangeEnd = j+1; + } + else + { + rangeEnd++; + } + j++; + } + else + { + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + j-=rangeEnd-rangeStart; + jSize-=rangeEnd-rangeStart; + rangeStart = -1; + rangeEnd = -1; + } + else + j++; } - j++; } while (j < end && j < jSize); + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + } } viewport.setStartRes(seq.findIndex(startRes)-1); @@ -1045,6 +1203,9 @@ public class AlignFrame viewport.updateConservation(); } resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); + alignPanel.repaint(); } @@ -1135,7 +1296,7 @@ public class AlignFrame */ public void font_actionPerformed(ActionEvent e) { - FontChooser fc = new FontChooser(alignPanel); + new FontChooser(alignPanel); } /** @@ -1143,14 +1304,15 @@ 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! * @@ -1252,15 +1414,15 @@ public class AlignFrame { viewport.showSequenceFeatures(sequenceFeatures.isSelected()); - if (viewport.showSequenceFeatures && - ! ( (Alignment) viewport.alignment).featuresAdded) + if (viewport.showSequenceFeatures) { - SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport. - alignment, + new SequenceFeatureFetcher(viewport. + alignment, alignPanel); - ( (Alignment) viewport.alignment).featuresAdded = true; } + featureSettings.setEnabled(true); + alignPanel.repaint(); } @@ -1271,14 +1433,6 @@ public class AlignFrame */ public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - if (annotationPanelMenuItem.isSelected() && - viewport.getWrapAlignment()) - { - annotationPanelMenuItem.setSelected(false); - - return; - } - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } @@ -1610,8 +1764,6 @@ public class AlignFrame conservationMenuItem.setSelected(false); viewport.setConservationSelected(false); - ColourSchemeI cs = viewport.getGlobalColourScheme(); - changeColour(viewport.getGlobalColourScheme()); modifyPID_actionPerformed(null); @@ -1822,21 +1974,7 @@ public class AlignFrame return; } - try - { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(pcaPanel); - Desktop.addInternalFrame(frame, "Principal component analysis", - 400, 400); - } - catch (java.lang.OutOfMemoryError ex) - { - JOptionPane.showInternalMessageDialog(this, - "Too many sequences selected\nfor Principal Component Analysis!!", - "Out of memory", - JOptionPane.WARNING_MESSAGE); - } + new PCAPanel(viewport); } /** @@ -2070,7 +2208,16 @@ public class AlignFrame { SequenceI seq = null; SequenceI[] msa = null; +/* + if (predictindex==-1) { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "The alignment contains no columns or residues usable for prediction!", + "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE); + this. + return; + } +*/ if ( (viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() > 0)) { @@ -2239,11 +2386,11 @@ public class AlignFrame */ public void BuildWebServiceMenu() { - if ( (Desktop.discoverer.services != null) - && (Desktop.discoverer.services.size() > 0)) + if ( (Discoverer.services != null) + && (Discoverer.services.size() > 0)) { - Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred"); + Vector msaws = (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); Vector wsmenu = new Vector(); if (msaws != null) { @@ -2259,8 +2406,8 @@ public class AlignFrame public void actionPerformed(ActionEvent e) { SequenceI[] msa = gatherSequencesForAlignment(); - MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa, - false, true); + new jalview.ws.MsaWSClient(sh, title, msa, + false, true, viewport.getAlignment().getDataset()); } @@ -2276,8 +2423,8 @@ public class AlignFrame public void actionPerformed(ActionEvent e) { SequenceI[] msa = gatherSequencesForAlignment(); - MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa, - true, true); + new jalview.ws.MsaWSClient(sh, title, msa, + true, true, viewport.getAlignment().getDataset()); } @@ -2301,18 +2448,28 @@ public class AlignFrame { public void actionPerformed(ActionEvent e) { - SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction(); + SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction()); + if (msa==null) { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "There are no columns or residues usable for prediction!\n" + +"There must be valid residues in at least one\n" + +"of the sequences in the alignment,\n" + +"or in the currently selected region.", + "Invalid Input for Secondary Structure Prediction", + JOptionPane.WARNING_MESSAGE); + return; + } + if (msa.length == 1) { // Single Sequence prediction - jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, - title, msa[0]); + new jalview.ws.JPredClient(sh,title, msa[0]); } else { if (msa.length > 1) { - // Single Sequence prediction + // Aligned Sequences prediction jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, title, msa); } @@ -2339,4 +2496,136 @@ public class AlignFrame // TODO: group services by location as well as function. } + /* public void vamsasStore_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Export to Vamsas file"); + chooser.setToolTipText("Export"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); + //vs.store(chooser.getSelectedFile().getAbsolutePath() ); + vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); + } + }*/ + + public void featureSettings_actionPerformed(ActionEvent e) + { + new FeatureSettings(viewport, alignPanel); + } + + + +public void showTranslation_actionPerformed(ActionEvent e) +{ + int s, sSize = viewport.alignment.getHeight(); + SequenceI [] newSeq = new SequenceI[sSize]; + + int res, resSize; + StringBuffer protein; + String seq; + for(s=0; s