X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=81e55644b6b34e941aa0fc24f6970fd085d1dc30;hb=966e2e639242c252f4ed9e5f0e3e91b0389bd2de;hp=9bc4bc0146189b9e002ac4665abc3839cb025a6b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9bc4bc0..81e5564 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -13,12 +13,13 @@ * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software + * along with this program; if not, write to the Free Softwarechang * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import java.beans.*; +import java.io.*; import java.util.*; import java.awt.*; @@ -26,7 +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.*; @@ -34,48 +34,269 @@ import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; +import javax.swing.event.AncestorEvent; +/** + * DOCUMENT ME! + * + * @author $author$ + * @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; - public String currentFileFormat = "Jalview"; + AlignmentPanel alignPanel; + AlignViewport viewport; + + Vector viewports = new Vector(); + Vector alignPanels = new Vector(); + + /** DOCUMENT ME!! */ + public String currentFileFormat = null; Stack historyList = new Stack(); Stack redoList = new Stack(); private int treeCount = 0; + + /** + * Creates a new AlignFrame object. + * + * @param al DOCUMENT ME! + */ public AlignFrame(AlignmentI al) { viewport = new AlignViewport(al); + viewports.add(viewport); + + + if(viewport.vconsensus==null) + { + //Out of memory calculating consensus. + BLOSUM62Colour.setEnabled(false); + PIDColour.setEnabled(false); + conservationMenuItem.setEnabled(false); + modifyConservation.setEnabled(false); + abovePIDThreshold.setEnabled(false); + modifyPID.setEnabled(false); + } 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"); + + if(sortby.equals("Id")) + sortIDMenuItem_actionPerformed(null); + else if(sortby.equals("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(null); + + // remove(tabbedPane); + getContentPane().add(alignPanel, BorderLayout.CENTER); + + - getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); + // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); - addInternalFrameListener(new InternalFrameAdapter() + ///Dataset tab + ///////////////////////// + if(al.getDataset()==null) { - public void internalFrameActivated(InternalFrameEvent evt) + 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() + { + public void propertyChange(PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + alignmentChanged(); + } + } + }); + + + if (Desktop.desktop != null) + { + addServiceListeners(); + setGUINucleotide(al.isNucleotide()); + } + } + + /* Set up intrinsic listeners for dynamically generated GUI bits. */ + private void addServiceListeners() + { + final java.beans.PropertyChangeListener thisListener; + // Do this once to get current state + BuildWebServiceMenu(); + Desktop.discoverer.addPropertyChangeListener( + thisListener = new java.beans.PropertyChangeListener() + { + public void propertyChange(PropertyChangeEvent evt) { - javax.swing.SwingUtilities.invokeLater(new Runnable() + // System.out.println("Discoverer property change."); + if (evt.getPropertyName().equals("services")) { - public void run() + // System.out.println("Rebuilding web service menu"); + BuildWebServiceMenu(); + } + } + }); + addInternalFrameListener(new javax.swing.event. + InternalFrameAdapter() + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + // System.out.println("deregistering discoverer listener"); + Desktop.discoverer.removePropertyChangeListener(thisListener); + closeMenuItem_actionPerformed(null); + } + ; + }); + + } + + 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! + * + * @param String DOCUMENT ME! + */ + + public void parseGroupsFile(String file) + { + try + { + BufferedReader in = new BufferedReader(new FileReader(file)); + SequenceI seq = null; + String line, type, desc, token; + + int index, start, end; + StringTokenizer st; + 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() == 2) + { + type = st.nextToken(); + UserColourScheme ucs = new UserColourScheme(st.nextToken()); + fr.setColour(type, ucs.findColour("A")); + continue; + } + + while (st.hasMoreElements()) + { + desc = st.nextToken(); + token = st.nextToken(); + if (!token.equals("ID_NOT_SPECIFIED")) { - alignPanel.requestFocus(); + index = viewport.alignment.findIndex(viewport.alignment.findName( + token)); + st.nextToken(); } - }); + else + { + index = Integer.parseInt(st.nextToken()); + } + + start = Integer.parseInt(st.nextToken()); + end = Integer.parseInt(st.nextToken()); + + seq = viewport.alignment.getSequenceAt(index); + start = seq.findIndex(start) - 1; + end = seq.findIndex(end) - 1; + + 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.showSequenceFeatures = true; + + alignPanel.repaint(); + + } + catch (Exception ex) + { + System.out.println("Error parsing groups file: " + ex); + } + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(this); } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void saveAlignmentMenu_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. @@ -100,73 +321,130 @@ 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); - if (currentFileFormat.equals("Jalview")) - { - String shortName = title; + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - if (shortName.indexOf(java.io.File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); - } + saveAlignment(choice, currentFileFormat); + } + } - String choice = chooser.getSelectedFile().getPath(); - Jalview2XML.SaveState(this, choice, shortName); + public boolean saveAlignment(String file, String format) + { + if (format.equalsIgnoreCase("Jalview")) + { + String shortName = title; - // USE Jalview2XML to save this file - return; + if (shortName.indexOf(java.io.File.separatorChar) > -1) + { + shortName = shortName.substring(shortName.lastIndexOf( + java.io.File.separatorChar) + 1); } - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + Jalview2XML.SaveAlignment(this, file, shortName); - String output = FormatAdapter.formatSequences(currentFileFormat, - viewport.getAlignment().getSequences()); + // USE Jalview2XML to save this file + return true; + } + else + { + String output = new FormatAdapter().formatSequences(format, + viewport.getAlignment(). + getSequences()); + if (output == null) + { + return false; + } try { - java.io.PrintWriter out = new java.io.PrintWriter(new java.io. - FileWriter( - choice)); - out.println(output); + java.io.PrintWriter out = new java.io.PrintWriter( + new java.io.FileWriter(file)); + + out.print(output); out.close(); + return true; } catch (Exception ex) { + ex.printStackTrace(); } } + return false; } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void outputText_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); 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())); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ 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) + { + alignPanel.makePNGImageMap(file, image); } - protected void createPNG_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void createPNG(File f) { - alignPanel.makePNG(); + alignPanel.makePNG(f); } - protected void epsFile_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void createEPS(File f) { - alignPanel.makeEPS(); + alignPanel.makeEPS(f); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void printMenuItem_actionPerformed(ActionEvent e) { //Putting in a thread avoids Swing painting problems @@ -174,10 +452,16 @@ public class AlignFrame thread.start(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void closeMenuItem_actionPerformed(ActionEvent e) { try { + PaintRefresher.components.remove(viewport.alignment); this.setClosed(true); } catch (Exception ex) @@ -185,6 +469,9 @@ public class AlignFrame } } + /** + * DOCUMENT ME! + */ void updateEditMenuBar() { if (historyList.size() > 0) @@ -214,28 +501,42 @@ public class AlignFrame } } + /** + * DOCUMENT ME! + * + * @param hi DOCUMENT ME! + */ public void addHistoryItem(HistoryItem hi) { historyList.push(hi); updateEditMenuBar(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void undoMenuItem_actionPerformed(ActionEvent e) { HistoryItem hi = (HistoryItem) historyList.pop(); redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); restoreHistoryItem(hi); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void redoMenuItem_actionPerformed(ActionEvent e) { HistoryItem hi = (HistoryItem) redoList.pop(); restoreHistoryItem(hi); updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } // used by undo and redo @@ -280,13 +581,15 @@ public class AlignFrame updateEditMenuBar(); - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + /** + * DOCUMENT ME! + * + * @param up DOCUMENT ME! + */ public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -344,6 +647,17 @@ public class AlignFrame alignPanel.repaint(); } + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + Desktop.jalviewClipboard = null; + } + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void copy_actionPerformed(ActionEvent e) { if (viewport.getSelectionGroup() == null) @@ -354,9 +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++) { @@ -365,7 +679,8 @@ public class AlignFrame orderedSeqs.put(index + "", seq); } - int index = 0; + int index = 0, startRes, endRes; + char ch; for (int i = 0; i < sg.getSize(); i++) { @@ -386,21 +701,60 @@ public class AlignFrame } } - buffer.append(seq.getName() + "\t" + - seq.findPosition(sg.getStartRes()) + "\t" + - seq.findPosition(sg.getEndRes()) + "\t" + - sg.getSequenceAt(i).getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + //FIND START RES + //Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); + + //FIND END RES + //Need to find the residue preceeding index if gap + endRes = 0; + + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) + { + endRes++; + } + } + + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } + + 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()}; } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void pasteThis_actionPerformed(ActionEvent e) { addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, @@ -408,6 +762,11 @@ public class AlignFrame paste(false); } + /** + * DOCUMENT ME! + * + * @param newAlignment DOCUMENT ME! + */ void paste(boolean newAlignment) { try @@ -421,33 +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")) @@ -464,31 +825,58 @@ public class AlignFrame } else { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + //!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.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } catch (Exception ex) { + // could be anything being pasted in here } - // could be anything being pasted in here + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void cut_actionPerformed(ActionEvent e) { copy_actionPerformed(null); delete_actionPerformed(null); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void delete_actionPerformed(ActionEvent e) { - boolean seqsdeleted = false; if (viewport.getSelectionGroup() == null) { @@ -499,6 +887,11 @@ public class AlignFrame HistoryItem.HIDE)); SequenceGroup sg = viewport.getSelectionGroup(); + boolean allSequences = false; + if (sg.sequences.size() == viewport.alignment.getHeight()) + { + allSequences = true; + } for (int i = 0; i < sg.sequences.size(); i++) { @@ -506,9 +899,15 @@ public class AlignFrame int index = viewport.getAlignment().findIndex(seq); seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); + // If the cut affects all sequences, remove highlighted columns + if (allSequences) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + if (seq.getSequence().length() < 1) { - seqsdeleted = true; viewport.getAlignment().deleteSequence(seq); } else @@ -520,13 +919,10 @@ public class AlignFrame viewport.setSelectionGroup(null); viewport.alignment.deleteGroup(sg); - if (seqsdeleted) - { - viewport.firePropertyChange("alignment", null, + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); + if (viewport.getAlignment().getHeight() < 1) { @@ -538,12 +934,13 @@ public class AlignFrame { } } - - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void deleteGroups_actionPerformed(ActionEvent e) { viewport.alignment.deleteAllGroups(); @@ -551,6 +948,11 @@ public class AlignFrame alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); @@ -558,35 +960,59 @@ public class AlignFrame for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { - sg.addSequence(viewport.getAlignment().getSequenceAt(i)); + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth()); + sg.setEndRes(viewport.alignment.getWidth() - 1); viewport.setSelectionGroup(sg); - PaintRefresher.Refresh(null); + PaintRefresher.Refresh(null, viewport.alignment); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - PaintRefresher.Refresh(null); + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.annotationPanel.activeRes = null; + PaintRefresher.Refresh(null, viewport.alignment); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + selectAllSequenceMenuItem_actionPerformed(null); + + return; + } + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i)); + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } - PaintRefresher.Refresh(null); + PaintRefresher.Refresh(null, viewport.alignment); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { ColumnSelection colSel = viewport.getColumnSelection(); @@ -617,10 +1043,15 @@ public class AlignFrame } } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void remove2RightMenuItem_actionPerformed(ActionEvent e) { ColumnSelection colSel = viewport.getColumnSelection(); @@ -650,58 +1081,185 @@ public class AlignFrame } } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + SequenceI current; int jSize; - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + Vector seqs = null; + + int start = 0; + int end = viewport.alignment.getWidth(); + + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().sequences != null + && viewport.getSelectionGroup().sequences.size() > 0) { - current = viewport.getAlignment().getSequenceAt(i); + seqs = viewport.getSelectionGroup().sequences; + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes()+1; + } + else + { + seqs = viewport.alignment.getSequences(); + } + + for (int i = 0; i < seqs.size(); i++) + { + current = (SequenceI) seqs.elementAt(i); jSize = current.getLength(); - for (int j = 0; j < jSize; j++) + // 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++; + } + } + while (j < end && j < jSize); + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); } } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + public void alignmentChanged() + { + if(viewport.vconsensus!=null) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); + + alignPanel.repaint(); + } + + void resetAllColourSchemes() + { + ColourSchemeI cs = viewport.globalColourScheme; + if(cs!=null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). + resetClustalX(viewport.alignment.getSequences(), + viewport.alignment.getWidth()); + } + + cs.setConsensus(viewport.vconsensus); + if (cs.conservationApplied()) + { + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + + cs.setConservation(c); + } + } + + int s, sSize = viewport.alignment.getGroups().size(); + for(s=0; sDisplayed Tree menu. + * Creates a new menu item for a TreePanel with an appropriate + * jalview.analysis.AlignmentSorter call. Listeners are added + * to remove the menu item when the treePanel is closed, and adjust + * the tree leaf to sequence mapping when the alignment is modified. + * @param treePanel Displayed tree window. + * @param title SortBy menu item title. + */ void addTreeMenuItem(final TreePanel treePanel, String title) { final JMenuItem item = new JMenuItem(title); @@ -1352,22 +2156,15 @@ public class AlignFrame } ; }); - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue()); - treePanel.repaint(); - } - } - }); } - public void clustalAlignMenuItem_actionPerformed(ActionEvent e) + /** + * Work out whether the whole set of sequences + * or just the selected set will be submitted for multiple alignment. + * + */ + private SequenceI[] gatherSequencesForAlignment() { - // TODO:resolve which menu item was actually selected // Now, check we have enough sequences SequenceI[] msa = null; @@ -1398,60 +2195,29 @@ public class AlignFrame } } } - - if (msa != null) - { - jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", - title, msa, false, true); - } + return msa; } - public void ClustalRealign_actionPerformed(ActionEvent e) - { - // TODO:resolve which menu item was actually selected - // Now, check we have enough sequences - SequenceI[] msa = null; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 1)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); - int sz; - msa = new SequenceI[sz = seqs.getSize()]; - - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) - { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - - if (msa != null) - { - jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", - title, msa, true, true); - } - } - - protected void jpred_actionPerformed(ActionEvent e) + /** + * Decides what is submitted to a secondary structure prediction service, + * the currently selected sequence, or the currently selected alignment + * (where the first sequence in the set is the one that the prediction + * will be for). + */ + SequenceI[] gatherSeqOrMsaForSecStrPrediction() { 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)) { @@ -1491,63 +2257,26 @@ public class AlignFrame } } } - if (msa != null) { - JPredClient ct = new JPredClient(title, msa); - } - else if (seq != null) - { - JPredClient ct = new JPredClient(title, seq); + return msa; } else { - System.err.print( - "JALVIEW ERROR! - Unexpected JPred selection state!\n"); - } - } - - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) - { - // TODO:resolve which menu item was actually selected - // Now, check we have enough sequences - SequenceI[] msa = null; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 1)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); - int sz; - msa = new SequenceI[sz = seqs.getSize()]; - - for (int i = 0; i < sz; i++) + if (seq != null) { - msa[i] = (SequenceI) seqs.getSequenceAt(i); + return new SequenceI[] + { + seq}; } } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) - { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - - if (msa != null) - { - MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa, - false, true); - } + return null; } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file @@ -1569,7 +2298,7 @@ public class AlignFrame { jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File"); - ShowNewickTree(fin, choice); + viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { @@ -1582,27 +2311,50 @@ public class AlignFrame } } - public void ShowNewickTree(NewickFile nf, String title) + + public TreePanel ShowNewickTree(NewickFile nf, String title) { + return ShowNewickTree(nf,title,600,500,4,5); + } + /** + * DOCUMENT ME! + * + * @param nf DOCUMENT ME! + * @param title DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) + { + TreePanel tp = null; + try { nf.parse(); if (nf.getTree() != null) { - TreePanel tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), nf, - "FromFile", - title); - Desktop.addInternalFrame(tp, title, 600, 500); + tp = new TreePanel(viewport, + viewport.getAlignment().getSequences(), nf, + "FromFile", + title); + + tp.setSize(w,h); + + if(x>0 && y>0) + tp.setLocation(x,y); + + + Desktop.addInternalFrame(tp, title, w, h); addTreeMenuItem(tp, title); - viewport.setCurrentTree(tp.getTree()); } } catch (Exception ex) { ex.printStackTrace(); } + + return tp; } class PrintThread @@ -1627,4 +2379,253 @@ public class AlignFrame } } } + + /** + * Generates menu items and listener event actions for web service clients + * + */ + public void BuildWebServiceMenu() + { + if ( (Discoverer.services != null) + && (Discoverer.services.size() > 0)) + { + Vector msaws = (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); + Vector wsmenu = new Vector(); + if (msaws != null) + { + // Add any Multiple Sequence Alignment Services + final JMenu msawsmenu = new JMenu("Alignment"); + for (int i = 0, j = msaws.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws. + get(i); + final JMenuItem method = new JMenuItem(sh.getName()); + method.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + SequenceI[] msa = gatherSequencesForAlignment(); + new jalview.ws.MsaWSClient(sh, title, msa, + false, true, viewport.getAlignment().getDataset()); + + } + + }); + msawsmenu.add(method); + // Deal with services that we know accept partial alignments. + if (sh.getName().indexOf("lustal") > -1) + { + // We know that ClustalWS can accept partial alignments for refinement. + final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign"); + methodR.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + SequenceI[] msa = gatherSequencesForAlignment(); + new jalview.ws.MsaWSClient(sh, title, msa, + true, true, viewport.getAlignment().getDataset()); + + } + + }); + msawsmenu.add(methodR); + + } + } + wsmenu.add(msawsmenu); + } + if (secstrpr != null) + { + // Add any secondary structure prediction services + final JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); + for (int i = 0, j = secstrpr.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) + secstrpr.get(i); + final JMenuItem method = new JMenuItem(sh.getName()); + method.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + 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 + new jalview.ws.JPredClient(sh,title, msa[0]); + } + else + { + if (msa.length > 1) + { + // Aligned Sequences prediction + jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, + title, msa); + } + } + } + }); + secstrmenu.add(method); + } + wsmenu.add(secstrmenu); + } + this.webService.removeAll(); + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add( (JMenu) wsmenu.get(i)); + } + } + else + { + this.webService.removeAll(); + this.webService.add(this.webServiceNoServices); + } + // TODO: add in rediscovery function + // TODO: reduce code redundancy. + // 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