X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=e4ed302efb3e345694029be10ffc855d8be8b12b;hb=97173a9190084b142021b3822e383de600a2e8a2;hp=cabb24f502198a6fa7270cebee2df895268d041e;hpb=9bea55eea55110a19b17d0127903802013fa60ea;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index cabb24f..e4ed302 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,137 +1,337 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * - * AM Waterhouse - *******************/ - - - - + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * 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 + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; -import jalview.jbgui.GAlignFrame; -import jalview.schemes.*; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.io.*; -import jalview.ws.*; +import java.beans.*; +import java.io.*; +import java.util.*; + import java.awt.*; +import java.awt.datatransfer.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; import javax.swing.event.*; -import java.util.*; -import java.awt.datatransfer.*; +import jalview.analysis.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.jbgui.*; +import jalview.schemes.*; +import jalview.ws.*; -public class AlignFrame extends GAlignFrame +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignFrame + extends GAlignFrame { - final AlignmentPanel alignPanel; - final AlignViewport viewport; + /** 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; + + /** 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) { - try{ - String ip = java.net.InetAddress.getLocalHost().getHostAddress(); - if( !ip.startsWith("10.")) - webService.setVisible(false); - } - catch(java.net.UnknownHostException e){} viewport = new AlignViewport(al); - alignPanel = new AlignmentPanel(this, viewport); alignPanel.annotationPanel.adjustPanelHeight(); - alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize()); - alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize()); - alignPanel.setAnnotationVisible( viewport.getShowAnnotation() ); + alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel. + annotationPanel.getPreferredSize()); + alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel. + getPreferredSize()); + alignPanel.setAnnotationVisible(viewport.getShowAnnotation()); getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameActivated(InternalFrameEvent evt) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void internalFrameActivated(InternalFrameEvent evt) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() { - public void run() - { alignPanel.requestFocus(); } - }); + alignPanel.requestFocus(); + } + }); + } + }); + addServiceListeners(); + } + + /* Set up intrinsic listeners for dynamically generated GUI bits. */ + private void addServiceListeners() + { - } - }); + final AlignFrame thisFrame = this; + final java.beans.PropertyChangeListener thisListener; + // Do this once to get current state + thisFrame.BuildWebServiceMenu(); + Desktop.discoverer.addPropertyChangeListener( + thisListener = new java.beans.PropertyChangeListener() + { + public void propertyChange(PropertyChangeEvent evt) + { + // System.out.println("Discoverer property change."); + if (evt.getPropertyName().equals("services")) + { + // System.out.println("Rebuilding web service menu"); + thisFrame.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); + } + ; + }); } - protected void saveAs_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ + + public void parseGroupsFile(String file) { - String suffix [] = null; - if(e.getActionCommand().equals("FASTA")) - suffix = new String[]{"fa", "fasta"}; - else if(e.getActionCommand().equals("MSF")) - suffix = new String[]{"msf"}; - else if(e.getActionCommand().equals("CLUSTAL")) - suffix = new String[]{"aln"}; - else if(e.getActionCommand().equals("BLC")) - suffix = new String[]{"blc"}; - else if(e.getActionCommand().equals("PIR")) - suffix = new String[]{"pir"}; - else if(e.getActionCommand().equals("PFAM")) - suffix = new String[]{"pfam"}; + try + { + BufferedReader in = new BufferedReader(new FileReader(file)); + SequenceI seq = null; + String line, text, token; + UserColourScheme ucs; + int index, start, end; + StringTokenizer st; + SequenceGroup sg; + while ( (line = in.readLine()) != null) + { + st = new StringTokenizer(line, "\t"); + if (st.countTokens() != 6) + { + System.out.println("Groups file " + file + + " is invalid. Read help file."); + System.exit(1); + } + + while (st.hasMoreElements()) + { + text = st.nextToken(); + token = st.nextToken(); + if (!token.equals("ID_NOT_SPECIFIED")) + { + 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()); + 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); + + viewport.alignment.addGroup(sg); + } + } + + } + catch (Exception ex) + { + System.out.println("Error parsing groups file: " + ex); + } + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void saveAlignmentMenu_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY"), + new String[] + { + "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", + "jar" + }, + new String[] + { + "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" + }, currentFileFormat); - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY") - , suffix, e.getActionCommand()+" file"); + chooser.setAcceptAllFileFilterUsed(false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format."); + chooser.setDialogTitle("Save Alignment to file"); chooser.setToolTipText("Save"); + int value = chooser.showSaveDialog(this); - if(value == JalviewFileChooser.APPROVE_OPTION) + + if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); + currentFileFormat = chooser.getSelectedFormat(); + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat); + + String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()); - try{ - java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) ); + + saveAlignment(choice, currentFileFormat); + } + } + + public boolean saveAlignment(String file, String format) + { + if (format.equalsIgnoreCase("Jalview")) + { + String shortName = title; + + if (shortName.indexOf(java.io.File.separatorChar) > -1) + { + shortName = shortName.substring(shortName.lastIndexOf( + java.io.File.separatorChar) + 1); + } + + Jalview2XML.SaveAlignment(this, file, shortName); + + // USE Jalview2XML to save this file + return true; + } + else + { + String output = FormatAdapter.formatSequences(format, + viewport.getAlignment(). + getSequences()); + if (output == null) + { + return false; + } + + try + { + java.io.PrintWriter out = new java.io.PrintWriter( + new java.io.FileWriter(file)); out.println(output); out.close(); + return true; + } + catch (Exception ex) + { + ex.printStackTrace(); } - catch(Exception ex){} } - + return false; } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - JInternalFrame frame = new JInternalFrame(); - cap.formatForOutput(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500); - cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences())); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, + 500); + cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), + viewport.getAlignment(). + getSequences())); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { - HTMLOutput htmlOutput = new HTMLOutput(viewport); - htmlOutput = null; + new HTMLOutput(viewport); } - protected void createPNG_actionPerformed(ActionEvent e) + public void createImageMap(File file, String image) { - alignPanel.makePNG(); + alignPanel.makePNGImageMap(file, image); } - protected void epsFile_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void createPNG(File f) { - alignPanel.makeEPS(); + alignPanel.makePNG(f); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void createEPS(File f) + { + alignPanel.makeEPS(f); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void printMenuItem_actionPerformed(ActionEvent e) { //Putting in a thread avoids Swing painting problems @@ -139,61 +339,47 @@ public class AlignFrame extends GAlignFrame thread.start(); } - class PrintThread extends Thread - { - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - printJob.setPrintable(alignPanel, pf); - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - - } - - - - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void closeMenuItem_actionPerformed(ActionEvent e) { - try{ + try + { this.setClosed(true); - }catch(Exception ex){} + } + catch (Exception ex) + { + } } - Stack historyList = new Stack(); - Stack redoList = new Stack(); - + /** + * DOCUMENT ME! + */ void updateEditMenuBar() { - if(historyList.size()>0) - { - undoMenuItem.setEnabled(true); - Object [] history = (Object[])historyList.get(0); - undoMenuItem.setText("Undo "+history[0]); - } + if (historyList.size() > 0) + { + undoMenuItem.setEnabled(true); + + HistoryItem hi = (HistoryItem) historyList.peek(); + undoMenuItem.setText("Undo " + hi.getDescription()); + } else { undoMenuItem.setEnabled(false); undoMenuItem.setText("Undo"); } - if(redoList.size()>0) - { - redoMenuItem.setEnabled(true); - Object [] history = (Object[])redoList.get(0); - redoMenuItem.setText("Redo "+history[0]); - } + if (redoList.size() > 0) + { + redoMenuItem.setEnabled(true); + + HistoryItem hi = (HistoryItem) redoList.peek(); + redoMenuItem.setText("Redo " + hi.getDescription()); + } else { redoMenuItem.setEnabled(false); @@ -201,60 +387,125 @@ public class AlignFrame extends GAlignFrame } } - public void addHistoryItem(String type) + /** + * DOCUMENT ME! + * + * @param hi DOCUMENT ME! + */ + public void addHistoryItem(HistoryItem hi) { - // must make sure we add new sequence objects her, not refs to the existing sequences - redoList.clear(); - SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()]; - for(int i=0; i (hi.getSequences().size() - 1); i--) + { + viewport.alignment.deleteSequence(i); + } + } } - ///////// - redoList.add(0, new Object[] {history[0], seq}); + updateEditMenuBar(); - seq = (SequenceI[]) history[1]; - viewport.setAlignment( new Alignment(seq) ); - updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); + 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(); + if (sg == null) + { return; + } if (up) { for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); + if (!sg.sequences.contains(seq)) + { continue; + } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + if (sg.sequences.contains(temp)) + { continue; + } viewport.alignment.getSequences().setElementAt(temp, i); viewport.alignment.getSequences().setElementAt(seq, i - 1); @@ -265,12 +516,18 @@ public class AlignFrame extends GAlignFrame for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); + if (!sg.sequences.contains(seq)) + { continue; + } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + if (sg.sequences.contains(temp)) + { continue; + } viewport.alignment.getSequences().setElementAt(temp, i); viewport.alignment.getSequences().setElementAt(seq, i + 1); @@ -280,469 +537,868 @@ public class AlignFrame extends GAlignFrame alignPanel.repaint(); } - - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void copy_actionPerformed(ActionEvent e) { - if(viewport.getSelectionGroup()==null) - return; + if (viewport.getSelectionGroup() == null) + { + return; + } - SequenceGroup sg = viewport.getSelectionGroup(); + SequenceGroup sg = viewport.getSelectionGroup(); - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - StringBuffer buffer= new StringBuffer(); + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + StringBuffer buffer = new StringBuffer(); - for(int i=0; i 0) + { + endRes += seq.getStart() - 1; + } + + buffer.append(seq.getName() + "\t" + + startRes + "\t" + + endRes + "\t" + + seq.getSequence(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); + } + c.setContents(new StringSelection(buffer.toString()), null); + } + /** + * 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("Paste"); + addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, + HistoryItem.PASTE)); paste(false); } + /** + * DOCUMENT ME! + * + * @param newAlignment DOCUMENT ME! + */ void paste(boolean newAlignment) { - try{ + try + { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); Transferable contents = c.getContents(this); + if (contents == null) + { return; + } String str = (String) contents.getTransferData(DataFlavor.stringFlavor); StringTokenizer st = new StringTokenizer(str); ArrayList seqs = new ArrayList(); + 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); + Sequence sequence = new Sequence(name, st.nextToken(), start, + end); - if(!newAlignment) + if (!newAlignment) + { viewport.alignment.addSequence(sequence); + } else + { seqs.add(sequence); + } } - if(newAlignment) + if (newAlignment) { SequenceI[] newSeqs = new SequenceI[seqs.size()]; seqs.toArray(newSeqs); + AlignFrame af = new AlignFrame(new Alignment(newSeqs)); - Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); + String newtitle = new String("Copied sequences"); + + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + + Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); } else { + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); viewport.updateConservation(); viewport.updateConsensus(); alignPanel.repaint(); } + } + catch (Exception ex) + { + } - }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) { - addHistoryItem("Delete"); + boolean seqsdeleted = false; + if (viewport.getSelectionGroup() == null) + { return; + } + + addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, + 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++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.getAlignment().findIndex(seq); + seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - SequenceGroup sg = viewport.getSelectionGroup(); - for (int i=0;i < sg.sequences.size(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - 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) - viewport.getAlignment().deleteSequence(seq); + if (seq.getSequence().length() < 1) + { + seqsdeleted = true; + viewport.getAlignment().deleteSequence(seq); + } else - viewport.getAlignment().getSequences().setElementAt(seq, index); - } + { + viewport.getAlignment().getSequences().setElementAt(seq, index); + } + } - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); - viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight()); - if(viewport.getAlignment().getHeight()<1) - try - { - this.setClosed(true); - }catch(Exception ex){} - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.setSelectionGroup(null); + viewport.alignment.deleteGroup(sg); - } + if (seqsdeleted) + { + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + } + viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + this.setClosed(true); + } + catch (Exception ex) + { + } + } - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - Object [] history = (Object[])redoList.remove(0); - SequenceI[] seq = (SequenceI[]) history[1]; - viewport.setAlignment( new Alignment(seq) ); - updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + viewport.updateConservation(); + viewport.updateConsensus(); + alignPanel.repaint(); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void deleteGroups_actionPerformed(ActionEvent e) { viewport.alignment.deleteAllGroups(); viewport.setSelectionGroup(null); - alignPanel.repaint(); } - - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); - for (int i=0; i 0) { + addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, + HistoryItem.HIDE)); + int min = colSel.getMin(); viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0,min); + colSel.compensateForEdit(0, min); - if(viewport.getSelectionGroup()!=null) + if (viewport.getSelectionGroup() != null) + { viewport.getSelectionGroup().adjustForRemoveLeft(min); + } Vector groups = viewport.alignment.getGroups(); - for(int i=0; i 0) { + addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, + HistoryItem.HIDE)); + int max = colSel.getMax(); viewport.getAlignment().trimRight(max); - if(viewport.getSelectionGroup()!=null) + + if (viewport.getSelectionGroup() != null) + { viewport.getSelectionGroup().adjustForRemoveRight(max); + } Vector groups = viewport.alignment.getGroups(); - for(int i=0; i 0) { - current = viewport.getAlignment().getSequenceAt(i); + seqs = viewport.getSelectionGroup().sequences; + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + 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++) - if(jalview.util.Comparison.isGap(current.getCharAt(j))) + + int j = start; + + do + { + if (jalview.util.Comparison.isGap(current.getCharAt(j))) { current.deleteCharAt(j); j--; jSize--; } + j++; + } + while (j < end && j < jSize); } + viewport.updateConservation(); viewport.updateConsensus(); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void padGapsMenuitem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment, + HistoryItem.HIDE)); + + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + + viewport.updateConservation(); + viewport.updateConsensus(); + alignPanel.repaint(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void findMenuItem_actionPerformed(ActionEvent e) { JInternalFrame frame = new JInternalFrame(); Finder finder = new Finder(viewport, alignPanel, frame); frame.setContentPane(finder); - Desktop.addInternalFrame(frame, "Find", 340,110, false); + Desktop.addInternalFrame(frame, "Find", 340, 110); frame.setLayer(JLayeredPane.PALETTE_LAYER); - } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void font_actionPerformed(ActionEvent e) { - FontChooser fc = new FontChooser( alignPanel ); + FontChooser fc = new FontChooser(alignPanel); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void fullSeqId_actionPerformed(ActionEvent e) { - viewport.setShowFullId( fullSeqId.isSelected() ); + viewport.setShowFullId(fullSeqId.isSelected()); - alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() ); + alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth()); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void colourTextMenuItem_actionPerformed(ActionEvent e) { - viewport.setColourText( colourTextMenuItem.isSelected() ); - alignPanel.repaint(); + viewport.setColourText(colourTextMenuItem.isSelected()); + alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void wrapMenuItem_actionPerformed(ActionEvent e) { - viewport.setWrapAlignment( wrapMenuItem.isSelected() ); - alignPanel.setWrapAlignment( wrapMenuItem.isSelected() ); - scaleAbove.setVisible( wrapMenuItem.isSelected() ); - scaleLeft.setVisible( wrapMenuItem.isSelected() ); - scaleRight.setVisible( wrapMenuItem.isSelected() ); + viewport.setWrapAlignment(wrapMenuItem.isSelected()); + alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); + scaleAbove.setVisible(wrapMenuItem.isSelected()); + scaleLeft.setVisible(wrapMenuItem.isSelected()); + scaleRight.setVisible(wrapMenuItem.isSelected()); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); alignPanel.repaint(); } - - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowBoxes( viewBoxesMenuItem.isSelected() ); + viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void viewTextMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowText( viewTextMenuItem.isSelected() ); + viewport.setShowText(viewTextMenuItem.isSelected()); alignPanel.repaint(); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ public void sequenceFeatures_actionPerformed(ActionEvent evt) { viewport.showSequenceFeatures(sequenceFeatures.isSelected()); - if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded) + + if (viewport.showSequenceFeatures && + ! ( (Alignment) viewport.alignment).featuresAdded) { - AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel); - ((Alignment)viewport.alignment).featuresAdded = true; + SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport. + alignment, + alignPanel); + ( (Alignment) viewport.alignment).featuresAdded = true; } + alignPanel.repaint(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment()) + if (annotationPanelMenuItem.isSelected() && + viewport.getWrapAlignment()) { annotationPanelMenuItem.setSelected(false); + return; } - viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() ); - alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() ); + + viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) + { return; + } JInternalFrame frame = new JInternalFrame(); OverviewPanel overview = new OverviewPanel(alignPanel); - frame.setContentPane(overview); + frame.setContentPane(overview); Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt) + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) { - alignPanel.setOverviewPanel(null); - }; + alignPanel.setOverviewPanel(null); + } + ; }); - alignPanel.setOverviewPanel( overview ); - - + alignPanel.setOverviewPanel(overview); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void noColourmenuItem_actionPerformed(ActionEvent e) { - changeColour( null ); + changeColour(null); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void clustalColour_actionPerformed(ActionEvent e) { - abovePIDThreshold.setSelected(false); - changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth())); + changeColour(new ClustalxColourScheme( + viewport.alignment.getSequences(), viewport.alignment.getWidth())); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void hydrophobicityColour_actionPerformed(ActionEvent e) { - changeColour( new HydrophobicColourScheme() ); + changeColour(new HydrophobicColourScheme()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void helixColour_actionPerformed(ActionEvent e) { - changeColour(new HelixColourScheme() ); + changeColour(new HelixColourScheme()); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void buriedColour_actionPerformed(ActionEvent e) { - changeColour(new BuriedColourScheme() ); + changeColour(new BuriedColourScheme()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); } - - + /** + * DOCUMENT ME! + * + * @param cs DOCUMENT ME! + */ void changeColour(ColourSchemeI cs) { int threshold = 0; - if ( viewport.getAbovePIDThreshold() ) + if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); if (cs instanceof ResidueColourScheme) - ( (ResidueColourScheme) cs).setThreshold(threshold); + { + ( (ResidueColourScheme) cs).setThreshold(threshold, + viewport. + getIgnoreGapsConsensus()); + } else if (cs instanceof ScoreColourScheme) - ( (ScoreColourScheme) cs).setThreshold(threshold); + { + ( (ScoreColourScheme) cs).setThreshold(threshold, + viewport.getIgnoreGapsConsensus()); + } viewport.setGlobalColourScheme(cs); } else if (cs instanceof ResidueColourScheme) - ( (ResidueColourScheme) cs).setThreshold(0); + { + ( (ResidueColourScheme) cs).setThreshold(0, + viewport.getIgnoreGapsConsensus()); + } else if (cs instanceof ScoreColourScheme) - ( (ScoreColourScheme) cs).setThreshold(0); - - + { + ( (ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus()); + } if (viewport.getConservationSelected()) { @@ -759,118 +1415,167 @@ public class AlignFrame extends GAlignFrame ccs = new ConservationColourScheme(c, cs); - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - ccs.setConsensus( viewport.vconsensus ); viewport.setGlobalColourScheme(ccs); - SliderPanel.setConservationSlider(alignPanel, ccs, "Background"); - + ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, + "Background"); } else { - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - if (cs != null) - cs.setConsensus(viewport.vconsensus); - viewport.setGlobalColourScheme(cs); - } + // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! + if (cs != null) + { + cs.setConsensus(viewport.vconsensus); + } + viewport.setGlobalColourScheme(cs); + } - if(viewport.getColourAppliesToAllGroups()) + if (viewport.getColourAppliesToAllGroups()) { Vector groups = viewport.alignment.getGroups(); - for(int i=0; i0) - || viewport.getAlignment().getHeight()<4) + if ( ( (viewport.getSelectionGroup() != null) && + (viewport.getSelectionGroup().getSize() < 4) && + (viewport.getSelectionGroup().getSize() > 0)) || + (viewport.getAlignment().getHeight() < 4)) { - JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n" - +"at least 4 input sequences.", - "Sequence selection insufficient", - JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(this, + "Principal component analysis must take\n" + + "at least 4 input sequences.", + "Sequence selection insufficient", + JOptionPane.WARNING_MESSAGE); + return; } - try{ + 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); - } - - + 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); + } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "PID", "Average distance tree using PID"); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } + /** + * DOCUMENT ME! + * + * @param type DOCUMENT ME! + * @param pwType DOCUMENT ME! + * @param title DOCUMENT ME! + */ void NewTreePanel(String type, String pwType, String title) { - //are the sequences aligned? - if(!viewport.alignment.isAligned()) - { - JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.", - "Sequences not aligned", JOptionPane.WARNING_MESSAGE); - return; - } - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) + + if ( (viewport.getSelectionGroup() != null) && + (viewport.getSelectionGroup().getSize() > 3)) { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); + int s = 0; + SequenceGroup sg = viewport.getSelectionGroup(); + + /* Decide if the selection is a column region */ + while (s < sg.sequences.size()) + { + if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() < + sg.getEndRes()) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The selected region to create a tree may\nonly contain residues or gaps.\n" + + "Try using the Pad function in the edit menu,\n" + + "or one of the multiple sequence alignment web services.", + "Sequences in selection are not aligned", + JOptionPane.WARNING_MESSAGE); + + return; + } + } + + title = title + " on region"; + tp = new TreePanel(viewport, + viewport.getSelectionGroup().sequences, type, pwType, + sg.getStartRes(), sg.getEndRes()); } else { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The sequences must be aligned before creating a tree.\n" + + "Try using the Pad function in the edit menu,\n" + + "or one of the multiple sequence alignment web services.", + "Sequences not aligned", + JOptionPane.WARNING_MESSAGE); + + return; + } + + tp = new TreePanel(viewport, + viewport.getAlignment().getSequences(), type, pwType, + 0, + viewport.alignment.getWidth()); } - addTreeMenuItem(tp, title); + addTreeMenuItem(tp, title); + viewport.setCurrentTree(tp.getTree()); + + Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500); + } + + /** + * DOCUMENT ME! + * + * @param title DOCUMENT ME! + * @param order DOCUMENT ME! + */ + public void addSortByOrderMenuItem(String title, final AlignmentOrder order) + { + final JMenuItem item = new JMenuItem("by " + title); + sort.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Sort", viewport.alignment, + HistoryItem.SORT)); - Desktop.addInternalFrame(tp, title, 600, 500); + // TODO: JBPNote - have to map order entries to curent SequenceI pointers + AlignmentSorter.sortBy(viewport.getAlignment(), order); + alignPanel.repaint(); + } + }); } + /** + * Maintain the Order by->Displayed 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); + + treeCount++; + + if (treeCount == 1) + { + sort.add(sortByTreeMenu); + } + sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - addHistoryItem("sort"); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); + addHistoryItem(new HistoryItem("Tree Sort", + viewport.alignment, HistoryItem.SORT)); + AlignmentSorter.sortByTree(viewport.getAlignment(), + treePanel.getTree()); alignPanel.repaint(); } }); - treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + treePanel.addInternalFrameListener(new javax.swing.event. + InternalFrameAdapter() { - public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt) + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) { + treeCount--; sortByTreeMenu.remove(item); - }; - }); + if (treeCount == 0) + { + sort.remove(sortByTreeMenu); + } + } + ; + }); + 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() { - WebserviceInfo info = new WebserviceInfo("Clustal web service", - "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+ - " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." - +" Nucleic Acids Research, submitted, June 1994.", - 450, 150); - - ClustalThread thread = new ClustalThread(info); - thread.start(); - } + // Now, check we have enough sequences + SequenceI[] msa = null; - class ClustalThread extends Thread + if ( (viewport.getSelectionGroup() != null) && + (viewport.getSelectionGroup().getSize() > 1)) { - WebserviceInfo info; - public ClustalThread(WebserviceInfo info) - {this.info = info; } + // 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()]; - public void run() + for (int i = 0; i < sz; i++) { - info.setStatus(WebserviceInfo.STATE_RUNNING); - jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss(); - Vector sv = viewport.getAlignment().getSequences(); - SequenceI[] seqs = new SequenceI[sv.size()]; + msa[i] = (SequenceI) seqs.getSequenceAt(i); + } + } + else + { + Vector seqs = viewport.getAlignment().getSequences(); - int i = 0; - do - { - seqs[i] = (SequenceI) sv.elementAt(i); - } - while (++i < sv.size()); + if (seqs.size() > 1) + { + msa = new SequenceI[seqs.size()]; - SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method - if (alignment != null) - { - AlignFrame af = new AlignFrame(new Alignment(alignment)); - Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"), - NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); - af.clustalColour_actionPerformed(null); - af.clustalColour.setSelected(true); - info.setStatus(WebserviceInfo.STATE_STOPPED_OK); - } - else + for (int i = 0; i < seqs.size(); i++) { - info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); - info.appendProgressText("Problem obtaining clustal alignment"); + msa[i] = (SequenceI) seqs.elementAt(i); } } } + return msa; + } - 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 (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0) + if ( (viewport.getSelectionGroup() != null) && + (viewport.getSelectionGroup().getSize() > 0)) { // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! SequenceGroup seqs = viewport.getSelectionGroup(); - if (seqs.getSize() == 1 || !viewport.alignment.isAligned()) + + if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned()) { - JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0)); + seq = (SequenceI) seqs.getSequenceAt(0); } else { int sz; - SequenceI[] msa = new SequenceI[sz=seqs.getSize()]; + msa = new SequenceI[sz = seqs.getSize()]; + for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) seqs.getSequenceAt(i); } - - JPredClient ct = new JPredClient(msa); } - } else { Vector seqs = viewport.getAlignment().getSequences(); - if (seqs.size() == 1 || !viewport.alignment.isAligned()) + if ( (seqs.size() == 1) || !viewport.alignment.isAligned()) { - JPredClient ct = new JPredClient( (SequenceI) - seqs.elementAt(0)); + seq = (SequenceI) seqs.elementAt(0); } else { - SequenceI[] msa = new SequenceI[seqs.size()]; + msa = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) seqs.elementAt(i); } - - JPredClient ct = new JPredClient(msa); } - } - } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) - { - // TODO:resolve which menu item was actually selected - // Now, check we have enough sequences - 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; - SequenceI[] msa = new SequenceI[sz=seqs.getSize()]; - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - - MsaWSClient ct = new jalview.ws.MsaWSClient(msa); - } - else + if (msa != null) + { + return msa; + } + else + { + if (seq != null) { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) { - SequenceI[] msa = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - - MsaWSClient ct = new MsaWSClient(msa); - } - + return new SequenceI[] + { + seq}; } } - - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + return null; + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty("LAST_DIRECTORY")); + getProperty( + "LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Select a newick-like tree file"); chooser.setToolTipText("Load a tree file"); + int value = chooser.showOpenDialog(null); + if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - TreePanel treepanel = null; + try { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File"); - fin.parse(); - - if (fin.getTree() != null) - { - TreePanel tp = null; - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - fin, "FromFile", choice); - Desktop.addInternalFrame(tp, title, 600, 500); - addTreeMenuItem(tp, title); - } + jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, + "File"); + viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { @@ -1221,4 +2125,167 @@ public class AlignFrame extends GAlignFrame } } + /** + * DOCUMENT ME! + * + * @param nf DOCUMENT ME! + * @param title DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public TreePanel ShowNewickTree(NewickFile nf, String title) + { + TreePanel tp = null; + + try + { + nf.parse(); + + if (nf.getTree() != null) + { + tp = new TreePanel(viewport, + viewport.getAlignment().getSequences(), nf, + "FromFile", + title); + Desktop.addInternalFrame(tp, title, 600, 500); + addTreeMenuItem(tp, title); + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + return tp; + } + + class PrintThread + extends Thread + { + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + printJob.setPrintable(alignPanel, pf); + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } + catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } + } + + /** + * Generates menu items and listener event actions for web service clients + * + */ + public void BuildWebServiceMenu() + { + if ( (Desktop.discoverer.services != null) + && (Desktop.discoverer.services.size() > 0)) + { + Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Desktop.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(); + MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa, + false, true); + + } + + }); + 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(); + MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa, + true, true); + + } + + }); + 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 = gatherSeqOrMsaForSecStrPrediction(); + if (msa.length == 1) + { + // Single Sequence prediction + jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, + title, msa[0]); + } + else + { + if (msa.length > 1) + { + // Single Sequence 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. + } + }