X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d154e2ea4f905796517af33d169c69a3589c55aa;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=0c0e3d7a623c2e68f7e998be62a7e918101bbe52;hpb=550cb05fd9def5e4f82b4353681cba939241b745;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 0c0e3d7..d154e2e 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,1325 +1,2136 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - - - - -package jalview.gui; - -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 jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; -import java.beans.PropertyChangeEvent; - -public class AlignFrame extends GAlignFrame -{ - final AlignmentPanel alignPanel; - final AlignViewport viewport; - public static final int NEW_WINDOW_WIDTH = 700; - public static final int NEW_WINDOW_HEIGHT = 500; - public String currentFileFormat = "Jalview"; - - public AlignFrame(AlignmentI al) - { - 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() ); - - getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); - - addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameActivated(InternalFrameEvent evt) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { alignPanel.requestFocus(); } - }); - - } - }); - - } - - 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); - - chooser.setAcceptAllFileFilterUsed(false); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); - int value = chooser.showSaveDialog(this); - if(value == JalviewFileChooser.APPROVE_OPTION) - { - currentFileFormat = chooser.getSelectedFormat(); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat); - - if (currentFileFormat.equals("Jalview")) - { - String shortName = title.replace('/', '_'); - title = title.replace('\\', '_'); - String choice = chooser.getSelectedFile().getPath(); - Jalview2XML.SaveState(this, choice, shortName); - // USE Jalview2XML to save this file - return; - } - - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences()); - try{ - java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) ); - out.println(output); - out.close(); - } - catch(Exception ex){} - } - - } - - 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.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences())); - } - - protected void htmlMenuItem_actionPerformed(ActionEvent e) - { - HTMLOutput htmlOutput = new HTMLOutput(viewport); - htmlOutput = null; - } - - protected void createPNG_actionPerformed(ActionEvent e) - { - alignPanel.makePNG(); - } - - protected void epsFile_actionPerformed(ActionEvent e) - { - alignPanel.makeEPS(); - } - - - public void printMenuItem_actionPerformed(ActionEvent e) - { - //Putting in a thread avoids Swing painting problems - PrintThread thread = new PrintThread(); - 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(); - } - } - } - - } - - - - - public void closeMenuItem_actionPerformed(ActionEvent e) - { - try{ - this.setClosed(true); - }catch(Exception ex){} - } - - Stack historyList = new Stack(); - Stack redoList = new Stack(); - private int treeCount = 0; - - void updateEditMenuBar() - { - 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); - HistoryItem hi = (HistoryItem)redoList.peek(); - redoMenuItem.setText("Redo "+hi.getDescription()); - } - else - { - redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); - } - } - - public void addHistoryItem(HistoryItem hi) - { - historyList.push(hi); - updateEditMenuBar(); - } - - protected void undoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem)historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); - restoreHistoryItem(hi); - } - - - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem)redoList.pop(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); - } - - - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) - { - if(hi.getType()== HistoryItem.SORT) - { - for(int i=0; ihi.getSequences().size()-1; i--) - viewport.alignment.deleteSequence(i); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - updateEditMenuBar(); - - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); - } - - 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); - } - } - else - { - 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); - } - } - - alignPanel.repaint(); - } - - - - protected void copy_actionPerformed(ActionEvent e) - { - if(viewport.getSelectionGroup()==null) - return; - - SequenceGroup sg = viewport.getSelectionGroup(); - - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - StringBuffer buffer= new StringBuffer(); - - Hashtable orderedSeqs = new Hashtable(); - 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); - - 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) - viewport.getSelectionGroup().adjustForRemoveRight(max); - - Vector groups = viewport.alignment.getGroups(); - for(int i=0; i0) - || viewport.getAlignment().getHeight()<4) - { - JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n" - +"at least 4 input sequences.", - "Sequence selection insufficient", - JOptionPane.WARNING_MESSAGE); - 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); - } - - - } - - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); - } - - 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.\n" - +"Try using the Pad function in the edit menu.", - "Sequences not aligned", JOptionPane.WARNING_MESSAGE); - return; - } - - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); - } - else - { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); - } - - addTreeMenuItem(tp, title); - - Desktop.addInternalFrame(tp, title, 600, 500); - } - - 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)); - // TODO: JBPNote - have to map order entries to curent SequenceI pointers - AlignmentSorter.sortBy(viewport.getAlignment(), order); - alignPanel.repaint(); - } - }); - } - - 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(new HistoryItem("Tree Sort", viewport.alignment, - HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.repaint(); - } - }); - - treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - 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) - { - // 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) -{ - SequenceI seq=null; - SequenceI[] msa=null; - - 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()) - { - seq = (SequenceI)seqs.getSequenceAt(0); - } - else - { - 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 || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.elementAt(0); - } - else - { - msa = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - if (msa!=null) { - JPredClient ct = new JPredClient(title, msa); - } else - if (seq!=null) { - JPredClient ct = new JPredClient(title, seq); - } else { - System.out.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++) - { - 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) { - MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true); - } - } - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { - // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - 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); - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File"); - ShowNewickTree(fin, choice); - } - catch (Exception ex) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "Problem reading tree file", - ex.getMessage(), - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - } - } - - public void ShowNewickTree(NewickFile nf, String title) - { - try{ - nf.parse(); - if (nf.getTree() != null) - { - TreePanel tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), - nf, "FromFile", title); - Desktop.addInternalFrame(tp, title, 600, 500); - addTreeMenuItem(tp, title); - viewport.setCurrentTree(tp.getTree()); - } - }catch(Exception ex){ex.printStackTrace();} - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * 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.analysis.*; + +import jalview.datamodel.*; + +import jalview.io.*; + +import jalview.jbgui.*; + +import jalview.schemes.*; + +import jalview.ws.*; + +import java.awt.*; +import java.awt.datatransfer.*; +import java.awt.event.*; +import java.awt.print.*; + +import java.io.*; + +import java.beans.*; + +import java.util.*; + +import javax.swing.*; +import javax.swing.event.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignFrame extends GAlignFrame +{ + /** 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) + { + 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()); + + getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); + + addInternalFrameListener(new InternalFrameAdapter() + { + public void internalFrameActivated(InternalFrameEvent evt) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + alignPanel.requestFocus(); + } + }); + } + }); + } + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void parseGroupsFile(String file) + { + 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); + + chooser.setAcceptAllFileFilterUsed(false); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save Alignment to file"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + currentFileFormat = chooser.getSelectedFormat(); + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat); + + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", 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(); + } + } + 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(), + viewport.getAlignment().getSequences())); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void htmlMenuItem_actionPerformed(ActionEvent e) + { + new HTMLOutput(viewport); + } + + public void createImageMap(File file, String image) + { + alignPanel.makePNGImageMap(file, image); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void createPNG(File f) + { + 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 + PrintThread thread = new PrintThread(); + thread.start(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void closeMenuItem_actionPerformed(ActionEvent e) + { + try + { + this.setClosed(true); + } + catch (Exception ex) + { + } + } + + /** + * DOCUMENT ME! + */ + void updateEditMenuBar() + { + 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); + + HistoryItem hi = (HistoryItem) redoList.peek(); + redoMenuItem.setText("Redo " + hi.getDescription()); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setText("Redo"); + } + } + + /** + * 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); + } + + /** + * 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(); + } + + // used by undo and redo + void restoreHistoryItem(HistoryItem hi) + { + if (hi.getType() == HistoryItem.SORT) + { + for (int i = 0; i < hi.getSequences().size(); i++) + { + viewport.alignment.getSequences().setElementAt(hi.getSequences() + .elementAt(i), + i); + } + } + else + { + for (int i = 0; i < hi.getSequences().size(); i++) + { + SequenceI restore = (SequenceI) hi.getSequences().elementAt(i); + + if (restore.getLength() == 0) + { + restore.setSequence(hi.getHidden().elementAt(i).toString()); + viewport.alignment.getSequences().insertElementAt(restore, + hi.getAlignIndex(i)); + } + else + { + restore.setSequence(hi.getHidden().elementAt(i).toString()); + } + } + + if (hi.getType() == HistoryItem.PASTE) + { + for (int i = viewport.alignment.getHeight() - 1; + i > (hi.getSequences().size() - 1); i--) + { + viewport.alignment.deleteSequence(i); + } + } + } + + 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(); + + 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); + } + } + else + { + 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); + } + } + + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void copy_actionPerformed(ActionEvent e) + { + if (viewport.getSelectionGroup() == null) + { + return; + } + + SequenceGroup sg = viewport.getSelectionGroup(); + + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + StringBuffer buffer = new StringBuffer(); + + Hashtable orderedSeqs = new Hashtable(); + + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.alignment.findIndex(seq); + orderedSeqs.put(index + "", seq); + } + + int index = 0; + + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = null; + + while (seq == null) + { + if (orderedSeqs.containsKey(index + "")) + { + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; + + break; + } + else + { + index++; + } + } + + 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"); + } + + 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(new HistoryItem("Paste Sequences", viewport.alignment, + HistoryItem.PASTE)); + paste(false); + } + + /** + * DOCUMENT ME! + * + * @param newAlignment DOCUMENT ME! + */ + void paste(boolean newAlignment) + { + 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); + + if (!newAlignment) + { + viewport.alignment.addSequence(sequence); + } + else + { + seqs.add(sequence); + } + } + + if (newAlignment) + { + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + seqs.toArray(newSeqs); + + AlignFrame af = new AlignFrame(new Alignment(newSeqs)); + 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) + { + } + + // 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) + { + return; + } + + addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, + HistoryItem.HIDE)); + + 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 (seq.getSequence().length() < 1) + { + seqsdeleted = true; + viewport.getAlignment().deleteSequence(seq); + } + else + { + viewport.getAlignment().getSequences().setElementAt(seq, index); + } + } + + 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) + { + } + } + + 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 < viewport.getAlignment().getSequences().size(); + i++) + { + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + } + + sg.setEndRes(viewport.alignment.getWidth()); + viewport.setSelectionGroup(sg); + 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); + 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), false); + } + + PaintRefresher.Refresh(null, viewport.alignment); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + { + ColumnSelection colSel = viewport.getColumnSelection(); + + if (colSel.size() > 0) + { + addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, + HistoryItem.HIDE)); + + int min = colSel.getMin(); + viewport.getAlignment().trimLeft(min); + colSel.compensateForEdit(0, min); + + if (viewport.getSelectionGroup() != null) + { + viewport.getSelectionGroup().adjustForRemoveLeft(min); + } + + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.get(i); + + if (!sg.adjustForRemoveLeft(min)) + { + viewport.alignment.deleteGroup(sg); + } + } + + alignPanel.repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void remove2RightMenuItem_actionPerformed(ActionEvent e) + { + ColumnSelection colSel = viewport.getColumnSelection(); + + if (colSel.size() > 0) + { + addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, + HistoryItem.HIDE)); + + int max = colSel.getMax(); + viewport.getAlignment().trimRight(max); + + if (viewport.getSelectionGroup() != null) + { + viewport.getSelectionGroup().adjustForRemoveRight(max); + } + + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.get(i); + + if (!sg.adjustForRemoveRight(max)) + { + viewport.alignment.deleteGroup(sg); + } + } + + alignPanel.repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Remove Gapped Columns", + viewport.alignment, HistoryItem.HIDE)); + + viewport.getAlignment().removeGaps(); + viewport.updateConservation(); + viewport.updateConsensus(); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, + HistoryItem.HIDE)); + + SequenceI current; + int jSize; + + Vector seqs = null; + + int start = 0; + int end = viewport.alignment.getWidth(); + + if (viewport.getSelectionGroup() != null) + { + 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(); + + int j = start; + + do + { + if (jalview.util.Comparison.isGap(current.getCharAt(j))) + { + current.deleteCharAt(j); + j--; + jSize--; + } + + j++; + } + while (j < end); + } + + 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); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void font_actionPerformed(ActionEvent e) + { + FontChooser fc = new FontChooser(alignPanel); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void fullSeqId_actionPerformed(ActionEvent e) + { + viewport.setShowFullId(fullSeqId.isSelected()); + + 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(); + } + + /** + * 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()); + 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()); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void viewTextMenuItem_actionPerformed(ActionEvent e) + { + 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) + { + 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()) + { + annotationPanelMenuItem.setSelected(false); + + return; + } + + 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); + 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) + { + alignPanel.setOverviewPanel(null); + } + ; + }); + + alignPanel.setOverviewPanel(overview); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { + changeColour(null); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void clustalColour_actionPerformed(ActionEvent e) + { + 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()); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void helixColour_actionPerformed(ActionEvent e) + { + 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()); + } + + /** + * 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()) + { + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); + + if (cs instanceof ResidueColourScheme) + { + ((ResidueColourScheme) cs).setThreshold(threshold); + } + else if (cs instanceof ScoreColourScheme) + { + ((ScoreColourScheme) cs).setThreshold(threshold); + } + + viewport.setGlobalColourScheme(cs); + } + else if (cs instanceof ResidueColourScheme) + { + ((ResidueColourScheme) cs).setThreshold(0); + } + else if (cs instanceof ScoreColourScheme) + { + ((ScoreColourScheme) cs).setThreshold(0); + } + + if (viewport.getConservationSelected()) + { + ConservationColourScheme ccs = null; + + 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); + + ccs = new ConservationColourScheme(c, cs); + + // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! + ccs.setConsensus(viewport.vconsensus); + viewport.setGlobalColourScheme(ccs); + + ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, + "Background"); + } + else + { + // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! + if (cs != null) + { + cs.setConsensus(viewport.vconsensus); + } + + viewport.setGlobalColourScheme(cs); + } + + if (viewport.getColourAppliesToAllGroups()) + { + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + + if (cs == null) + { + sg.cs = null; + } + else if (cs instanceof ClustalxColourScheme) + { + sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + } + else if (cs instanceof UserColourScheme) + { + sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours()); + } + else + { + try + { + sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + } + catch (Exception ex) + { + } + } + + if (viewport.getAbovePIDThreshold()) + { + if (sg.cs instanceof ResidueColourScheme) + { + ((ResidueColourScheme) sg.cs).setThreshold(threshold); + } + else if (sg.cs instanceof ScoreColourScheme) + { + ((ScoreColourScheme) sg.cs).setThreshold(threshold); + } + + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.getWidth())); + } + + if (viewport.getConservationSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, sg.sequences, 0, + viewport.alignment.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + + ConservationColourScheme ccs = new ConservationColourScheme(c, + sg.cs); + + // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! + ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.getWidth())); + sg.cs = ccs; + } + else if (cs != null) + { + // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.getWidth())); + } + } + } + + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void modifyPID_actionPerformed(ActionEvent e) + { + if (viewport.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); + SliderPanel.showPIDSlider(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void modifyConservation_actionPerformed(ActionEvent e) + { + if (viewport.getConservationSelected()) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.globalColourScheme, "Background"); + SliderPanel.showConservationSlider(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { + viewport.setConservationSelected(conservationMenuItem.isSelected()); + + viewport.setAbovePIDThreshold(false); + abovePIDThreshold.setSelected(false); + + ColourSchemeI cs = viewport.getGlobalColourScheme(); + + if (cs instanceof ConservationColourScheme) + { + changeColour(((ConservationColourScheme) cs).cs); + } + else + { + changeColour(cs); + } + + modifyConservation_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void abovePIDThreshold_actionPerformed(ActionEvent e) + { + viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); + + conservationMenuItem.setSelected(false); + viewport.setConservationSelected(false); + + ColourSchemeI cs = viewport.getGlobalColourScheme(); + + if (cs instanceof ConservationColourScheme) + { + changeColour(((ConservationColourScheme) cs).cs); + } + else + { + changeColour(cs); + } + + modifyPID_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void userDefinedColour_actionPerformed(ActionEvent e) + { + new UserDefinedColours(alignPanel, null); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void PIDColour_actionPerformed(ActionEvent e) + { + changeColour(new PIDColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + changeColour(new Blosum62ColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, + HistoryItem.SORT)); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void sortIDMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + HistoryItem.SORT)); + AlignmentSorter.sortByID(viewport.getAlignment()); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void sortGroupMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + HistoryItem.SORT)); + + AlignmentSorter.sortByGroup(viewport.getAlignment()); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + { + RedundancyPanel sp = new RedundancyPanel(alignPanel, this); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(sp); + Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, + 100, false); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + { + if ((viewport.getSelectionGroup() == null) || + (viewport.getSelectionGroup().getSize() < 2)) + { + JOptionPane.showInternalMessageDialog(this, + "You must select at least 2 sequences.", "Invalid Selection", + JOptionPane.WARNING_MESSAGE); + } + else + { + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(new PairwiseAlignPanel(viewport)); + Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void PCAMenuItem_actionPerformed(ActionEvent e) + { + 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); + + 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); + } + } + + /** + * 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 BLOSUM62"); + } + + /** + * DOCUMENT ME! + * + * @param type DOCUMENT ME! + * @param pwType DOCUMENT ME! + * @param title DOCUMENT ME! + */ + void NewTreePanel(String type, String pwType, String title) + { + final TreePanel tp; + + if ((viewport.getSelectionGroup() != null) && + (viewport.getSelectionGroup().getSize() > 3)) + { + 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 + { + //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); + 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)); + + // TODO: JBPNote - have to map order entries to curent SequenceI pointers + AlignmentSorter.sortBy(viewport.getAlignment(), order); + alignPanel.repaint(); + } + }); + } + + /** + * DOCUMENT ME! + * + * @param treePanel DOCUMENT ME! + * @param title DOCUMENT ME! + */ + 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(new HistoryItem("Tree Sort", + viewport.alignment, HistoryItem.SORT)); + AlignmentSorter.sortByTree(viewport.getAlignment(), + treePanel.getTree()); + alignPanel.repaint(); + } + }); + + treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + 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(); + } + } + }); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void clustalAlignMenuItem_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, false, true); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + 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); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void jpred_actionPerformed(ActionEvent e) + { + SequenceI seq = null; + SequenceI[] msa = null; + + 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()) + { + seq = (SequenceI) seqs.getSequenceAt(0); + } + else + { + 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) || !viewport.alignment.isAligned()) + { + seq = (SequenceI) seqs.elementAt(0); + } + else + { + msa = new SequenceI[seqs.size()]; + + for (int i = 0; i < seqs.size(); i++) + { + msa[i] = (SequenceI) seqs.elementAt(i); + } + } + } + + if (msa != null) + { + JPredClient ct = new JPredClient(title, msa); + } + else if (seq != null) + { + JPredClient ct = new JPredClient(title, seq); + } + else + { + System.err.print( + "JALVIEW ERROR! - Unexpected JPred selection state!\n"); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + 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++) + { + 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) + { + MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa, + false, true); + } + } + + /** + * 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")); + 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); + + try + { + jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, + "File"); + viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + } + catch (Exception ex) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "Problem reading tree file", ex.getMessage(), + JOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + } + } + + /** + * 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(); + } + } + } + } +}