X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f82efb5b9b25bade7cbc11287ced0586f4c9c0d2;hb=0b23947e2cdcd704d3f313b23ba271e43d097344;hp=727e1c6e2cd31da3f9c00a63d9ed7f4f15ec8f8e;hpb=11cfcb7281e45c5958b839e55da66cfbb9582fa7;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 727e1c6..f82efb5 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,2172 +1,3168 @@
-/*
- * 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, startRes, endRes;
- char ch;
-
- 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++;
- }
- }
-
- //FIND START RES
- //Returns residue following index if gap
- startRes = seq.findPosition(sg.getStartRes());
-
- //FIND END RES
- //Need to find the residue preceeding index if gap
- endRes = 0;
-
- for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
- {
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
- {
- endRes++;
- }
- }
-
- if(endRes>0)
- {
- endRes += seq.getStart() -1;
- }
-
- 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(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();
- 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);
-
- // If the cut affects all sequences, remove highlighted columns
- if(allSequences)
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);
- }
-
-
- if (seq.getSequence().length() < 1)
- {
- seqsdeleted = true;
- viewport.getAlignment().deleteSequence(seq);
- }
- else
- {
- 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()-1);
- 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
- && viewport.getSelectionGroup().sequences != null
- && viewport.getSelectionGroup().sequences.size()>0)
- {
- 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 && 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);
- 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();
- }
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 Softwarechang
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.commands.*;
+import jalview.ws.*;
+import java.awt.dnd.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame extends GAlignFrame implements DropTargetListener
+{
+ /** DOCUMENT ME!! */
+ public static final int DEFAULT_WIDTH = 700;
+
+ /** DOCUMENT ME!! */
+ public static final int DEFAULT_HEIGHT = 500;
+ public AlignmentPanel alignPanel;
+
+ AlignViewport viewport;
+
+ Vector alignPanels = new Vector();
+
+
+ /** DOCUMENT ME!! */
+ public String currentFileFormat = null;
+
+ public String fileName = null;
+
+ private int treeCount = 0;
+
+ /**
+ * Creates a new AlignFrame object.
+ *
+ * @param al DOCUMENT ME!
+ */
+ public AlignFrame(AlignmentI al, int width, int height)
+ {
+ this(al, null, width, height);
+ }
+
+
+ /**
+ * new alignment window with hidden columns
+ * @param al AlignmentI
+ * @param hiddenColumns ColumnSelection or null
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height)
+ {
+ this.setSize(width, height);
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+ if(al.getDataset()==null)
+ {
+ al.setDataset(null);
+ }
+
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ /**
+ * Make a new AlignFrame from exisiting alignmentPanels
+ * @param ap AlignmentPanel
+ * @param av AlignViewport
+ */
+ public AlignFrame(AlignmentPanel ap)
+ {
+ viewport = ap.av;
+ alignPanel = ap;
+ addAlignmentPanel(ap, false);
+ init();
+ }
+
+ void init()
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+
+ if (viewport.conservation == null)
+ {
+ BLOSUM62Colour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
+ }
+
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+ if (sortby.equals("Id"))
+ sortIDMenuItem_actionPerformed(null);
+ else if (sortby.equals("Pairwise Identity"))
+ sortPairwiseMenuItem_actionPerformed(null);
+
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(viewport.alignment.isNucleotide());
+ }
+
+ setMenusFromViewport(viewport);
+
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ addKeyListener();
+
+
+ }
+
+ void addKeyListener()
+ {
+ final AlignFrame af = this;
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ if (viewport.cursorMode
+ && evt.getKeyCode() >= KeyEvent.VK_0
+ && evt.getKeyCode() <= KeyEvent.VK_9)
+ {
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
+
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_V:
+ if (!evt.isControlDown())
+ {
+ AlignmentPanel newap =
+ new Jalview2XML().copyAlignPanel(alignPanel, true);
+
+ if(viewport.viewName==null)
+ viewport.viewName="View 1";
+
+ newap.av.historyList = viewport.historyList;
+ newap.av.redoList = viewport.redoList;
+ newap.av.viewName = "View " +
+ (Desktop.getViewCount(viewport.getSequenceSetId())+1);
+
+ addAlignmentPanel(newap, false);
+
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount()-1);
+
+ }
+ break;
+ case KeyEvent.VK_G:
+ Desktop.instance.gatherViews(af);
+ break;
+
+ case KeyEvent.VK_X:
+ if (!evt.isControlDown())
+ {
+ Desktop.instance.explodeViews(af);
+ }
+ break;
+
+
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
+
+ break;
+
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ moveSelectedSequences(false);
+ break;
+
+ case KeyEvent.VK_UP:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, -1);
+ }
+ else
+ moveSelectedSequences(true);
+ break;
+
+ case KeyEvent.VK_LEFT:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor( -1, 0);
+ }
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(1, 0);
+ }
+ break;
+
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+ }
+ break;
+
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (!viewport.cursorMode)
+ {
+ cut_actionPerformed(null);
+ }
+ else
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+
+ break;
+
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
+
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
+
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
+
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText("Keyboard editing mode is " +
+ (viewport.cursorMode ? "on" : "off"));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ alignPanel.seqPanel.seqCanvas.repaint();
+ break;
+
+ case KeyEvent.VK_F1:
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break
+ ;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+
+ boolean hide = false;
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+ showAllSeqs_actionPerformed(null);
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ viewport.selectionGroup = sg;
+ }
+ else if (!hide)
+ showAllColumns_actionPerformed(null);
+ }
+ break;
+ }
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
+ alignPanel.scrollUp(true);
+ else
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ break;
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ alignPanel.scrollUp(false);
+ else
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ break;
+ }
+ }
+ });
+ }
+
+
+ public void addAlignmentPanel(final AlignmentPanel ap,
+ boolean newPanel)
+ {
+ ap.alignFrame = this;
+
+ alignPanels.addElement(ap);
+
+ int aSize = alignPanels.size();
+
+ tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+
+ if (aSize == 1 && ap.av.viewName==null)
+ {
+ this.getContentPane().add(ap, BorderLayout.CENTER);
+ }
+ else
+ {
+ if (aSize == 2)
+ {
+ AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
+
+ this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+ }
+
+ tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+
+ ap.setVisible(false);
+ }
+
+ if(newPanel)
+ {
+ ap.av.updateConsensus(ap);
+ ap.av.updateConservation(ap);
+ }
+ }
+
+
+ public AlignViewport getViewport()
+ {
+ return viewport;
+ }
+
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */
+ private void addServiceListeners()
+ {
+ final java.beans.PropertyChangeListener thisListener;
+ // Do this once to get current state
+ BuildWebServiceMenu();
+ Desktop.discoverer.addPropertyChangeListener(
+ thisListener = new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // System.out.println("Discoverer property change.");
+ if (evt.getPropertyName().equals("services"))
+ {
+ // System.out.println("Rebuilding web service menu");
+ BuildWebServiceMenu();
+ }
+ }
+ });
+
+ addInternalFrameListener(new javax.swing.event.
+ InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("deregistering discoverer listener");
+ Desktop.discoverer.removePropertyChangeListener(thisListener);
+ closeMenuItem_actionPerformed(null);
+ }
+ ;
+ });
+ }
+
+ public void setGUINucleotide(boolean nucleotide)
+ {
+ showTranslation.setVisible( nucleotide );
+ conservationMenuItem.setEnabled( !nucleotide );
+ modifyConservation.setEnabled( !nucleotide );
+
+ //Remember AlignFrame always starts as protein
+ if(!nucleotide)
+ {
+ calculateMenu.remove(calculateMenu.getItemCount()-2);
+ }
+ }
+
+ /**
+ * Need to call this method when tabs are selected for multiple views,
+ * or when loading from Jalview2XML.java
+ * @param av AlignViewport
+ */
+ void setMenusFromViewport(AlignViewport av)
+ {
+ colourTextMenuItem.setSelected(av.showColourText);
+ abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ conservationMenuItem.setSelected(av.getConservationSelected());
+ seqLimits.setSelected(av.getShowJVSuffix());
+ renderGapsMenuItem.setSelected(av.renderGaps);
+ wrapMenuItem.setSelected(av.wrapAlignment);
+ annotationPanelMenuItem.setState(av.showAnnotation);
+ viewBoxesMenuItem.setSelected(av.showBoxes);
+ viewTextMenuItem.setSelected(av.showText);
+
+ setColourSelected(ColourSchemeProperty.
+ getColourName(av.getGlobalColourScheme()));
+
+ showSeqFeatures.setSelected(av.showSequenceFeatures);
+ hiddenMarkers.setState(av.showHiddenMarkers);
+ applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ smoothFont.setState(av.antiAlias);
+
+ updateEditMenuBar();
+ }
+
+
+ Hashtable progressBars;
+ public void setProgressBar(String message, long id)
+ {
+ if(progressBars == null)
+ progressBars = new Hashtable();
+
+ JPanel progressPanel;
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if(progressBars.get( new Long(id) )!=null)
+ {
+ progressPanel = (JPanel)progressBars.get( new Long(id) );
+ statusPanel.remove(progressPanel);
+ progressBars.remove( progressPanel );
+ progressPanel = null;
+ if(message!=null)
+ statusBar.setText(message);
+
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(new Long(id), progressPanel);
+ }
+
+ validate();
+ }
+
+
+
+
+ /*
+ Added so Castor Mapping file can obtain Jalview Version
+ */
+ public String getVersion()
+ {
+ return jalview.bin.Cache.getProperty("VERSION");
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
+
+ public void save_actionPerformed(ActionEvent e)
+ {
+ if(fileName==null || currentFileFormat==null)
+ saveAs_actionPerformed(null);
+ else
+ saveAlignment(fileName, currentFileFormat);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveAs_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,
+ 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();
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "You must select a file format before saving!",
+ "File format not specified",
+ JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
+
+ fileName = chooser.getSelectedFile().getPath();
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat);
+
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
+
+ saveAlignment(fileName, 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);
+ }
+
+ new Jalview2XML().SaveAlignment(this, file, shortName);
+
+ statusBar.setText("Successfully saved to file: "
+ +fileName+" in "
+ +format +" format.");
+
+
+ // USE Jalview2XML to save this file
+ return true;
+ }
+ else
+ {
+
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ + "\nDo you want to save only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ format,
+ viewport.alignment.getSequencesArray(),
+ omitHidden);
+
+ if (output == null)
+ {
+ return false;
+ }
+
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
+ out.close();
+ this.setTitle(file);
+ statusBar.setText("Successfully saved to file: "
+ +fileName+" in "
+ +format +" format.");
+ return true;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ String [] omitHidden = null;
+
+ if(viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ +"\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if(reply==JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600,
+ 500);
+
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ viewport.alignment.getSequencesArray(),
+ omitHidden));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ new HTMLOutput(viewport,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ 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();
+ }
+
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
+ viewport.alignment.getAlignmentAnnotation()
+ );
+ }
+
+
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Jalview Annotations or Features File");
+ chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(choice);
+ }
+
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void closeMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ if(alignPanels!=null)
+ {
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(ap);
+ }
+ // alignPanels = null;
+ }
+ // else
+ // System.out.println("null one here");
+
+ // alignPanel = null;
+ // viewport = null;
+
+ this.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ */
+ void updateEditMenuBar()
+ {
+
+ if (viewport.historyList.size() > 0)
+ {
+ undoMenuItem.setEnabled(true);
+ CommandI command = (CommandI) viewport.historyList.peek();
+ undoMenuItem.setText("Undo " + command.getDescription());
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ }
+
+ if (viewport.redoList.size() > 0)
+ {
+ redoMenuItem.setEnabled(true);
+
+ CommandI command = (CommandI) viewport.redoList.peek();
+ redoMenuItem.setText("Redo " + command.getDescription());
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
+ }
+ }
+
+
+ public void addHistoryItem(CommandI command)
+ {
+ if(command.getSize()>0)
+ {
+ viewport.historyList.push(command);
+ viewport.redoList.clear();
+ updateEditMenuBar();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ }
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ CommandI command = (CommandI)viewport.historyList.pop();
+ viewport.redoList.push(command);
+ command.undoCommand();
+
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ updateEditMenuBar();
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+
+ updateEditMenuBar();
+ 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.getSequences(false).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+
+ if (sg.getSequences(false).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.getSequences(false).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+ if (sg.getSequences(false).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)
+ {
+ System.gc();
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ omitHidden = viewport.getViewAsString(true);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ "Fasta",
+ seqs,
+ omitHidden);
+
+ StringSelection ss = new StringSelection(output);
+
+ try
+ {
+ //Its really worth setting the clipboard contents
+ //to empty before setting the large StringSelection!!
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
+ }
+ catch (OutOfMemoryError er)
+ {
+ er.printStackTrace();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory copying region!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ return;
+ }
+
+ Vector hiddenColumns = null;
+ if(viewport.hasHiddenColumns)
+ {
+ hiddenColumns =new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ for(int i=0; i>>This is a fix for the moment, until a better solution is found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+
+ }
+
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: "+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)
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ Vector seqs = new Vector();
+ int cutLength = sg.getEndRes()-sg.getStartRes()+1;
+ boolean seqsCut = false;
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(false); i++)
+ {
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ if(seq.getLength()<=cutLength)
+ seqsCut = true;
+ }
+
+
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize(false) == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+
+ SequenceI [] cut = new SequenceI[seqs.size()];
+ for(int i=0; i 0)
+ {
+ if(trimLeft)
+ column = colSel.getMin();
+ else
+ column = colSel.getMax();
+
+ SequenceI [] seqs;
+ if(viewport.getSelectionGroup()!=null)
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ else
+ seqs = viewport.alignment.getSequencesArray();
+
+
+ TrimRegionCommand trimRegion;
+ if(trimLeft)
+ {
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ }
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ }
+
+ statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+ addHistoryItem(trimRegion);
+
+ Vector groups = viewport.alignment.getGroups();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ {
+ viewport.alignment.deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ int start = 0, end = viewport.alignment.getWidth()-1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ seqs = viewport.alignment.getSequencesArray();
+
+
+ RemoveGapColCommand removeGapCols =
+ new RemoveGapColCommand("Remove Gapped Columns",
+ seqs,
+ start, end,
+ viewport.getGapCharacter());
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ int start = 0, end = viewport.alignment.getWidth()-1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ seqs = viewport.alignment.getSequencesArray();
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+ seqs,
+ start, end,
+ viewport.getGapCharacter()));
+
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ viewport.padGaps = padGapsMenuitem.isSelected();
+
+ viewport.firePropertyChange("alignment",
+ null,
+ viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * 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);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ new FontChooser(alignPanel);
+ }
+
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+ viewport.antiAlias = smoothFont.isSelected();
+ alignPanel.annotationPanel.image = null;
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowJVSuffix(seqLimits.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!
+ */
+ public void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ scaleAbove.setVisible(wrapMenuItem.isSelected());
+ scaleLeft.setVisible(wrapMenuItem.isSelected());
+ scaleRight.setVisible(wrapMenuItem.isSelected());
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ }
+
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenSeqs();
+ }
+
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ repaint();
+ }
+
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+ viewport.hideAllSelectedSeqs();
+ alignPanel.repaint();
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.repaint();
+ }
+
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+ 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();
+ }
+
+
+ public FeatureSettings featureSettings;
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
+ if(featureSettings !=null )
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
+ featureSettings = new FeatureSettings(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+ alignPanel.repaint();
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ 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());
+ }
+
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColourChooser(viewport, alignPanel);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs DOCUMENT ME!
+ */
+ public void changeColour(ColourSchemeI cs)
+ {
+ int threshold = 0;
+
+ if(cs!=null)
+ {
+ if (viewport.getAbovePIDThreshold())
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
+
+ cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else
+ {
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ if (viewport.getConservationSelected())
+ {
+
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ cs.setConservation(c);
+
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+ "Background"));
+ }
+ else
+ {
+ cs.setConservation(null);
+ }
+
+ cs.setConsensus(viewport.hconsensus);
+ }
+
+ 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;
+ continue;
+ }
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(true), 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()
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(true), 0,
+ sg.getWidth()));
+ }
+ else
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
+
+ if (viewport.getConservationSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(true), 0,
+ viewport.alignment.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+ sg.cs.setConservation(c);
+ }
+ else
+ sg.cs.setConservation(null);
+ }
+ }
+
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(),
+ "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ {
+ 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);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ 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);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyPID_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ if (e.getActionCommand().equals("User Defined..."))
+ {
+ new UserDefinedColours(alignPanel, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+ getUserColourSchemes().get(e.getActionCommand());
+
+ changeColour(udc);
+ }
+ }
+
+ public void updateUserColourMenu()
+ {
+
+ Component[] menuItems = colourMenu.getMenuComponents();
+ int i, iSize = menuItems.length;
+ for (i = 0; i < iSize; i++)
+ {
+ if (menuItems[i].getName() != null &&
+ menuItems[i].getName().equals("USER_DEFINED"))
+ {
+ colourMenu.remove(menuItems[i]);
+ iSize--;
+ }
+ }
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if(option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
+ }
+
+ /**
+ * 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)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(),
+ viewport.getAlignment().getSequenceAt(0));
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ new RedundancyPanel(alignPanel, this);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ if ( (viewport.getSelectionGroup() == null) ||
+ (viewport.getSelectionGroup().getSize(false) < 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(false) < 4) &&
+ (viewport.getSelectionGroup().getSize(false) > 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;
+ }
+
+ new PCAPanel(viewport);
+ }
+
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if(viewport.autoCalculateConsensus)
+ {
+ viewport.firePropertyChange("alignment",
+ null,
+ viewport.getAlignment().getSequences());
+ }
+ }
+
+
+ /**
+ * 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)
+ {
+ TreePanel tp;
+
+ if (viewport.getSelectionGroup() != null) {
+ if (viewport.getSelectionGroup().getSize(false) < 3) {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "You need to have more than two sequences selected to build a tree!",
+ "Not enough sequences",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ int s = 0;
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ /* Decide if the selection is a column region */
+ while (s < sg.getSize(false))
+ {
+ if ( ( (SequenceI) sg.getSequences(false).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(alignPanel, type, pwType);
+ }
+ 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;
+ }
+
+ if(viewport.alignment.getHeight()<2)
+ return;
+
+ tp = new TreePanel(alignPanel, type, pwType);
+ }
+
+ addTreeMenuItem(tp, title);
+
+ 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)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);
+
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
+
+ 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)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(viewport.getAlignment(),
+ treePanel.getTree());
+
+ addHistoryItem(new OrderCommand("Tree Sort",
+ oldOrder,
+ viewport.alignment));
+
+
+ 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);
+ }
+ }
+ ;
+ });
+ }
+
+ /**
+ * Work out whether the whole set of sequences
+ * or just the selected set will be submitted for multiple alignment.
+ *
+ */
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+ {
+ // Now, check we have enough sequences
+ AlignmentView msa = null;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 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(false)];
+
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ } */
+ msa = viewport.getAlignmentView(true);
+ }
+ 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);
+ }
+ }*/
+ msa = viewport.getAlignmentView(false);
+ }
+ return msa;
+ }
+
+ /**
+ * 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).
+ */
+ AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ {
+ AlignmentView seqs = null;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 0))
+ {
+ seqs = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ seqs = viewport.getAlignmentView(false);
+ }
+ // limit sequences - JBPNote in future - could spawn multiple prediction jobs
+ // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ if (!viewport.alignment.isAligned())
+ {
+ seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
+ }
+ return seqs;
+ }
+ /**
+ * 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();
+ }
+ }
+ }
+
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title)
+ {
+ return ShowNewickTree(nf,title,600,500,4,5);
+ }
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+ {
+ return ShowNewickTree(nf,title, input, 600,500,4,5);
+ }
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+ return ShowNewickTree(nf, title, null, w, h, x, y);
+ }
+ /**
+ * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
+ *
+ * @param nf the tree
+ * @param title tree viewer title
+ * @param input Associated alignment input data (or null)
+ * @param w width
+ * @param h height
+ * @param x position
+ * @param y position
+ * @return TreePanel handle
+ */
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
+ TreePanel tp = null;
+
+ try
+ {
+ nf.parse();
+
+ if (nf.getTree() != null)
+ {
+ tp = new TreePanel(alignPanel,
+ "FromFile",
+ title,
+ nf, input);
+
+ tp.setSize(w,h);
+
+ if(x>0 && y>0)
+ tp.setLocation(x,y);
+
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ 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 ( (Discoverer.services != null)
+ && (Discoverer.services.size() > 0))
+ {
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector wsmenu = new Vector();
+ final AlignFrame af = this;
+ 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)
+ {
+ AlignmentView msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ false, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ 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)
+ {
+ AlignmentView msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ true, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ 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)
+ {
+ AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
+ if (msa.getSequences().length == 1)
+ {
+ // Single Sequence prediction
+ new jalview.ws.JPredClient(sh, title, false, msa, af, true);
+ }
+ else
+ {
+ if (msa.getSequences().length > 1)
+ {
+ // Sequence profile based prediction
+ new jalview.ws.JPredClient(sh,
+ title, true, msa, af, true);
+ }
+ }
+ }
+ });
+ secstrmenu.add(method);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ this.webService.removeAll();
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add( (JMenu) wsmenu.get(i));
+ }
+ }
+ else
+ {
+ this.webService.removeAll();
+ this.webService.add(this.webServiceNoServices);
+ }
+ // TODO: add in rediscovery function
+ // TODO: reduce code redundancy.
+ // TODO: group services by location as well as function.
+ }
+
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Export to Vamsas file");
+ chooser.setToolTipText("Export");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+ }
+ }*/
+
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ String [] seqstring = viewport.getViewAsString(true);
+
+ int s, sSize = selection.length;
+ SequenceI [] newSeq = new SequenceI[sSize];
+
+ int res, resSize;
+ StringBuffer protein;
+ String seq;
+ for(s=0; s -1 || file.indexOf("file:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
+ alignment, file);
+
+ if (!isAnnotation)
+ {
+ boolean isGroupsFile = parseFeaturesFile(file,protocol);
+ if (!isGroupsFile)
+ {
+ String format = new IdentifyFile().Identify(file, protocol);
+
+ if(format.equalsIgnoreCase("JnetFile"))
+ {
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(),
+ 0, false);
+ alignPanel.adjustAnnotationHeight();
+ alignPanel.repaint();
+ }
+ else
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ }
+ else
+ {
+ // (isAnnotation)
+ alignPanel.adjustAnnotationHeight();
+ }
+
+ }catch(Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ public void tabSelectionChanged(int index)
+ {
+ if (index > -1)
+ {
+ alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+ viewport = alignPanel.av;
+ setMenusFromViewport(viewport);
+ }
+ }
+
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
+ if(SwingUtilities.isRightMouseButton(e))
+ {
+ String reply = JOptionPane.showInternalInputDialog(this,
+ "Enter View Name",
+ "Edit View Name",
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply != null)
+ {
+ viewport.viewName = reply;
+ tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+ }
+ }
+ }
+
+
+ public AlignViewport getCurrentView()
+ {
+ return viewport;
+ }
+}