2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Softwarechang
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import java.beans.*;
\r
26 import java.awt.datatransfer.*;
\r
27 import java.awt.event.*;
\r
28 import java.awt.print.*;
\r
29 import javax.swing.*;
\r
30 import javax.swing.event.*;
\r
32 import jalview.analysis.*;
\r
33 import jalview.datamodel.*;
\r
34 import jalview.io.*;
\r
35 import jalview.jbgui.*;
\r
36 import jalview.schemes.*;
\r
37 import jalview.ws.*;
\r
43 * @version $Revision$
\r
45 public class AlignFrame
\r
48 /** DOCUMENT ME!! */
\r
49 public static final int NEW_WINDOW_WIDTH = 700;
\r
51 /** DOCUMENT ME!! */
\r
52 public static final int NEW_WINDOW_HEIGHT = 500;
\r
53 final AlignmentPanel alignPanel;
\r
54 final AlignViewport viewport;
\r
56 /** DOCUMENT ME!! */
\r
57 public String currentFileFormat = null;
\r
58 Stack historyList = new Stack();
\r
59 Stack redoList = new Stack();
\r
60 private int treeCount = 0;
\r
63 * Creates a new AlignFrame object.
\r
65 * @param al DOCUMENT ME!
\r
67 public AlignFrame(AlignmentI al)
\r
69 viewport = new AlignViewport(al);
\r
71 alignPanel = new AlignmentPanel(this, viewport);
\r
72 alignPanel.annotationPanel.adjustPanelHeight();
\r
73 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
\r
74 annotationPanel.getPreferredSize());
\r
75 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
\r
76 getPreferredSize());
\r
77 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
\r
79 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
\r
81 if(sortby.equals("Id"))
\r
82 sortIDMenuItem_actionPerformed(null);
\r
83 else if(sortby.equals("Pairwise Identity"))
\r
84 sortPairwiseMenuItem_actionPerformed(null);
\r
86 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
\r
88 viewport.addPropertyChangeListener(new PropertyChangeListener()
\r
90 public void propertyChange(PropertyChangeEvent evt)
\r
92 if (evt.getPropertyName().equals("alignment"))
\r
99 addServiceListeners();
\r
102 /* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
103 private void addServiceListeners()
\r
105 final java.beans.PropertyChangeListener thisListener;
\r
106 // Do this once to get current state
\r
107 BuildWebServiceMenu();
\r
108 Desktop.discoverer.addPropertyChangeListener(
\r
109 thisListener = new java.beans.PropertyChangeListener()
\r
111 public void propertyChange(PropertyChangeEvent evt)
\r
113 // System.out.println("Discoverer property change.");
\r
114 if (evt.getPropertyName().equals("services"))
\r
116 // System.out.println("Rebuilding web service menu");
\r
117 BuildWebServiceMenu();
\r
121 addInternalFrameListener(new javax.swing.event.
\r
122 InternalFrameAdapter()
\r
124 public void internalFrameClosed(
\r
125 javax.swing.event.InternalFrameEvent evt)
\r
127 // System.out.println("deregistering discoverer listener");
\r
128 Desktop.discoverer.removePropertyChangeListener(thisListener);
\r
129 closeMenuItem_actionPerformed(null);
\r
139 * @param String DOCUMENT ME!
\r
142 public void parseGroupsFile(String file)
\r
146 BufferedReader in = new BufferedReader(new FileReader(file));
\r
147 SequenceI seq = null;
\r
148 String line, text, token;
\r
149 UserColourScheme ucs;
\r
150 int index, start, end;
\r
151 StringTokenizer st;
\r
153 while ( (line = in.readLine()) != null)
\r
155 st = new StringTokenizer(line, "\t");
\r
156 if (st.countTokens() != 6)
\r
158 System.out.println("Groups file " + file +
\r
159 " is invalid. Read help file.");
\r
163 while (st.hasMoreElements())
\r
165 text = st.nextToken();
\r
166 token = st.nextToken();
\r
167 if (!token.equals("ID_NOT_SPECIFIED"))
\r
169 index = viewport.alignment.findIndex(viewport.alignment.findName(
\r
175 index = Integer.parseInt(st.nextToken());
\r
178 start = Integer.parseInt(st.nextToken());
\r
179 end = Integer.parseInt(st.nextToken());
\r
180 ucs = new UserColourScheme(st.nextToken());
\r
182 seq = viewport.alignment.getSequenceAt(index);
\r
183 start = seq.findIndex(start) - 1;
\r
184 end = seq.findIndex(end) - 1;
\r
186 sg = new SequenceGroup(text, ucs, true, true, false, start, end);
\r
187 sg.addSequence(seq, true);
\r
189 viewport.alignment.addGroup(sg);
\r
194 catch (Exception ex)
\r
196 System.out.println("Error parsing groups file: " + ex);
\r
203 * @param e DOCUMENT ME!
\r
205 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
207 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
212 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
\r
217 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
\r
218 }, currentFileFormat);
\r
220 chooser.setAcceptAllFileFilterUsed(false);
\r
221 chooser.setFileView(new JalviewFileView());
\r
222 chooser.setDialogTitle("Save Alignment to file");
\r
223 chooser.setToolTipText("Save");
\r
225 int value = chooser.showSaveDialog(this);
\r
227 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
229 currentFileFormat = chooser.getSelectedFormat();
\r
230 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
\r
231 currentFileFormat);
\r
233 String choice = chooser.getSelectedFile().getPath();
\r
234 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
236 saveAlignment(choice, currentFileFormat);
\r
240 public boolean saveAlignment(String file, String format)
\r
242 if (format.equalsIgnoreCase("Jalview"))
\r
244 String shortName = title;
\r
246 if (shortName.indexOf(java.io.File.separatorChar) > -1)
\r
248 shortName = shortName.substring(shortName.lastIndexOf(
\r
249 java.io.File.separatorChar) + 1);
\r
252 Jalview2XML.SaveAlignment(this, file, shortName);
\r
254 // USE Jalview2XML to save this file
\r
259 String output = FormatAdapter.formatSequences(format,
\r
260 viewport.getAlignment().
\r
262 if (output == null)
\r
269 java.io.PrintWriter out = new java.io.PrintWriter(
\r
270 new java.io.FileWriter(file));
\r
276 catch (Exception ex)
\r
278 ex.printStackTrace();
\r
287 * @param e DOCUMENT ME!
\r
289 protected void outputText_actionPerformed(ActionEvent e)
\r
291 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
292 Desktop.addInternalFrame(cap,
\r
293 "Alignment output - " + e.getActionCommand(), 600,
\r
295 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
\r
296 viewport.getAlignment().
\r
303 * @param e DOCUMENT ME!
\r
305 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
307 new HTMLOutput(viewport);
\r
310 public void createImageMap(File file, String image)
\r
312 alignPanel.makePNGImageMap(file, image);
\r
318 * @param e DOCUMENT ME!
\r
320 public void createPNG(File f)
\r
322 alignPanel.makePNG(f);
\r
328 * @param e DOCUMENT ME!
\r
330 public void createEPS(File f)
\r
332 alignPanel.makeEPS(f);
\r
338 * @param e DOCUMENT ME!
\r
340 public void printMenuItem_actionPerformed(ActionEvent e)
\r
342 //Putting in a thread avoids Swing painting problems
\r
343 PrintThread thread = new PrintThread();
\r
350 * @param e DOCUMENT ME!
\r
352 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
356 PaintRefresher.components.remove(viewport.alignment);
\r
357 this.setClosed(true);
\r
359 catch (Exception ex)
\r
367 void updateEditMenuBar()
\r
369 if (historyList.size() > 0)
\r
371 undoMenuItem.setEnabled(true);
\r
373 HistoryItem hi = (HistoryItem) historyList.peek();
\r
374 undoMenuItem.setText("Undo " + hi.getDescription());
\r
378 undoMenuItem.setEnabled(false);
\r
379 undoMenuItem.setText("Undo");
\r
382 if (redoList.size() > 0)
\r
384 redoMenuItem.setEnabled(true);
\r
386 HistoryItem hi = (HistoryItem) redoList.peek();
\r
387 redoMenuItem.setText("Redo " + hi.getDescription());
\r
391 redoMenuItem.setEnabled(false);
\r
392 redoMenuItem.setText("Redo");
\r
399 * @param hi DOCUMENT ME!
\r
401 public void addHistoryItem(HistoryItem hi)
\r
403 historyList.push(hi);
\r
404 updateEditMenuBar();
\r
410 * @param e DOCUMENT ME!
\r
412 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
414 HistoryItem hi = (HistoryItem) historyList.pop();
\r
415 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
416 HistoryItem.HIDE));
\r
417 restoreHistoryItem(hi);
\r
418 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
424 * @param e DOCUMENT ME!
\r
426 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
428 HistoryItem hi = (HistoryItem) redoList.pop();
\r
429 restoreHistoryItem(hi);
\r
430 updateEditMenuBar();
\r
431 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
434 // used by undo and redo
\r
435 void restoreHistoryItem(HistoryItem hi)
\r
437 if (hi.getType() == HistoryItem.SORT)
\r
439 for (int i = 0; i < hi.getSequences().size(); i++)
\r
441 viewport.alignment.getSequences().setElementAt(hi.getSequences()
\r
448 for (int i = 0; i < hi.getSequences().size(); i++)
\r
450 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
\r
452 if (restore.getLength() == 0)
\r
454 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
455 viewport.alignment.getSequences().insertElementAt(restore,
\r
456 hi.getAlignIndex(i));
\r
460 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
464 if (hi.getType() == HistoryItem.PASTE)
\r
466 for (int i = viewport.alignment.getHeight() - 1;
\r
467 i > (hi.getSequences().size() - 1); i--)
\r
469 viewport.alignment.deleteSequence(i);
\r
474 updateEditMenuBar();
\r
476 viewport.firePropertyChange("alignment", null,
\r
477 viewport.getAlignment().getSequences());
\r
483 * @param up DOCUMENT ME!
\r
485 public void moveSelectedSequences(boolean up)
\r
487 SequenceGroup sg = viewport.getSelectionGroup();
\r
496 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
498 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
500 if (!sg.sequences.contains(seq))
\r
505 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
507 if (sg.sequences.contains(temp))
\r
512 viewport.alignment.getSequences().setElementAt(temp, i);
\r
513 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
518 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
520 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
522 if (!sg.sequences.contains(seq))
\r
527 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
529 if (sg.sequences.contains(temp))
\r
534 viewport.alignment.getSequences().setElementAt(temp, i);
\r
535 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
539 alignPanel.repaint();
\r
545 * @param e DOCUMENT ME!
\r
547 protected void copy_actionPerformed(ActionEvent e)
\r
549 if (viewport.getSelectionGroup() == null)
\r
554 SequenceGroup sg = viewport.getSelectionGroup();
\r
556 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
557 StringBuffer buffer = new StringBuffer();
\r
559 Hashtable orderedSeqs = new Hashtable();
\r
561 for (int i = 0; i < sg.getSize(); i++)
\r
563 SequenceI seq = sg.getSequenceAt(i);
\r
564 int index = viewport.alignment.findIndex(seq);
\r
565 orderedSeqs.put(index + "", seq);
\r
568 int index = 0, startRes, endRes;
\r
571 for (int i = 0; i < sg.getSize(); i++)
\r
573 SequenceI seq = null;
\r
575 while (seq == null)
\r
577 if (orderedSeqs.containsKey(index + ""))
\r
579 seq = (SequenceI) orderedSeqs.get(index + "");
\r
590 //Returns residue following index if gap
\r
591 startRes = seq.findPosition(sg.getStartRes());
\r
594 //Need to find the residue preceeding index if gap
\r
597 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
599 ch = seq.getCharAt(j);
\r
600 if (!jalview.util.Comparison.isGap( (ch)))
\r
608 endRes += seq.getStart() - 1;
\r
611 buffer.append(seq.getName() + "\t" +
\r
614 seq.getSequence(sg.getStartRes(),
\r
615 sg.getEndRes() + 1) + "\n");
\r
618 c.setContents(new StringSelection(buffer.toString()), null);
\r
624 * @param e DOCUMENT ME!
\r
626 protected void pasteNew_actionPerformed(ActionEvent e)
\r
634 * @param e DOCUMENT ME!
\r
636 protected void pasteThis_actionPerformed(ActionEvent e)
\r
638 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
639 HistoryItem.PASTE));
\r
646 * @param newAlignment DOCUMENT ME!
\r
648 void paste(boolean newAlignment)
\r
652 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
653 Transferable contents = c.getContents(this);
\r
655 if (contents == null)
\r
660 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
\r
661 StringTokenizer st = new StringTokenizer(str);
\r
662 ArrayList seqs = new ArrayList();
\r
664 while (st.hasMoreElements())
\r
666 String name = st.nextToken();
\r
667 int start = Integer.parseInt(st.nextToken());
\r
668 int end = Integer.parseInt(st.nextToken());
\r
669 Sequence sequence = new Sequence(name, st.nextToken(), start,
\r
674 viewport.alignment.addSequence(sequence);
\r
678 seqs.add(sequence);
\r
684 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
685 seqs.toArray(newSeqs);
\r
687 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
\r
688 String newtitle = new String("Copied sequences");
\r
690 if (title.startsWith("Copied sequences"))
\r
696 newtitle = newtitle.concat("- from " + title);
\r
699 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
700 NEW_WINDOW_HEIGHT);
\r
704 viewport.setEndSeq(viewport.alignment.getHeight());
\r
705 viewport.alignment.getWidth();
\r
706 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
709 catch (Exception ex)
\r
711 // could be anything being pasted in here
\r
720 * @param e DOCUMENT ME!
\r
722 protected void cut_actionPerformed(ActionEvent e)
\r
724 copy_actionPerformed(null);
\r
725 delete_actionPerformed(null);
\r
731 * @param e DOCUMENT ME!
\r
733 protected void delete_actionPerformed(ActionEvent e)
\r
735 boolean seqsdeleted = false;
\r
737 if (viewport.getSelectionGroup() == null)
\r
742 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
743 HistoryItem.HIDE));
\r
745 SequenceGroup sg = viewport.getSelectionGroup();
\r
746 boolean allSequences = false;
\r
747 if (sg.sequences.size() == viewport.alignment.getHeight())
\r
749 allSequences = true;
\r
752 for (int i = 0; i < sg.sequences.size(); i++)
\r
754 SequenceI seq = sg.getSequenceAt(i);
\r
755 int index = viewport.getAlignment().findIndex(seq);
\r
756 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
758 // If the cut affects all sequences, remove highlighted columns
\r
761 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
762 sg.getEndRes() + 1);
\r
765 if (seq.getSequence().length() < 1)
\r
767 seqsdeleted = true;
\r
768 viewport.getAlignment().deleteSequence(seq);
\r
772 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
776 viewport.setSelectionGroup(null);
\r
777 viewport.alignment.deleteGroup(sg);
\r
781 viewport.firePropertyChange("alignment", null,
\r
782 viewport.getAlignment().getSequences());
\r
786 if (viewport.getAlignment().getHeight() < 1)
\r
790 this.setClosed(true);
\r
792 catch (Exception ex)
\r
801 * @param e DOCUMENT ME!
\r
803 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
805 viewport.alignment.deleteAllGroups();
\r
806 viewport.setSelectionGroup(null);
\r
807 alignPanel.repaint();
\r
813 * @param e DOCUMENT ME!
\r
815 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
817 SequenceGroup sg = new SequenceGroup();
\r
819 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
822 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
825 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
826 viewport.setSelectionGroup(sg);
\r
827 PaintRefresher.Refresh(null, viewport.alignment);
\r
833 * @param e DOCUMENT ME!
\r
835 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
837 viewport.setSelectionGroup(null);
\r
838 viewport.getColumnSelection().clear();
\r
839 viewport.setSelectionGroup(null);
\r
840 alignPanel.annotationPanel.activeRes = null;
\r
841 PaintRefresher.Refresh(null, viewport.alignment);
\r
847 * @param e DOCUMENT ME!
\r
849 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
851 SequenceGroup sg = viewport.getSelectionGroup();
\r
855 selectAllSequenceMenuItem_actionPerformed(null);
\r
860 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
863 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
866 PaintRefresher.Refresh(null, viewport.alignment);
\r
872 * @param e DOCUMENT ME!
\r
874 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
876 ColumnSelection colSel = viewport.getColumnSelection();
\r
878 if (colSel.size() > 0)
\r
880 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
881 HistoryItem.HIDE));
\r
883 int min = colSel.getMin();
\r
884 viewport.getAlignment().trimLeft(min);
\r
885 colSel.compensateForEdit(0, min);
\r
887 if (viewport.getSelectionGroup() != null)
\r
889 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
892 Vector groups = viewport.alignment.getGroups();
\r
894 for (int i = 0; i < groups.size(); i++)
\r
896 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
898 if (!sg.adjustForRemoveLeft(min))
\r
900 viewport.alignment.deleteGroup(sg);
\r
904 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
911 * @param e DOCUMENT ME!
\r
913 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
915 ColumnSelection colSel = viewport.getColumnSelection();
\r
917 if (colSel.size() > 0)
\r
919 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
920 HistoryItem.HIDE));
\r
922 int max = colSel.getMax();
\r
923 viewport.getAlignment().trimRight(max);
\r
925 if (viewport.getSelectionGroup() != null)
\r
927 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
930 Vector groups = viewport.alignment.getGroups();
\r
932 for (int i = 0; i < groups.size(); i++)
\r
934 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
936 if (!sg.adjustForRemoveRight(max))
\r
938 viewport.alignment.deleteGroup(sg);
\r
942 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
949 * @param e DOCUMENT ME!
\r
951 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
953 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
954 viewport.alignment, HistoryItem.HIDE));
\r
956 //This is to maintain viewport position on first residue
\r
957 //of first sequence
\r
958 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
959 int startRes = seq.findPosition(viewport.startRes);
\r
961 viewport.getAlignment().removeGaps();
\r
963 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
965 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
971 * @param e DOCUMENT ME!
\r
973 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
975 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
976 HistoryItem.HIDE));
\r
978 //This is to maintain viewport position on first residue
\r
979 //of first sequence
\r
980 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
981 int startRes = seq.findPosition(viewport.startRes);
\r
987 Vector seqs = null;
\r
990 int end = viewport.alignment.getWidth();
\r
992 if (viewport.getSelectionGroup() != null
\r
993 && viewport.getSelectionGroup().sequences != null
\r
994 && viewport.getSelectionGroup().sequences.size() > 0)
\r
996 seqs = viewport.getSelectionGroup().sequences;
\r
997 start = viewport.getSelectionGroup().getStartRes();
\r
998 end = viewport.getSelectionGroup().getEndRes();
\r
1002 seqs = viewport.alignment.getSequences();
\r
1005 for (int i = 0; i < seqs.size(); i++)
\r
1007 current = (SequenceI) seqs.elementAt(i);
\r
1008 jSize = current.getLength();
\r
1014 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1016 current.deleteCharAt(j);
\r
1022 while (j < end && j < jSize);
\r
1025 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1028 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1031 public void alignmentChanged()
\r
1033 viewport.updateConsensus();
\r
1034 viewport.updateConservation();
\r
1035 resetAllColourSchemes();
\r
1036 alignPanel.repaint();
\r
1039 void resetAllColourSchemes()
\r
1041 ColourSchemeI cs = viewport.globalColourScheme;
\r
1044 if (cs instanceof ClustalxColourScheme)
\r
1046 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1047 resetClustalX(viewport.alignment.getSequences(),
\r
1048 viewport.alignment.getWidth());
\r
1051 cs.setConsensus(viewport.vconsensus);
\r
1052 if (cs.conservationApplied())
\r
1054 Alignment al = (Alignment) viewport.alignment;
\r
1055 Conservation c = new Conservation("All",
\r
1056 ResidueProperties.propHash, 3,
\r
1057 al.getSequences(), 0,
\r
1058 al.getWidth() - 1);
\r
1060 c.verdict(false, viewport.ConsPercGaps);
\r
1062 cs.setConservation(c);
\r
1066 int s, sSize = viewport.alignment.getGroups().size();
\r
1067 for(s=0; s<sSize; s++)
\r
1069 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1070 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1072 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1074 sg.recalcConservation();
\r
1081 * @param e DOCUMENT ME!
\r
1083 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1085 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1086 HistoryItem.HIDE));
\r
1088 SequenceI current;
\r
1089 int Width = viewport.getAlignment().getWidth();
\r
1091 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1094 current = viewport.getAlignment().getSequenceAt(i);
\r
1096 if (current.getLength() < Width)
\r
1098 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1102 alignmentChanged();
\r
1108 * @param e DOCUMENT ME!
\r
1110 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1112 JInternalFrame frame = new JInternalFrame();
\r
1113 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1114 frame.setContentPane(finder);
\r
1115 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1116 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1122 * @param e DOCUMENT ME!
\r
1124 public void font_actionPerformed(ActionEvent e)
\r
1126 FontChooser fc = new FontChooser(alignPanel);
\r
1132 * @param e DOCUMENT ME!
\r
1134 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1136 viewport.setShowFullId(fullSeqId.isSelected());
\r
1138 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1139 alignPanel.repaint();
\r
1145 * @param e DOCUMENT ME!
\r
1147 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1149 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1150 alignPanel.repaint();
\r
1156 * @param e DOCUMENT ME!
\r
1158 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1160 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1161 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1162 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1163 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1164 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1165 alignPanel.repaint();
\r
1171 * @param e DOCUMENT ME!
\r
1173 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1175 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1176 alignPanel.repaint();
\r
1182 * @param e DOCUMENT ME!
\r
1184 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1186 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1187 alignPanel.repaint();
\r
1193 * @param e DOCUMENT ME!
\r
1195 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1197 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1198 alignPanel.repaint();
\r
1204 * @param e DOCUMENT ME!
\r
1206 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1208 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1209 alignPanel.repaint();
\r
1215 * @param e DOCUMENT ME!
\r
1217 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1219 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1220 alignPanel.repaint();
\r
1226 * @param e DOCUMENT ME!
\r
1228 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1230 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1231 alignPanel.repaint();
\r
1237 * @param evt DOCUMENT ME!
\r
1239 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1241 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1243 if (viewport.showSequenceFeatures &&
\r
1244 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1246 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1249 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1252 alignPanel.repaint();
\r
1258 * @param e DOCUMENT ME!
\r
1260 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1262 if (annotationPanelMenuItem.isSelected() &&
\r
1263 viewport.getWrapAlignment())
\r
1265 annotationPanelMenuItem.setSelected(false);
\r
1270 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1271 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1277 * @param e DOCUMENT ME!
\r
1279 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1281 if (alignPanel.overviewPanel != null)
\r
1286 JInternalFrame frame = new JInternalFrame();
\r
1287 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1288 frame.setContentPane(overview);
\r
1289 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1290 frame.getWidth(), frame.getHeight());
\r
1292 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1293 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1295 public void internalFrameClosed(
\r
1296 javax.swing.event.InternalFrameEvent evt)
\r
1298 alignPanel.setOverviewPanel(null);
\r
1303 alignPanel.setOverviewPanel(overview);
\r
1309 * @param e DOCUMENT ME!
\r
1311 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1313 changeColour(null);
\r
1319 * @param e DOCUMENT ME!
\r
1321 public void clustalColour_actionPerformed(ActionEvent e)
\r
1323 changeColour(new ClustalxColourScheme(
\r
1324 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1330 * @param e DOCUMENT ME!
\r
1332 public void zappoColour_actionPerformed(ActionEvent e)
\r
1334 changeColour(new ZappoColourScheme());
\r
1340 * @param e DOCUMENT ME!
\r
1342 public void taylorColour_actionPerformed(ActionEvent e)
\r
1344 changeColour(new TaylorColourScheme());
\r
1350 * @param e DOCUMENT ME!
\r
1352 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1354 changeColour(new HydrophobicColourScheme());
\r
1360 * @param e DOCUMENT ME!
\r
1362 public void helixColour_actionPerformed(ActionEvent e)
\r
1364 changeColour(new HelixColourScheme());
\r
1370 * @param e DOCUMENT ME!
\r
1372 public void strandColour_actionPerformed(ActionEvent e)
\r
1374 changeColour(new StrandColourScheme());
\r
1380 * @param e DOCUMENT ME!
\r
1382 public void turnColour_actionPerformed(ActionEvent e)
\r
1384 changeColour(new TurnColourScheme());
\r
1390 * @param e DOCUMENT ME!
\r
1392 public void buriedColour_actionPerformed(ActionEvent e)
\r
1394 changeColour(new BuriedColourScheme());
\r
1400 * @param e DOCUMENT ME!
\r
1402 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1404 changeColour(new NucleotideColourScheme());
\r
1410 * @param e DOCUMENT ME!
\r
1412 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1414 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1420 * @param cs DOCUMENT ME!
\r
1422 void changeColour(ColourSchemeI cs)
\r
1424 int threshold = 0;
\r
1428 if (viewport.getAbovePIDThreshold())
\r
1430 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1433 cs.setThreshold(threshold,
\r
1434 viewport.getIgnoreGapsConsensus());
\r
1436 viewport.setGlobalColourScheme(cs);
\r
1440 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1443 if (viewport.getConservationSelected())
\r
1446 Alignment al = (Alignment) viewport.alignment;
\r
1447 Conservation c = new Conservation("All",
\r
1448 ResidueProperties.propHash, 3,
\r
1449 al.getSequences(), 0,
\r
1450 al.getWidth() - 1);
\r
1453 c.verdict(false, viewport.ConsPercGaps);
\r
1455 cs.setConservation(c);
\r
1457 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1462 cs.setConservation(null);
\r
1465 cs.setConsensus(viewport.vconsensus);
\r
1468 viewport.setGlobalColourScheme(cs);
\r
1470 if (viewport.getColourAppliesToAllGroups())
\r
1472 Vector groups = viewport.alignment.getGroups();
\r
1474 for (int i = 0; i < groups.size(); i++)
\r
1476 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1484 if (cs instanceof ClustalxColourScheme)
\r
1486 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1488 else if (cs instanceof UserColourScheme)
\r
1490 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1496 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1498 catch (Exception ex)
\r
1503 if (viewport.getAbovePIDThreshold()
\r
1504 || cs instanceof PIDColourScheme
\r
1505 || cs instanceof Blosum62ColourScheme)
\r
1507 sg.cs.setThreshold(threshold,
\r
1508 viewport.getIgnoreGapsConsensus());
\r
1510 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1514 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1517 if (viewport.getConservationSelected())
\r
1519 Conservation c = new Conservation("Group",
\r
1520 ResidueProperties.propHash, 3,
\r
1522 viewport.alignment.getWidth() - 1);
\r
1524 c.verdict(false, viewport.ConsPercGaps);
\r
1525 sg.cs.setConservation(c);
\r
1528 sg.cs.setConservation(null);
\r
1532 if (alignPanel.getOverviewPanel() != null)
\r
1534 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1537 alignPanel.repaint();
\r
1543 * @param e DOCUMENT ME!
\r
1545 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1547 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1549 SliderPanel.setPIDSliderSource(alignPanel,
\r
1550 viewport.getGlobalColourScheme(),
\r
1552 SliderPanel.showPIDSlider();
\r
1559 * @param e DOCUMENT ME!
\r
1561 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1563 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1565 SliderPanel.setConservationSlider(alignPanel,
\r
1566 viewport.globalColourScheme,
\r
1568 SliderPanel.showConservationSlider();
\r
1575 * @param e DOCUMENT ME!
\r
1577 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1579 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1581 viewport.setAbovePIDThreshold(false);
\r
1582 abovePIDThreshold.setSelected(false);
\r
1584 changeColour(viewport.getGlobalColourScheme());
\r
1586 modifyConservation_actionPerformed(null);
\r
1592 * @param e DOCUMENT ME!
\r
1594 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1596 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1598 conservationMenuItem.setSelected(false);
\r
1599 viewport.setConservationSelected(false);
\r
1601 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1603 changeColour(viewport.getGlobalColourScheme());
\r
1605 modifyPID_actionPerformed(null);
\r
1611 * @param e DOCUMENT ME!
\r
1613 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1615 if (e.getActionCommand().equals("User Defined..."))
\r
1617 new UserDefinedColours(alignPanel, null);
\r
1621 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1622 getUserColourSchemes().get(e.getActionCommand());
\r
1624 changeColour(udc);
\r
1628 public void updateUserColourMenu()
\r
1631 Component[] menuItems = colourMenu.getMenuComponents();
\r
1632 int i, iSize = menuItems.length;
\r
1633 for (i = 0; i < iSize; i++)
\r
1635 if (menuItems[i].getName() != null &&
\r
1636 menuItems[i].getName().equals("USER_DEFINED"))
\r
1638 colourMenu.remove(menuItems[i]);
\r
1642 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1644 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1645 getUserColourSchemes().keys();
\r
1647 while (userColours.hasMoreElements())
\r
1649 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1650 nextElement().toString());
\r
1651 radioItem.setName("USER_DEFINED");
\r
1652 radioItem.addMouseListener(new MouseAdapter()
\r
1654 public void mousePressed(MouseEvent evt)
\r
1656 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1658 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1660 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1661 "Remove from default list?",
\r
1662 "Remove user defined colour",
\r
1663 JOptionPane.YES_NO_OPTION);
\r
1664 if(option == JOptionPane.YES_OPTION)
\r
1666 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1667 colourMenu.remove(radioItem);
\r
1670 radioItem.addActionListener(new ActionListener()
\r
1672 public void actionPerformed(ActionEvent evt)
\r
1674 userDefinedColour_actionPerformed(evt);
\r
1680 radioItem.addActionListener(new ActionListener()
\r
1682 public void actionPerformed(ActionEvent evt)
\r
1684 userDefinedColour_actionPerformed(evt);
\r
1688 colourMenu.insert(radioItem, 15);
\r
1689 colours.add(radioItem);
\r
1697 * @param e DOCUMENT ME!
\r
1699 public void PIDColour_actionPerformed(ActionEvent e)
\r
1701 changeColour(new PIDColourScheme());
\r
1707 * @param e DOCUMENT ME!
\r
1709 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1711 changeColour(new Blosum62ColourScheme());
\r
1717 * @param e DOCUMENT ME!
\r
1719 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1721 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1722 HistoryItem.SORT));
\r
1723 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1724 viewport.getAlignment().getSequenceAt(0));
\r
1725 alignPanel.repaint();
\r
1731 * @param e DOCUMENT ME!
\r
1733 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1735 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1736 HistoryItem.SORT));
\r
1737 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1738 alignPanel.repaint();
\r
1744 * @param e DOCUMENT ME!
\r
1746 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1748 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1749 HistoryItem.SORT));
\r
1751 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1752 alignPanel.repaint();
\r
1758 * @param e DOCUMENT ME!
\r
1760 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1762 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1763 JInternalFrame frame = new JInternalFrame();
\r
1764 frame.setContentPane(sp);
\r
1765 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1772 * @param e DOCUMENT ME!
\r
1774 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1776 if ( (viewport.getSelectionGroup() == null) ||
\r
1777 (viewport.getSelectionGroup().getSize() < 2))
\r
1779 JOptionPane.showInternalMessageDialog(this,
\r
1780 "You must select at least 2 sequences.",
\r
1781 "Invalid Selection",
\r
1782 JOptionPane.WARNING_MESSAGE);
\r
1786 JInternalFrame frame = new JInternalFrame();
\r
1787 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1788 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1795 * @param e DOCUMENT ME!
\r
1797 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1799 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1800 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1801 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1802 (viewport.getAlignment().getHeight() < 4))
\r
1804 JOptionPane.showInternalMessageDialog(this,
\r
1805 "Principal component analysis must take\n" +
\r
1806 "at least 4 input sequences.",
\r
1807 "Sequence selection insufficient",
\r
1808 JOptionPane.WARNING_MESSAGE);
\r
1815 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1816 JInternalFrame frame = new JInternalFrame();
\r
1817 frame.setContentPane(pcaPanel);
\r
1818 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1821 catch (java.lang.OutOfMemoryError ex)
\r
1823 JOptionPane.showInternalMessageDialog(this,
\r
1824 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1826 JOptionPane.WARNING_MESSAGE);
\r
1833 * @param e DOCUMENT ME!
\r
1835 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1837 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1843 * @param e DOCUMENT ME!
\r
1845 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1847 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1853 * @param e DOCUMENT ME!
\r
1855 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1857 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1863 * @param e DOCUMENT ME!
\r
1865 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1867 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1873 * @param type DOCUMENT ME!
\r
1874 * @param pwType DOCUMENT ME!
\r
1875 * @param title DOCUMENT ME!
\r
1877 void NewTreePanel(String type, String pwType, String title)
\r
1879 final TreePanel tp;
\r
1881 if ( (viewport.getSelectionGroup() != null) &&
\r
1882 (viewport.getSelectionGroup().getSize() > 3))
\r
1885 SequenceGroup sg = viewport.getSelectionGroup();
\r
1887 /* Decide if the selection is a column region */
\r
1888 while (s < sg.sequences.size())
\r
1890 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1893 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1894 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1895 "Try using the Pad function in the edit menu,\n" +
\r
1896 "or one of the multiple sequence alignment web services.",
\r
1897 "Sequences in selection are not aligned",
\r
1898 JOptionPane.WARNING_MESSAGE);
\r
1904 title = title + " on region";
\r
1905 tp = new TreePanel(viewport,
\r
1906 viewport.getSelectionGroup().sequences, type, pwType,
\r
1907 sg.getStartRes(), sg.getEndRes());
\r
1911 //are the sequences aligned?
\r
1912 if (!viewport.alignment.isAligned())
\r
1914 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1915 "The sequences must be aligned before creating a tree.\n" +
\r
1916 "Try using the Pad function in the edit menu,\n" +
\r
1917 "or one of the multiple sequence alignment web services.",
\r
1918 "Sequences not aligned",
\r
1919 JOptionPane.WARNING_MESSAGE);
\r
1924 tp = new TreePanel(viewport,
\r
1925 viewport.getAlignment().getSequences(), type, pwType,
\r
1927 viewport.alignment.getWidth());
\r
1930 addTreeMenuItem(tp, title);
\r
1931 viewport.setCurrentTree(tp.getTree());
\r
1933 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1939 * @param title DOCUMENT ME!
\r
1940 * @param order DOCUMENT ME!
\r
1942 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1944 final JMenuItem item = new JMenuItem("by " + title);
\r
1946 item.addActionListener(new java.awt.event.ActionListener()
\r
1948 public void actionPerformed(ActionEvent e)
\r
1950 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1951 HistoryItem.SORT));
\r
1953 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1954 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1955 alignPanel.repaint();
\r
1961 * Maintain the Order by->Displayed Tree menu.
\r
1962 * Creates a new menu item for a TreePanel with an appropriate
\r
1963 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1964 * to remove the menu item when the treePanel is closed, and adjust
\r
1965 * the tree leaf to sequence mapping when the alignment is modified.
\r
1966 * @param treePanel Displayed tree window.
\r
1967 * @param title SortBy menu item title.
\r
1969 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1971 final JMenuItem item = new JMenuItem(title);
\r
1975 if (treeCount == 1)
\r
1977 sort.add(sortByTreeMenu);
\r
1980 sortByTreeMenu.add(item);
\r
1981 item.addActionListener(new java.awt.event.ActionListener()
\r
1983 public void actionPerformed(ActionEvent e)
\r
1985 addHistoryItem(new HistoryItem("Tree Sort",
\r
1986 viewport.alignment, HistoryItem.SORT));
\r
1987 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1988 treePanel.getTree());
\r
1989 alignPanel.repaint();
\r
1993 treePanel.addInternalFrameListener(new javax.swing.event.
\r
1994 InternalFrameAdapter()
\r
1996 public void internalFrameClosed(
\r
1997 javax.swing.event.InternalFrameEvent evt)
\r
2000 sortByTreeMenu.remove(item);
\r
2002 if (treeCount == 0)
\r
2004 sort.remove(sortByTreeMenu);
\r
2009 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
2011 public void propertyChange(PropertyChangeEvent evt)
\r
2013 if (evt.getPropertyName().equals("alignment"))
\r
2015 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
2016 treePanel.repaint();
\r
2023 * Work out whether the whole set of sequences
\r
2024 * or just the selected set will be submitted for multiple alignment.
\r
2027 private SequenceI[] gatherSequencesForAlignment()
\r
2029 // Now, check we have enough sequences
\r
2030 SequenceI[] msa = null;
\r
2032 if ( (viewport.getSelectionGroup() != null) &&
\r
2033 (viewport.getSelectionGroup().getSize() > 1))
\r
2035 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2036 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2038 msa = new SequenceI[sz = seqs.getSize()];
\r
2040 for (int i = 0; i < sz; i++)
\r
2042 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2047 Vector seqs = viewport.getAlignment().getSequences();
\r
2049 if (seqs.size() > 1)
\r
2051 msa = new SequenceI[seqs.size()];
\r
2053 for (int i = 0; i < seqs.size(); i++)
\r
2055 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2063 * Decides what is submitted to a secondary structure prediction service,
\r
2064 * the currently selected sequence, or the currently selected alignment
\r
2065 * (where the first sequence in the set is the one that the prediction
\r
2068 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2070 SequenceI seq = null;
\r
2071 SequenceI[] msa = null;
\r
2073 if ( (viewport.getSelectionGroup() != null) &&
\r
2074 (viewport.getSelectionGroup().getSize() > 0))
\r
2076 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2077 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2079 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2081 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2086 msa = new SequenceI[sz = seqs.getSize()];
\r
2088 for (int i = 0; i < sz; i++)
\r
2090 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2096 Vector seqs = viewport.getAlignment().getSequences();
\r
2098 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2100 seq = (SequenceI) seqs.elementAt(0);
\r
2104 msa = new SequenceI[seqs.size()];
\r
2106 for (int i = 0; i < seqs.size(); i++)
\r
2108 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2120 return new SequenceI[]
\r
2130 * @param e DOCUMENT ME!
\r
2132 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2134 // Pick the tree file
\r
2135 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2137 "LAST_DIRECTORY"));
\r
2138 chooser.setFileView(new JalviewFileView());
\r
2139 chooser.setDialogTitle("Select a newick-like tree file");
\r
2140 chooser.setToolTipText("Load a tree file");
\r
2142 int value = chooser.showOpenDialog(null);
\r
2144 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2146 String choice = chooser.getSelectedFile().getPath();
\r
2147 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2151 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2153 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2155 catch (Exception ex)
\r
2157 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2158 "Problem reading tree file",
\r
2160 JOptionPane.WARNING_MESSAGE);
\r
2161 ex.printStackTrace();
\r
2167 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2169 return ShowNewickTree(nf,title,600,500,4,5);
\r
2174 * @param nf DOCUMENT ME!
\r
2175 * @param title DOCUMENT ME!
\r
2177 * @return DOCUMENT ME!
\r
2179 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2181 TreePanel tp = null;
\r
2187 if (nf.getTree() != null)
\r
2189 tp = new TreePanel(viewport,
\r
2190 viewport.getAlignment().getSequences(), nf,
\r
2197 tp.setLocation(x,y);
\r
2200 Desktop.addInternalFrame(tp, title, w, h);
\r
2201 addTreeMenuItem(tp, title);
\r
2204 catch (Exception ex)
\r
2206 ex.printStackTrace();
\r
2217 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2218 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2219 printJob.setPrintable(alignPanel, pf);
\r
2221 if (printJob.printDialog())
\r
2227 catch (Exception PrintException)
\r
2229 PrintException.printStackTrace();
\r
2236 * Generates menu items and listener event actions for web service clients
\r
2239 public void BuildWebServiceMenu()
\r
2241 if ( (Desktop.discoverer.services != null)
\r
2242 && (Desktop.discoverer.services.size() > 0))
\r
2244 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2245 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2246 Vector wsmenu = new Vector();
\r
2247 if (msaws != null)
\r
2249 // Add any Multiple Sequence Alignment Services
\r
2250 final JMenu msawsmenu = new JMenu("Alignment");
\r
2251 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2253 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2255 final JMenuItem method = new JMenuItem(sh.getName());
\r
2256 method.addActionListener(new ActionListener()
\r
2258 public void actionPerformed(ActionEvent e)
\r
2260 SequenceI[] msa = gatherSequencesForAlignment();
\r
2261 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2267 msawsmenu.add(method);
\r
2268 // Deal with services that we know accept partial alignments.
\r
2269 if (sh.getName().indexOf("lustal") > -1)
\r
2271 // We know that ClustalWS can accept partial alignments for refinement.
\r
2272 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2273 methodR.addActionListener(new ActionListener()
\r
2275 public void actionPerformed(ActionEvent e)
\r
2277 SequenceI[] msa = gatherSequencesForAlignment();
\r
2278 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2284 msawsmenu.add(methodR);
\r
2288 wsmenu.add(msawsmenu);
\r
2290 if (secstrpr != null)
\r
2292 // Add any secondary structure prediction services
\r
2293 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2294 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2296 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2298 final JMenuItem method = new JMenuItem(sh.getName());
\r
2299 method.addActionListener(new ActionListener()
\r
2301 public void actionPerformed(ActionEvent e)
\r
2303 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2304 if (msa.length == 1)
\r
2306 // Single Sequence prediction
\r
2307 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2312 if (msa.length > 1)
\r
2314 // Single Sequence prediction
\r
2315 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2321 secstrmenu.add(method);
\r
2323 wsmenu.add(secstrmenu);
\r
2325 this.webService.removeAll();
\r
2326 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2328 webService.add( (JMenu) wsmenu.get(i));
\r
2333 this.webService.removeAll();
\r
2334 this.webService.add(this.webServiceNoServices);
\r
2336 // TODO: add in rediscovery function
\r
2337 // TODO: reduce code redundancy.
\r
2338 // TODO: group services by location as well as function.
\r