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 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
\r
81 addInternalFrameListener(new InternalFrameAdapter()
\r
83 public void internalFrameActivated(InternalFrameEvent evt)
\r
85 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
89 alignPanel.requestFocus();
\r
94 addServiceListeners();
\r
97 /* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
98 private void addServiceListeners()
\r
100 final java.beans.PropertyChangeListener thisListener;
\r
101 // Do this once to get current state
\r
102 BuildWebServiceMenu();
\r
103 Desktop.discoverer.addPropertyChangeListener(
\r
104 thisListener = new java.beans.PropertyChangeListener()
\r
106 public void propertyChange(PropertyChangeEvent evt)
\r
108 // System.out.println("Discoverer property change.");
\r
109 if (evt.getPropertyName().equals("services"))
\r
111 // System.out.println("Rebuilding web service menu");
\r
112 BuildWebServiceMenu();
\r
116 addInternalFrameListener(new javax.swing.event.
\r
117 InternalFrameAdapter()
\r
119 public void internalFrameClosed(
\r
120 javax.swing.event.InternalFrameEvent evt)
\r
122 // System.out.println("deregistering discoverer listener");
\r
123 Desktop.discoverer.removePropertyChangeListener(thisListener);
\r
124 closeMenuItem_actionPerformed(null);
\r
134 * @param String DOCUMENT ME!
\r
137 public void parseGroupsFile(String file)
\r
141 BufferedReader in = new BufferedReader(new FileReader(file));
\r
142 SequenceI seq = null;
\r
143 String line, text, token;
\r
144 UserColourScheme ucs;
\r
145 int index, start, end;
\r
146 StringTokenizer st;
\r
148 while ( (line = in.readLine()) != null)
\r
150 st = new StringTokenizer(line, "\t");
\r
151 if (st.countTokens() != 6)
\r
153 System.out.println("Groups file " + file +
\r
154 " is invalid. Read help file.");
\r
158 while (st.hasMoreElements())
\r
160 text = st.nextToken();
\r
161 token = st.nextToken();
\r
162 if (!token.equals("ID_NOT_SPECIFIED"))
\r
164 index = viewport.alignment.findIndex(viewport.alignment.findName(
\r
170 index = Integer.parseInt(st.nextToken());
\r
173 start = Integer.parseInt(st.nextToken());
\r
174 end = Integer.parseInt(st.nextToken());
\r
175 ucs = new UserColourScheme(st.nextToken());
\r
177 seq = viewport.alignment.getSequenceAt(index);
\r
178 start = seq.findIndex(start) - 1;
\r
179 end = seq.findIndex(end) - 1;
\r
181 sg = new SequenceGroup(text, ucs, true, true, false, start, end);
\r
182 sg.addSequence(seq, true);
\r
184 viewport.alignment.addGroup(sg);
\r
189 catch (Exception ex)
\r
191 System.out.println("Error parsing groups file: " + ex);
\r
198 * @param e DOCUMENT ME!
\r
200 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
202 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
207 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
\r
212 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
\r
213 }, currentFileFormat);
\r
215 chooser.setAcceptAllFileFilterUsed(false);
\r
216 chooser.setFileView(new JalviewFileView());
\r
217 chooser.setDialogTitle("Save Alignment to file");
\r
218 chooser.setToolTipText("Save");
\r
220 int value = chooser.showSaveDialog(this);
\r
222 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
224 currentFileFormat = chooser.getSelectedFormat();
\r
225 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
\r
226 currentFileFormat);
\r
228 String choice = chooser.getSelectedFile().getPath();
\r
229 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
231 saveAlignment(choice, currentFileFormat);
\r
235 public boolean saveAlignment(String file, String format)
\r
237 if (format.equalsIgnoreCase("Jalview"))
\r
239 String shortName = title;
\r
241 if (shortName.indexOf(java.io.File.separatorChar) > -1)
\r
243 shortName = shortName.substring(shortName.lastIndexOf(
\r
244 java.io.File.separatorChar) + 1);
\r
247 Jalview2XML.SaveAlignment(this, file, shortName);
\r
249 // USE Jalview2XML to save this file
\r
254 String output = FormatAdapter.formatSequences(format,
\r
255 viewport.getAlignment().
\r
257 if (output == null)
\r
264 java.io.PrintWriter out = new java.io.PrintWriter(
\r
265 new java.io.FileWriter(file));
\r
266 out.println(output);
\r
270 catch (Exception ex)
\r
272 ex.printStackTrace();
\r
281 * @param e DOCUMENT ME!
\r
283 protected void outputText_actionPerformed(ActionEvent e)
\r
285 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
286 Desktop.addInternalFrame(cap,
\r
287 "Alignment output - " + e.getActionCommand(), 600,
\r
289 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
\r
290 viewport.getAlignment().
\r
297 * @param e DOCUMENT ME!
\r
299 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
301 new HTMLOutput(viewport);
\r
304 public void createImageMap(File file, String image)
\r
306 alignPanel.makePNGImageMap(file, image);
\r
312 * @param e DOCUMENT ME!
\r
314 public void createPNG(File f)
\r
316 alignPanel.makePNG(f);
\r
322 * @param e DOCUMENT ME!
\r
324 public void createEPS(File f)
\r
326 alignPanel.makeEPS(f);
\r
332 * @param e DOCUMENT ME!
\r
334 public void printMenuItem_actionPerformed(ActionEvent e)
\r
336 //Putting in a thread avoids Swing painting problems
\r
337 PrintThread thread = new PrintThread();
\r
344 * @param e DOCUMENT ME!
\r
346 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
350 PaintRefresher.components.remove(viewport.alignment);
\r
351 this.setClosed(true);
\r
353 catch (Exception ex)
\r
361 void updateEditMenuBar()
\r
363 if (historyList.size() > 0)
\r
365 undoMenuItem.setEnabled(true);
\r
367 HistoryItem hi = (HistoryItem) historyList.peek();
\r
368 undoMenuItem.setText("Undo " + hi.getDescription());
\r
372 undoMenuItem.setEnabled(false);
\r
373 undoMenuItem.setText("Undo");
\r
376 if (redoList.size() > 0)
\r
378 redoMenuItem.setEnabled(true);
\r
380 HistoryItem hi = (HistoryItem) redoList.peek();
\r
381 redoMenuItem.setText("Redo " + hi.getDescription());
\r
385 redoMenuItem.setEnabled(false);
\r
386 redoMenuItem.setText("Redo");
\r
393 * @param hi DOCUMENT ME!
\r
395 public void addHistoryItem(HistoryItem hi)
\r
397 historyList.push(hi);
\r
398 updateEditMenuBar();
\r
404 * @param e DOCUMENT ME!
\r
406 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
408 HistoryItem hi = (HistoryItem) historyList.pop();
\r
409 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
410 HistoryItem.HIDE));
\r
411 restoreHistoryItem(hi);
\r
417 * @param e DOCUMENT ME!
\r
419 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
421 HistoryItem hi = (HistoryItem) redoList.pop();
\r
422 restoreHistoryItem(hi);
\r
423 updateEditMenuBar();
\r
424 viewport.updateConsensus();
\r
425 alignPanel.repaint();
\r
426 alignPanel.repaint();
\r
429 // used by undo and redo
\r
430 void restoreHistoryItem(HistoryItem hi)
\r
432 if (hi.getType() == HistoryItem.SORT)
\r
434 for (int i = 0; i < hi.getSequences().size(); i++)
\r
436 viewport.alignment.getSequences().setElementAt(hi.getSequences()
\r
443 for (int i = 0; i < hi.getSequences().size(); i++)
\r
445 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
\r
447 if (restore.getLength() == 0)
\r
449 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
450 viewport.alignment.getSequences().insertElementAt(restore,
\r
451 hi.getAlignIndex(i));
\r
455 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
459 if (hi.getType() == HistoryItem.PASTE)
\r
461 for (int i = viewport.alignment.getHeight() - 1;
\r
462 i > (hi.getSequences().size() - 1); i--)
\r
464 viewport.alignment.deleteSequence(i);
\r
469 updateEditMenuBar();
\r
471 viewport.updateConsensus();
\r
472 viewport.updateConservation();
\r
473 alignPanel.repaint();
\r
474 viewport.firePropertyChange("alignment", null,
\r
475 viewport.getAlignment().getSequences());
\r
481 * @param up DOCUMENT ME!
\r
483 public void moveSelectedSequences(boolean up)
\r
485 SequenceGroup sg = viewport.getSelectionGroup();
\r
494 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
496 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
498 if (!sg.sequences.contains(seq))
\r
503 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
505 if (sg.sequences.contains(temp))
\r
510 viewport.alignment.getSequences().setElementAt(temp, i);
\r
511 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
516 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
518 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
520 if (!sg.sequences.contains(seq))
\r
525 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
527 if (sg.sequences.contains(temp))
\r
532 viewport.alignment.getSequences().setElementAt(temp, i);
\r
533 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
537 alignPanel.repaint();
\r
543 * @param e DOCUMENT ME!
\r
545 protected void copy_actionPerformed(ActionEvent e)
\r
547 if (viewport.getSelectionGroup() == null)
\r
552 SequenceGroup sg = viewport.getSelectionGroup();
\r
554 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
555 StringBuffer buffer = new StringBuffer();
\r
557 Hashtable orderedSeqs = new Hashtable();
\r
559 for (int i = 0; i < sg.getSize(); i++)
\r
561 SequenceI seq = sg.getSequenceAt(i);
\r
562 int index = viewport.alignment.findIndex(seq);
\r
563 orderedSeqs.put(index + "", seq);
\r
566 int index = 0, startRes, endRes;
\r
569 for (int i = 0; i < sg.getSize(); i++)
\r
571 SequenceI seq = null;
\r
573 while (seq == null)
\r
575 if (orderedSeqs.containsKey(index + ""))
\r
577 seq = (SequenceI) orderedSeqs.get(index + "");
\r
588 //Returns residue following index if gap
\r
589 startRes = seq.findPosition(sg.getStartRes());
\r
592 //Need to find the residue preceeding index if gap
\r
595 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
597 ch = seq.getCharAt(j);
\r
598 if (!jalview.util.Comparison.isGap( (ch)))
\r
606 endRes += seq.getStart() - 1;
\r
609 buffer.append(seq.getName() + "\t" +
\r
612 seq.getSequence(sg.getStartRes(),
\r
613 sg.getEndRes() + 1) + "\n");
\r
616 c.setContents(new StringSelection(buffer.toString()), null);
\r
622 * @param e DOCUMENT ME!
\r
624 protected void pasteNew_actionPerformed(ActionEvent e)
\r
632 * @param e DOCUMENT ME!
\r
634 protected void pasteThis_actionPerformed(ActionEvent e)
\r
636 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
637 HistoryItem.PASTE));
\r
644 * @param newAlignment DOCUMENT ME!
\r
646 void paste(boolean newAlignment)
\r
650 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
651 Transferable contents = c.getContents(this);
\r
653 if (contents == null)
\r
658 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
\r
659 StringTokenizer st = new StringTokenizer(str);
\r
660 ArrayList seqs = new ArrayList();
\r
662 while (st.hasMoreElements())
\r
664 String name = st.nextToken();
\r
665 int start = Integer.parseInt(st.nextToken());
\r
666 int end = Integer.parseInt(st.nextToken());
\r
667 Sequence sequence = new Sequence(name, st.nextToken(), start,
\r
672 viewport.alignment.addSequence(sequence);
\r
676 seqs.add(sequence);
\r
682 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
683 seqs.toArray(newSeqs);
\r
685 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
\r
686 String newtitle = new String("Copied sequences");
\r
688 if (title.startsWith("Copied sequences"))
\r
694 newtitle = newtitle.concat("- from " + title);
\r
697 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
698 NEW_WINDOW_HEIGHT);
\r
702 viewport.firePropertyChange("alignment", null,
\r
703 viewport.getAlignment().getSequences());
\r
704 viewport.setEndSeq(viewport.alignment.getHeight());
\r
705 viewport.alignment.getWidth();
\r
706 viewport.updateConservation();
\r
707 viewport.updateConsensus();
\r
708 alignPanel.repaint();
\r
711 catch (Exception ex)
\r
715 // could be anything being pasted in here
\r
721 * @param e DOCUMENT ME!
\r
723 protected void cut_actionPerformed(ActionEvent e)
\r
725 copy_actionPerformed(null);
\r
726 delete_actionPerformed(null);
\r
732 * @param e DOCUMENT ME!
\r
734 protected void delete_actionPerformed(ActionEvent e)
\r
736 boolean seqsdeleted = false;
\r
738 if (viewport.getSelectionGroup() == null)
\r
743 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
744 HistoryItem.HIDE));
\r
746 SequenceGroup sg = viewport.getSelectionGroup();
\r
747 boolean allSequences = false;
\r
748 if (sg.sequences.size() == viewport.alignment.getHeight())
\r
750 allSequences = true;
\r
753 for (int i = 0; i < sg.sequences.size(); i++)
\r
755 SequenceI seq = sg.getSequenceAt(i);
\r
756 int index = viewport.getAlignment().findIndex(seq);
\r
757 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
759 // If the cut affects all sequences, remove highlighted columns
\r
762 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
763 sg.getEndRes() + 1);
\r
766 if (seq.getSequence().length() < 1)
\r
768 seqsdeleted = true;
\r
769 viewport.getAlignment().deleteSequence(seq);
\r
773 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
777 viewport.setSelectionGroup(null);
\r
778 viewport.alignment.deleteGroup(sg);
\r
782 viewport.firePropertyChange("alignment", null,
\r
783 viewport.getAlignment().getSequences());
\r
786 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
\r
788 if (viewport.getAlignment().getHeight() < 1)
\r
792 this.setClosed(true);
\r
794 catch (Exception ex)
\r
799 viewport.updateConservation();
\r
800 viewport.updateConsensus();
\r
801 alignPanel.repaint();
\r
807 * @param e DOCUMENT ME!
\r
809 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
811 viewport.alignment.deleteAllGroups();
\r
812 viewport.setSelectionGroup(null);
\r
813 alignPanel.repaint();
\r
819 * @param e DOCUMENT ME!
\r
821 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
823 SequenceGroup sg = new SequenceGroup();
\r
825 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
828 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
831 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
832 viewport.setSelectionGroup(sg);
\r
833 PaintRefresher.Refresh(null, viewport.alignment);
\r
839 * @param e DOCUMENT ME!
\r
841 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
843 viewport.setSelectionGroup(null);
\r
844 viewport.getColumnSelection().clear();
\r
845 viewport.setSelectionGroup(null);
\r
846 alignPanel.annotationPanel.activeRes = null;
\r
847 PaintRefresher.Refresh(null, viewport.alignment);
\r
853 * @param e DOCUMENT ME!
\r
855 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
857 SequenceGroup sg = viewport.getSelectionGroup();
\r
861 selectAllSequenceMenuItem_actionPerformed(null);
\r
866 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
869 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
872 PaintRefresher.Refresh(null, viewport.alignment);
\r
878 * @param e DOCUMENT ME!
\r
880 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
882 ColumnSelection colSel = viewport.getColumnSelection();
\r
884 if (colSel.size() > 0)
\r
886 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
887 HistoryItem.HIDE));
\r
889 int min = colSel.getMin();
\r
890 viewport.getAlignment().trimLeft(min);
\r
891 colSel.compensateForEdit(0, min);
\r
893 if (viewport.getSelectionGroup() != null)
\r
895 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
898 Vector groups = viewport.alignment.getGroups();
\r
900 for (int i = 0; i < groups.size(); i++)
\r
902 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
904 if (!sg.adjustForRemoveLeft(min))
\r
906 viewport.alignment.deleteGroup(sg);
\r
910 alignPanel.repaint();
\r
917 * @param e DOCUMENT ME!
\r
919 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
921 ColumnSelection colSel = viewport.getColumnSelection();
\r
923 if (colSel.size() > 0)
\r
925 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
926 HistoryItem.HIDE));
\r
928 int max = colSel.getMax();
\r
929 viewport.getAlignment().trimRight(max);
\r
931 if (viewport.getSelectionGroup() != null)
\r
933 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
936 Vector groups = viewport.alignment.getGroups();
\r
938 for (int i = 0; i < groups.size(); i++)
\r
940 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
942 if (!sg.adjustForRemoveRight(max))
\r
944 viewport.alignment.deleteGroup(sg);
\r
948 alignPanel.repaint();
\r
955 * @param e DOCUMENT ME!
\r
957 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
959 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
960 viewport.alignment, HistoryItem.HIDE));
\r
962 viewport.getAlignment().removeGaps();
\r
963 viewport.updateConservation();
\r
964 viewport.updateConsensus();
\r
965 alignPanel.repaint();
\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
981 Vector seqs = null;
\r
984 int end = viewport.alignment.getWidth();
\r
986 if (viewport.getSelectionGroup() != null
\r
987 && viewport.getSelectionGroup().sequences != null
\r
988 && viewport.getSelectionGroup().sequences.size() > 0)
\r
990 seqs = viewport.getSelectionGroup().sequences;
\r
991 start = viewport.getSelectionGroup().getStartRes();
\r
992 end = viewport.getSelectionGroup().getEndRes();
\r
996 seqs = viewport.alignment.getSequences();
\r
999 for (int i = 0; i < seqs.size(); i++)
\r
1001 current = (SequenceI) seqs.elementAt(i);
\r
1002 jSize = current.getLength();
\r
1008 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1010 current.deleteCharAt(j);
\r
1016 while (j < end && j < jSize);
\r
1019 viewport.updateConservation();
\r
1020 viewport.updateConsensus();
\r
1021 alignPanel.repaint();
\r
1027 * @param e DOCUMENT ME!
\r
1029 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1031 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1032 HistoryItem.HIDE));
\r
1034 SequenceI current;
\r
1035 int Width = viewport.getAlignment().getWidth();
\r
1037 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1040 current = viewport.getAlignment().getSequenceAt(i);
\r
1042 if (current.getLength() < Width)
\r
1044 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1048 viewport.updateConservation();
\r
1049 viewport.updateConsensus();
\r
1050 alignPanel.repaint();
\r
1056 * @param e DOCUMENT ME!
\r
1058 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1060 JInternalFrame frame = new JInternalFrame();
\r
1061 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1062 frame.setContentPane(finder);
\r
1063 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1064 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1070 * @param e DOCUMENT ME!
\r
1072 public void font_actionPerformed(ActionEvent e)
\r
1074 FontChooser fc = new FontChooser(alignPanel);
\r
1080 * @param e DOCUMENT ME!
\r
1082 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1084 viewport.setShowFullId(fullSeqId.isSelected());
\r
1086 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1087 alignPanel.repaint();
\r
1093 * @param e DOCUMENT ME!
\r
1095 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1097 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1098 alignPanel.repaint();
\r
1104 * @param e DOCUMENT ME!
\r
1106 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1108 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1109 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1110 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1111 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1112 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1113 alignPanel.repaint();
\r
1119 * @param e DOCUMENT ME!
\r
1121 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1123 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1124 alignPanel.repaint();
\r
1130 * @param e DOCUMENT ME!
\r
1132 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1134 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1135 alignPanel.repaint();
\r
1141 * @param e DOCUMENT ME!
\r
1143 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1145 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1146 alignPanel.repaint();
\r
1152 * @param e DOCUMENT ME!
\r
1154 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1156 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1157 alignPanel.repaint();
\r
1163 * @param e DOCUMENT ME!
\r
1165 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1167 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1168 alignPanel.repaint();
\r
1174 * @param e DOCUMENT ME!
\r
1176 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1178 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1179 alignPanel.repaint();
\r
1185 * @param evt DOCUMENT ME!
\r
1187 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1189 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1191 if (viewport.showSequenceFeatures &&
\r
1192 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1194 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1197 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1200 alignPanel.repaint();
\r
1206 * @param e DOCUMENT ME!
\r
1208 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1210 if (annotationPanelMenuItem.isSelected() &&
\r
1211 viewport.getWrapAlignment())
\r
1213 annotationPanelMenuItem.setSelected(false);
\r
1218 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1219 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1225 * @param e DOCUMENT ME!
\r
1227 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1229 if (alignPanel.overviewPanel != null)
\r
1234 JInternalFrame frame = new JInternalFrame();
\r
1235 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1236 frame.setContentPane(overview);
\r
1237 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1238 frame.getWidth(), frame.getHeight());
\r
1240 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1241 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1243 public void internalFrameClosed(
\r
1244 javax.swing.event.InternalFrameEvent evt)
\r
1246 alignPanel.setOverviewPanel(null);
\r
1251 alignPanel.setOverviewPanel(overview);
\r
1257 * @param e DOCUMENT ME!
\r
1259 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1261 changeColour(null);
\r
1267 * @param e DOCUMENT ME!
\r
1269 public void clustalColour_actionPerformed(ActionEvent e)
\r
1271 changeColour(new ClustalxColourScheme(
\r
1272 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1278 * @param e DOCUMENT ME!
\r
1280 public void zappoColour_actionPerformed(ActionEvent e)
\r
1282 changeColour(new ZappoColourScheme());
\r
1288 * @param e DOCUMENT ME!
\r
1290 public void taylorColour_actionPerformed(ActionEvent e)
\r
1292 changeColour(new TaylorColourScheme());
\r
1298 * @param e DOCUMENT ME!
\r
1300 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1302 changeColour(new HydrophobicColourScheme());
\r
1308 * @param e DOCUMENT ME!
\r
1310 public void helixColour_actionPerformed(ActionEvent e)
\r
1312 changeColour(new HelixColourScheme());
\r
1318 * @param e DOCUMENT ME!
\r
1320 public void strandColour_actionPerformed(ActionEvent e)
\r
1322 changeColour(new StrandColourScheme());
\r
1328 * @param e DOCUMENT ME!
\r
1330 public void turnColour_actionPerformed(ActionEvent e)
\r
1332 changeColour(new TurnColourScheme());
\r
1338 * @param e DOCUMENT ME!
\r
1340 public void buriedColour_actionPerformed(ActionEvent e)
\r
1342 changeColour(new BuriedColourScheme());
\r
1348 * @param e DOCUMENT ME!
\r
1350 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1352 changeColour(new NucleotideColourScheme());
\r
1358 * @param e DOCUMENT ME!
\r
1360 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1362 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1368 * @param cs DOCUMENT ME!
\r
1370 void changeColour(ColourSchemeI cs)
\r
1372 int threshold = 0;
\r
1376 if (viewport.getAbovePIDThreshold())
\r
1378 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1381 cs.setThreshold(threshold,
\r
1382 viewport.getIgnoreGapsConsensus());
\r
1384 viewport.setGlobalColourScheme(cs);
\r
1388 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1391 if (viewport.getConservationSelected())
\r
1394 Alignment al = (Alignment) viewport.alignment;
\r
1395 Conservation c = new Conservation("All",
\r
1396 ResidueProperties.propHash, 3,
\r
1397 al.getSequences(), 0,
\r
1398 al.getWidth() - 1);
\r
1401 c.verdict(false, viewport.ConsPercGaps);
\r
1403 cs.setConservation(c);
\r
1405 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1410 cs.setConservation(null);
\r
1413 cs.setConsensus(viewport.vconsensus);
\r
1416 viewport.setGlobalColourScheme(cs);
\r
1418 if (viewport.getColourAppliesToAllGroups())
\r
1420 Vector groups = viewport.alignment.getGroups();
\r
1422 for (int i = 0; i < groups.size(); i++)
\r
1424 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1432 if (cs instanceof ClustalxColourScheme)
\r
1434 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1436 else if (cs instanceof UserColourScheme)
\r
1438 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1444 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1446 catch (Exception ex)
\r
1451 if (viewport.getAbovePIDThreshold()
\r
1452 || cs instanceof PIDColourScheme
\r
1453 || cs instanceof Blosum62ColourScheme)
\r
1455 sg.cs.setThreshold(threshold,
\r
1456 viewport.getIgnoreGapsConsensus());
\r
1458 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1462 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1465 if (viewport.getConservationSelected())
\r
1467 Conservation c = new Conservation("Group",
\r
1468 ResidueProperties.propHash, 3,
\r
1470 viewport.alignment.getWidth() - 1);
\r
1472 c.verdict(false, viewport.ConsPercGaps);
\r
1473 sg.cs.setConservation(c);
\r
1476 sg.cs.setConservation(null);
\r
1480 if (alignPanel.getOverviewPanel() != null)
\r
1482 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1485 alignPanel.repaint();
\r
1491 * @param e DOCUMENT ME!
\r
1493 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1495 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1497 SliderPanel.setPIDSliderSource(alignPanel,
\r
1498 viewport.getGlobalColourScheme(),
\r
1500 SliderPanel.showPIDSlider();
\r
1507 * @param e DOCUMENT ME!
\r
1509 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1511 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1513 SliderPanel.setConservationSlider(alignPanel,
\r
1514 viewport.globalColourScheme,
\r
1516 SliderPanel.showConservationSlider();
\r
1523 * @param e DOCUMENT ME!
\r
1525 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1527 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1529 viewport.setAbovePIDThreshold(false);
\r
1530 abovePIDThreshold.setSelected(false);
\r
1532 changeColour(viewport.getGlobalColourScheme());
\r
1534 modifyConservation_actionPerformed(null);
\r
1540 * @param e DOCUMENT ME!
\r
1542 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1544 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1546 conservationMenuItem.setSelected(false);
\r
1547 viewport.setConservationSelected(false);
\r
1549 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1551 changeColour(viewport.getGlobalColourScheme());
\r
1553 modifyPID_actionPerformed(null);
\r
1559 * @param e DOCUMENT ME!
\r
1561 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1563 if (e.getActionCommand().equals("User Defined..."))
\r
1565 new UserDefinedColours(alignPanel, null);
\r
1569 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1570 getUserColourSchemes().get(e.getActionCommand());
\r
1572 changeColour(udc);
\r
1576 public void updateUserColourMenu()
\r
1579 Component[] menuItems = colourMenu.getMenuComponents();
\r
1580 int i, iSize = menuItems.length;
\r
1581 for (i = 0; i < iSize; i++)
\r
1583 if (menuItems[i].getName() != null &&
\r
1584 menuItems[i].getName().equals("USER_DEFINED"))
\r
1586 colourMenu.remove(menuItems[i]);
\r
1590 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1592 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1593 getUserColourSchemes().keys();
\r
1595 while (userColours.hasMoreElements())
\r
1597 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1598 nextElement().toString());
\r
1599 radioItem.setName("USER_DEFINED");
\r
1600 radioItem.addMouseListener(new MouseAdapter()
\r
1602 public void mousePressed(MouseEvent evt)
\r
1604 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1606 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1608 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1609 "Remove from default list?",
\r
1610 "Remove user defined colour",
\r
1611 JOptionPane.YES_NO_OPTION);
\r
1612 if(option == JOptionPane.YES_OPTION)
\r
1614 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1615 colourMenu.remove(radioItem);
\r
1618 radioItem.addActionListener(new ActionListener()
\r
1620 public void actionPerformed(ActionEvent evt)
\r
1622 userDefinedColour_actionPerformed(evt);
\r
1628 radioItem.addActionListener(new ActionListener()
\r
1630 public void actionPerformed(ActionEvent evt)
\r
1632 userDefinedColour_actionPerformed(evt);
\r
1636 colourMenu.insert(radioItem, 15);
\r
1637 colours.add(radioItem);
\r
1645 * @param e DOCUMENT ME!
\r
1647 public void PIDColour_actionPerformed(ActionEvent e)
\r
1649 changeColour(new PIDColourScheme());
\r
1655 * @param e DOCUMENT ME!
\r
1657 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1659 changeColour(new Blosum62ColourScheme());
\r
1665 * @param e DOCUMENT ME!
\r
1667 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1669 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1670 HistoryItem.SORT));
\r
1671 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1672 viewport.getAlignment().getSequenceAt(0));
\r
1673 alignPanel.repaint();
\r
1679 * @param e DOCUMENT ME!
\r
1681 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1683 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1684 HistoryItem.SORT));
\r
1685 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1686 alignPanel.repaint();
\r
1692 * @param e DOCUMENT ME!
\r
1694 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1696 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1697 HistoryItem.SORT));
\r
1699 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1700 alignPanel.repaint();
\r
1706 * @param e DOCUMENT ME!
\r
1708 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1710 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1711 JInternalFrame frame = new JInternalFrame();
\r
1712 frame.setContentPane(sp);
\r
1713 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1720 * @param e DOCUMENT ME!
\r
1722 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1724 if ( (viewport.getSelectionGroup() == null) ||
\r
1725 (viewport.getSelectionGroup().getSize() < 2))
\r
1727 JOptionPane.showInternalMessageDialog(this,
\r
1728 "You must select at least 2 sequences.",
\r
1729 "Invalid Selection",
\r
1730 JOptionPane.WARNING_MESSAGE);
\r
1734 JInternalFrame frame = new JInternalFrame();
\r
1735 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1736 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1743 * @param e DOCUMENT ME!
\r
1745 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1747 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1748 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1749 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1750 (viewport.getAlignment().getHeight() < 4))
\r
1752 JOptionPane.showInternalMessageDialog(this,
\r
1753 "Principal component analysis must take\n" +
\r
1754 "at least 4 input sequences.",
\r
1755 "Sequence selection insufficient",
\r
1756 JOptionPane.WARNING_MESSAGE);
\r
1763 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1764 JInternalFrame frame = new JInternalFrame();
\r
1765 frame.setContentPane(pcaPanel);
\r
1766 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1769 catch (java.lang.OutOfMemoryError ex)
\r
1771 JOptionPane.showInternalMessageDialog(this,
\r
1772 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1774 JOptionPane.WARNING_MESSAGE);
\r
1781 * @param e DOCUMENT ME!
\r
1783 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1785 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1791 * @param e DOCUMENT ME!
\r
1793 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1795 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1801 * @param e DOCUMENT ME!
\r
1803 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1805 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1811 * @param e DOCUMENT ME!
\r
1813 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1815 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1821 * @param type DOCUMENT ME!
\r
1822 * @param pwType DOCUMENT ME!
\r
1823 * @param title DOCUMENT ME!
\r
1825 void NewTreePanel(String type, String pwType, String title)
\r
1827 final TreePanel tp;
\r
1829 if ( (viewport.getSelectionGroup() != null) &&
\r
1830 (viewport.getSelectionGroup().getSize() > 3))
\r
1833 SequenceGroup sg = viewport.getSelectionGroup();
\r
1835 /* Decide if the selection is a column region */
\r
1836 while (s < sg.sequences.size())
\r
1838 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1841 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1842 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1843 "Try using the Pad function in the edit menu,\n" +
\r
1844 "or one of the multiple sequence alignment web services.",
\r
1845 "Sequences in selection are not aligned",
\r
1846 JOptionPane.WARNING_MESSAGE);
\r
1852 title = title + " on region";
\r
1853 tp = new TreePanel(viewport,
\r
1854 viewport.getSelectionGroup().sequences, type, pwType,
\r
1855 sg.getStartRes(), sg.getEndRes());
\r
1859 //are the sequences aligned?
\r
1860 if (!viewport.alignment.isAligned())
\r
1862 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1863 "The sequences must be aligned before creating a tree.\n" +
\r
1864 "Try using the Pad function in the edit menu,\n" +
\r
1865 "or one of the multiple sequence alignment web services.",
\r
1866 "Sequences not aligned",
\r
1867 JOptionPane.WARNING_MESSAGE);
\r
1872 tp = new TreePanel(viewport,
\r
1873 viewport.getAlignment().getSequences(), type, pwType,
\r
1875 viewport.alignment.getWidth());
\r
1878 addTreeMenuItem(tp, title);
\r
1879 viewport.setCurrentTree(tp.getTree());
\r
1881 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1887 * @param title DOCUMENT ME!
\r
1888 * @param order DOCUMENT ME!
\r
1890 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1892 final JMenuItem item = new JMenuItem("by " + title);
\r
1894 item.addActionListener(new java.awt.event.ActionListener()
\r
1896 public void actionPerformed(ActionEvent e)
\r
1898 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1899 HistoryItem.SORT));
\r
1901 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1902 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1903 alignPanel.repaint();
\r
1909 * Maintain the Order by->Displayed Tree menu.
\r
1910 * Creates a new menu item for a TreePanel with an appropriate
\r
1911 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1912 * to remove the menu item when the treePanel is closed, and adjust
\r
1913 * the tree leaf to sequence mapping when the alignment is modified.
\r
1914 * @param treePanel Displayed tree window.
\r
1915 * @param title SortBy menu item title.
\r
1917 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1919 final JMenuItem item = new JMenuItem(title);
\r
1923 if (treeCount == 1)
\r
1925 sort.add(sortByTreeMenu);
\r
1928 sortByTreeMenu.add(item);
\r
1929 item.addActionListener(new java.awt.event.ActionListener()
\r
1931 public void actionPerformed(ActionEvent e)
\r
1933 addHistoryItem(new HistoryItem("Tree Sort",
\r
1934 viewport.alignment, HistoryItem.SORT));
\r
1935 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1936 treePanel.getTree());
\r
1937 alignPanel.repaint();
\r
1941 treePanel.addInternalFrameListener(new javax.swing.event.
\r
1942 InternalFrameAdapter()
\r
1944 public void internalFrameClosed(
\r
1945 javax.swing.event.InternalFrameEvent evt)
\r
1948 sortByTreeMenu.remove(item);
\r
1950 if (treeCount == 0)
\r
1952 sort.remove(sortByTreeMenu);
\r
1957 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
1959 public void propertyChange(PropertyChangeEvent evt)
\r
1961 if (evt.getPropertyName().equals("alignment"))
\r
1963 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
1964 treePanel.repaint();
\r
1971 * Work out whether the whole set of sequences
\r
1972 * or just the selected set will be submitted for multiple alignment.
\r
1975 private SequenceI[] gatherSequencesForAlignment()
\r
1977 // Now, check we have enough sequences
\r
1978 SequenceI[] msa = null;
\r
1980 if ( (viewport.getSelectionGroup() != null) &&
\r
1981 (viewport.getSelectionGroup().getSize() > 1))
\r
1983 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1984 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1986 msa = new SequenceI[sz = seqs.getSize()];
\r
1988 for (int i = 0; i < sz; i++)
\r
1990 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1995 Vector seqs = viewport.getAlignment().getSequences();
\r
1997 if (seqs.size() > 1)
\r
1999 msa = new SequenceI[seqs.size()];
\r
2001 for (int i = 0; i < seqs.size(); i++)
\r
2003 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2011 * Decides what is submitted to a secondary structure prediction service,
\r
2012 * the currently selected sequence, or the currently selected alignment
\r
2013 * (where the first sequence in the set is the one that the prediction
\r
2016 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2018 SequenceI seq = null;
\r
2019 SequenceI[] msa = null;
\r
2021 if ( (viewport.getSelectionGroup() != null) &&
\r
2022 (viewport.getSelectionGroup().getSize() > 0))
\r
2024 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2025 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2027 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2029 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2034 msa = new SequenceI[sz = seqs.getSize()];
\r
2036 for (int i = 0; i < sz; i++)
\r
2038 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2044 Vector seqs = viewport.getAlignment().getSequences();
\r
2046 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2048 seq = (SequenceI) seqs.elementAt(0);
\r
2052 msa = new SequenceI[seqs.size()];
\r
2054 for (int i = 0; i < seqs.size(); i++)
\r
2056 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2068 return new SequenceI[]
\r
2078 * @param e DOCUMENT ME!
\r
2080 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2082 // Pick the tree file
\r
2083 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2085 "LAST_DIRECTORY"));
\r
2086 chooser.setFileView(new JalviewFileView());
\r
2087 chooser.setDialogTitle("Select a newick-like tree file");
\r
2088 chooser.setToolTipText("Load a tree file");
\r
2090 int value = chooser.showOpenDialog(null);
\r
2092 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2094 String choice = chooser.getSelectedFile().getPath();
\r
2095 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2099 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2101 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2103 catch (Exception ex)
\r
2105 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2106 "Problem reading tree file",
\r
2108 JOptionPane.WARNING_MESSAGE);
\r
2109 ex.printStackTrace();
\r
2115 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2117 return ShowNewickTree(nf,title,600,500,4,5);
\r
2122 * @param nf DOCUMENT ME!
\r
2123 * @param title DOCUMENT ME!
\r
2125 * @return DOCUMENT ME!
\r
2127 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2129 TreePanel tp = null;
\r
2135 if (nf.getTree() != null)
\r
2137 tp = new TreePanel(viewport,
\r
2138 viewport.getAlignment().getSequences(), nf,
\r
2145 tp.setLocation(x,y);
\r
2148 Desktop.addInternalFrame(tp, title, w, h);
\r
2149 addTreeMenuItem(tp, title);
\r
2152 catch (Exception ex)
\r
2154 ex.printStackTrace();
\r
2165 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2166 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2167 printJob.setPrintable(alignPanel, pf);
\r
2169 if (printJob.printDialog())
\r
2175 catch (Exception PrintException)
\r
2177 PrintException.printStackTrace();
\r
2184 * Generates menu items and listener event actions for web service clients
\r
2187 public void BuildWebServiceMenu()
\r
2189 if ( (Desktop.discoverer.services != null)
\r
2190 && (Desktop.discoverer.services.size() > 0))
\r
2192 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2193 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2194 Vector wsmenu = new Vector();
\r
2195 if (msaws != null)
\r
2197 // Add any Multiple Sequence Alignment Services
\r
2198 final JMenu msawsmenu = new JMenu("Alignment");
\r
2199 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2201 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2203 final JMenuItem method = new JMenuItem(sh.getName());
\r
2204 method.addActionListener(new ActionListener()
\r
2206 public void actionPerformed(ActionEvent e)
\r
2208 SequenceI[] msa = gatherSequencesForAlignment();
\r
2209 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2215 msawsmenu.add(method);
\r
2216 // Deal with services that we know accept partial alignments.
\r
2217 if (sh.getName().indexOf("lustal") > -1)
\r
2219 // We know that ClustalWS can accept partial alignments for refinement.
\r
2220 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2221 methodR.addActionListener(new ActionListener()
\r
2223 public void actionPerformed(ActionEvent e)
\r
2225 SequenceI[] msa = gatherSequencesForAlignment();
\r
2226 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2232 msawsmenu.add(methodR);
\r
2236 wsmenu.add(msawsmenu);
\r
2238 if (secstrpr != null)
\r
2240 // Add any secondary structure prediction services
\r
2241 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2242 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2244 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2246 final JMenuItem method = new JMenuItem(sh.getName());
\r
2247 method.addActionListener(new ActionListener()
\r
2249 public void actionPerformed(ActionEvent e)
\r
2251 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2252 if (msa.length == 1)
\r
2254 // Single Sequence prediction
\r
2255 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2260 if (msa.length > 1)
\r
2262 // Single Sequence prediction
\r
2263 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2269 secstrmenu.add(method);
\r
2271 wsmenu.add(secstrmenu);
\r
2273 this.webService.removeAll();
\r
2274 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2276 webService.add( (JMenu) wsmenu.get(i));
\r
2281 this.webService.removeAll();
\r
2282 this.webService.add(this.webServiceNoServices);
\r
2284 // TODO: add in rediscovery function
\r
2285 // TODO: reduce code redundancy.
\r
2286 // TODO: group services by location as well as function.
\r