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
271 catch (Exception ex)
\r
273 ex.printStackTrace();
\r
282 * @param e DOCUMENT ME!
\r
284 protected void outputText_actionPerformed(ActionEvent e)
\r
286 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
287 Desktop.addInternalFrame(cap,
\r
288 "Alignment output - " + e.getActionCommand(), 600,
\r
290 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
\r
291 viewport.getAlignment().
\r
298 * @param e DOCUMENT ME!
\r
300 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
302 new HTMLOutput(viewport);
\r
305 public void createImageMap(File file, String image)
\r
307 alignPanel.makePNGImageMap(file, image);
\r
313 * @param e DOCUMENT ME!
\r
315 public void createPNG(File f)
\r
317 alignPanel.makePNG(f);
\r
323 * @param e DOCUMENT ME!
\r
325 public void createEPS(File f)
\r
327 alignPanel.makeEPS(f);
\r
333 * @param e DOCUMENT ME!
\r
335 public void printMenuItem_actionPerformed(ActionEvent e)
\r
337 //Putting in a thread avoids Swing painting problems
\r
338 PrintThread thread = new PrintThread();
\r
345 * @param e DOCUMENT ME!
\r
347 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
351 PaintRefresher.components.remove(viewport.alignment);
\r
352 this.setClosed(true);
\r
354 catch (Exception ex)
\r
362 void updateEditMenuBar()
\r
364 if (historyList.size() > 0)
\r
366 undoMenuItem.setEnabled(true);
\r
368 HistoryItem hi = (HistoryItem) historyList.peek();
\r
369 undoMenuItem.setText("Undo " + hi.getDescription());
\r
373 undoMenuItem.setEnabled(false);
\r
374 undoMenuItem.setText("Undo");
\r
377 if (redoList.size() > 0)
\r
379 redoMenuItem.setEnabled(true);
\r
381 HistoryItem hi = (HistoryItem) redoList.peek();
\r
382 redoMenuItem.setText("Redo " + hi.getDescription());
\r
386 redoMenuItem.setEnabled(false);
\r
387 redoMenuItem.setText("Redo");
\r
394 * @param hi DOCUMENT ME!
\r
396 public void addHistoryItem(HistoryItem hi)
\r
398 historyList.push(hi);
\r
399 updateEditMenuBar();
\r
405 * @param e DOCUMENT ME!
\r
407 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
409 HistoryItem hi = (HistoryItem) historyList.pop();
\r
410 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
411 HistoryItem.HIDE));
\r
412 restoreHistoryItem(hi);
\r
413 resetAllColourSchemes();
\r
419 * @param e DOCUMENT ME!
\r
421 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
423 HistoryItem hi = (HistoryItem) redoList.pop();
\r
424 restoreHistoryItem(hi);
\r
425 updateEditMenuBar();
\r
426 viewport.updateConsensus();
\r
427 resetAllColourSchemes();
\r
428 alignPanel.repaint();
\r
431 // used by undo and redo
\r
432 void restoreHistoryItem(HistoryItem hi)
\r
434 if (hi.getType() == HistoryItem.SORT)
\r
436 for (int i = 0; i < hi.getSequences().size(); i++)
\r
438 viewport.alignment.getSequences().setElementAt(hi.getSequences()
\r
445 for (int i = 0; i < hi.getSequences().size(); i++)
\r
447 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
\r
449 if (restore.getLength() == 0)
\r
451 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
452 viewport.alignment.getSequences().insertElementAt(restore,
\r
453 hi.getAlignIndex(i));
\r
457 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
461 if (hi.getType() == HistoryItem.PASTE)
\r
463 for (int i = viewport.alignment.getHeight() - 1;
\r
464 i > (hi.getSequences().size() - 1); i--)
\r
466 viewport.alignment.deleteSequence(i);
\r
471 updateEditMenuBar();
\r
473 viewport.updateConsensus();
\r
474 viewport.updateConservation();
\r
475 alignPanel.repaint();
\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.firePropertyChange("alignment", null,
\r
705 viewport.getAlignment().getSequences());
\r
706 viewport.setEndSeq(viewport.alignment.getHeight());
\r
707 viewport.alignment.getWidth();
\r
708 viewport.updateConservation();
\r
709 viewport.updateConsensus();
\r
710 resetAllColourSchemes();
\r
711 alignPanel.repaint();
\r
714 catch (Exception ex)
\r
718 // could be anything being pasted in here
\r
724 * @param e DOCUMENT ME!
\r
726 protected void cut_actionPerformed(ActionEvent e)
\r
728 copy_actionPerformed(null);
\r
729 delete_actionPerformed(null);
\r
735 * @param e DOCUMENT ME!
\r
737 protected void delete_actionPerformed(ActionEvent e)
\r
739 boolean seqsdeleted = false;
\r
741 if (viewport.getSelectionGroup() == null)
\r
746 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
747 HistoryItem.HIDE));
\r
749 SequenceGroup sg = viewport.getSelectionGroup();
\r
750 boolean allSequences = false;
\r
751 if (sg.sequences.size() == viewport.alignment.getHeight())
\r
753 allSequences = true;
\r
756 for (int i = 0; i < sg.sequences.size(); i++)
\r
758 SequenceI seq = sg.getSequenceAt(i);
\r
759 int index = viewport.getAlignment().findIndex(seq);
\r
760 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
762 // If the cut affects all sequences, remove highlighted columns
\r
765 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
766 sg.getEndRes() + 1);
\r
769 if (seq.getSequence().length() < 1)
\r
771 seqsdeleted = true;
\r
772 viewport.getAlignment().deleteSequence(seq);
\r
776 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
780 viewport.setSelectionGroup(null);
\r
781 viewport.alignment.deleteGroup(sg);
\r
785 viewport.firePropertyChange("alignment", null,
\r
786 viewport.getAlignment().getSequences());
\r
789 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
\r
791 if (viewport.getAlignment().getHeight() < 1)
\r
795 this.setClosed(true);
\r
797 catch (Exception ex)
\r
802 viewport.updateConservation();
\r
803 viewport.updateConsensus();
\r
804 resetAllColourSchemes();
\r
805 alignPanel.repaint();
\r
811 * @param e DOCUMENT ME!
\r
813 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
815 viewport.alignment.deleteAllGroups();
\r
816 viewport.setSelectionGroup(null);
\r
817 alignPanel.repaint();
\r
823 * @param e DOCUMENT ME!
\r
825 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
827 SequenceGroup sg = new SequenceGroup();
\r
829 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
832 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
835 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
836 viewport.setSelectionGroup(sg);
\r
837 PaintRefresher.Refresh(null, viewport.alignment);
\r
843 * @param e DOCUMENT ME!
\r
845 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
847 viewport.setSelectionGroup(null);
\r
848 viewport.getColumnSelection().clear();
\r
849 viewport.setSelectionGroup(null);
\r
850 alignPanel.annotationPanel.activeRes = null;
\r
851 PaintRefresher.Refresh(null, viewport.alignment);
\r
857 * @param e DOCUMENT ME!
\r
859 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
861 SequenceGroup sg = viewport.getSelectionGroup();
\r
865 selectAllSequenceMenuItem_actionPerformed(null);
\r
870 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
873 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
876 PaintRefresher.Refresh(null, viewport.alignment);
\r
882 * @param e DOCUMENT ME!
\r
884 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
886 ColumnSelection colSel = viewport.getColumnSelection();
\r
888 if (colSel.size() > 0)
\r
890 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
891 HistoryItem.HIDE));
\r
893 int min = colSel.getMin();
\r
894 viewport.getAlignment().trimLeft(min);
\r
895 colSel.compensateForEdit(0, min);
\r
897 if (viewport.getSelectionGroup() != null)
\r
899 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
902 Vector groups = viewport.alignment.getGroups();
\r
904 for (int i = 0; i < groups.size(); i++)
\r
906 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
908 if (!sg.adjustForRemoveLeft(min))
\r
910 viewport.alignment.deleteGroup(sg);
\r
914 resetAllColourSchemes();
\r
915 alignPanel.repaint();
\r
922 * @param e DOCUMENT ME!
\r
924 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
926 ColumnSelection colSel = viewport.getColumnSelection();
\r
928 if (colSel.size() > 0)
\r
930 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
931 HistoryItem.HIDE));
\r
933 int max = colSel.getMax();
\r
934 viewport.getAlignment().trimRight(max);
\r
936 if (viewport.getSelectionGroup() != null)
\r
938 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
941 Vector groups = viewport.alignment.getGroups();
\r
943 for (int i = 0; i < groups.size(); i++)
\r
945 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
947 if (!sg.adjustForRemoveRight(max))
\r
949 viewport.alignment.deleteGroup(sg);
\r
953 resetAllColourSchemes();
\r
954 alignPanel.repaint();
\r
961 * @param e DOCUMENT ME!
\r
963 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
965 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
966 viewport.alignment, HistoryItem.HIDE));
\r
968 //This is to maintain viewport position on first residue
\r
969 //of first sequence
\r
970 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
971 int startRes = seq.findPosition(viewport.startRes);
\r
973 viewport.getAlignment().removeGaps();
\r
975 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
977 resetAllColourSchemes();
\r
978 viewport.updateConservation();
\r
979 viewport.updateConsensus();
\r
980 alignPanel.repaint();
\r
986 * @param e DOCUMENT ME!
\r
988 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
990 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
991 HistoryItem.HIDE));
\r
993 //This is to maintain viewport position on first residue
\r
994 //of first sequence
\r
995 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
996 int startRes = seq.findPosition(viewport.startRes);
\r
1002 Vector seqs = null;
\r
1005 int end = viewport.alignment.getWidth();
\r
1007 if (viewport.getSelectionGroup() != null
\r
1008 && viewport.getSelectionGroup().sequences != null
\r
1009 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1011 seqs = viewport.getSelectionGroup().sequences;
\r
1012 start = viewport.getSelectionGroup().getStartRes();
\r
1013 end = viewport.getSelectionGroup().getEndRes();
\r
1017 seqs = viewport.alignment.getSequences();
\r
1020 for (int i = 0; i < seqs.size(); i++)
\r
1022 current = (SequenceI) seqs.elementAt(i);
\r
1023 jSize = current.getLength();
\r
1029 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1031 current.deleteCharAt(j);
\r
1037 while (j < end && j < jSize);
\r
1040 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1043 viewport.updateConservation();
\r
1044 viewport.updateConsensus();
\r
1045 resetAllColourSchemes();
\r
1046 alignPanel.repaint();
\r
1050 void resetAllColourSchemes()
\r
1052 ColourSchemeI cs = viewport.globalColourScheme;
\r
1055 cs.setConsensus(viewport.vconsensus);
\r
1056 if(cs.conservationApplied())
\r
1058 Alignment al = (Alignment) viewport.alignment;
\r
1059 Conservation c = new Conservation("All",
\r
1060 ResidueProperties.propHash, 3,
\r
1061 al.getSequences(), 0,
\r
1062 al.getWidth() - 1);
\r
1064 c.verdict(false, viewport.ConsPercGaps);
\r
1066 cs.setConservation(c);
\r
1070 if(viewport.getGlobalColourScheme()!=null
\r
1071 && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
\r
1073 ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
\r
1074 resetClustalX(viewport.alignment.getSequences(),
\r
1075 viewport.alignment.getWidth());
\r
1078 int s, sSize = viewport.alignment.getGroups().size();
\r
1079 for(s=0; s<sSize; s++)
\r
1081 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1082 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1084 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1087 sg.recalcConservation();
\r
1095 * @param e DOCUMENT ME!
\r
1097 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1099 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1100 HistoryItem.HIDE));
\r
1102 SequenceI current;
\r
1103 int Width = viewport.getAlignment().getWidth();
\r
1105 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1108 current = viewport.getAlignment().getSequenceAt(i);
\r
1110 if (current.getLength() < Width)
\r
1112 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1116 viewport.updateConservation();
\r
1117 viewport.updateConsensus();
\r
1118 alignPanel.repaint();
\r
1124 * @param e DOCUMENT ME!
\r
1126 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1128 JInternalFrame frame = new JInternalFrame();
\r
1129 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1130 frame.setContentPane(finder);
\r
1131 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1132 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1138 * @param e DOCUMENT ME!
\r
1140 public void font_actionPerformed(ActionEvent e)
\r
1142 FontChooser fc = new FontChooser(alignPanel);
\r
1148 * @param e DOCUMENT ME!
\r
1150 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1152 viewport.setShowFullId(fullSeqId.isSelected());
\r
1154 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1155 alignPanel.repaint();
\r
1161 * @param e DOCUMENT ME!
\r
1163 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1165 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1166 alignPanel.repaint();
\r
1172 * @param e DOCUMENT ME!
\r
1174 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1176 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1177 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1178 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1179 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1180 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1181 alignPanel.repaint();
\r
1187 * @param e DOCUMENT ME!
\r
1189 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1191 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1192 alignPanel.repaint();
\r
1198 * @param e DOCUMENT ME!
\r
1200 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1202 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1203 alignPanel.repaint();
\r
1209 * @param e DOCUMENT ME!
\r
1211 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1213 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1214 alignPanel.repaint();
\r
1220 * @param e DOCUMENT ME!
\r
1222 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1224 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1225 alignPanel.repaint();
\r
1231 * @param e DOCUMENT ME!
\r
1233 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1235 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1236 alignPanel.repaint();
\r
1242 * @param e DOCUMENT ME!
\r
1244 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1246 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1247 alignPanel.repaint();
\r
1253 * @param evt DOCUMENT ME!
\r
1255 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1257 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1259 if (viewport.showSequenceFeatures &&
\r
1260 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1262 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1265 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1268 alignPanel.repaint();
\r
1274 * @param e DOCUMENT ME!
\r
1276 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1278 if (annotationPanelMenuItem.isSelected() &&
\r
1279 viewport.getWrapAlignment())
\r
1281 annotationPanelMenuItem.setSelected(false);
\r
1286 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1287 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1293 * @param e DOCUMENT ME!
\r
1295 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1297 if (alignPanel.overviewPanel != null)
\r
1302 JInternalFrame frame = new JInternalFrame();
\r
1303 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1304 frame.setContentPane(overview);
\r
1305 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1306 frame.getWidth(), frame.getHeight());
\r
1308 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1309 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1311 public void internalFrameClosed(
\r
1312 javax.swing.event.InternalFrameEvent evt)
\r
1314 alignPanel.setOverviewPanel(null);
\r
1319 alignPanel.setOverviewPanel(overview);
\r
1325 * @param e DOCUMENT ME!
\r
1327 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1329 changeColour(null);
\r
1335 * @param e DOCUMENT ME!
\r
1337 public void clustalColour_actionPerformed(ActionEvent e)
\r
1339 changeColour(new ClustalxColourScheme(
\r
1340 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1346 * @param e DOCUMENT ME!
\r
1348 public void zappoColour_actionPerformed(ActionEvent e)
\r
1350 changeColour(new ZappoColourScheme());
\r
1356 * @param e DOCUMENT ME!
\r
1358 public void taylorColour_actionPerformed(ActionEvent e)
\r
1360 changeColour(new TaylorColourScheme());
\r
1366 * @param e DOCUMENT ME!
\r
1368 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1370 changeColour(new HydrophobicColourScheme());
\r
1376 * @param e DOCUMENT ME!
\r
1378 public void helixColour_actionPerformed(ActionEvent e)
\r
1380 changeColour(new HelixColourScheme());
\r
1386 * @param e DOCUMENT ME!
\r
1388 public void strandColour_actionPerformed(ActionEvent e)
\r
1390 changeColour(new StrandColourScheme());
\r
1396 * @param e DOCUMENT ME!
\r
1398 public void turnColour_actionPerformed(ActionEvent e)
\r
1400 changeColour(new TurnColourScheme());
\r
1406 * @param e DOCUMENT ME!
\r
1408 public void buriedColour_actionPerformed(ActionEvent e)
\r
1410 changeColour(new BuriedColourScheme());
\r
1416 * @param e DOCUMENT ME!
\r
1418 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1420 changeColour(new NucleotideColourScheme());
\r
1426 * @param e DOCUMENT ME!
\r
1428 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1430 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1436 * @param cs DOCUMENT ME!
\r
1438 void changeColour(ColourSchemeI cs)
\r
1440 int threshold = 0;
\r
1444 if (viewport.getAbovePIDThreshold())
\r
1446 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1449 cs.setThreshold(threshold,
\r
1450 viewport.getIgnoreGapsConsensus());
\r
1452 viewport.setGlobalColourScheme(cs);
\r
1456 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1459 if (viewport.getConservationSelected())
\r
1462 Alignment al = (Alignment) viewport.alignment;
\r
1463 Conservation c = new Conservation("All",
\r
1464 ResidueProperties.propHash, 3,
\r
1465 al.getSequences(), 0,
\r
1466 al.getWidth() - 1);
\r
1469 c.verdict(false, viewport.ConsPercGaps);
\r
1471 cs.setConservation(c);
\r
1473 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1478 cs.setConservation(null);
\r
1481 cs.setConsensus(viewport.vconsensus);
\r
1484 viewport.setGlobalColourScheme(cs);
\r
1486 if (viewport.getColourAppliesToAllGroups())
\r
1488 Vector groups = viewport.alignment.getGroups();
\r
1490 for (int i = 0; i < groups.size(); i++)
\r
1492 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1500 if (cs instanceof ClustalxColourScheme)
\r
1502 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1504 else if (cs instanceof UserColourScheme)
\r
1506 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1512 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1514 catch (Exception ex)
\r
1519 if (viewport.getAbovePIDThreshold()
\r
1520 || cs instanceof PIDColourScheme
\r
1521 || cs instanceof Blosum62ColourScheme)
\r
1523 sg.cs.setThreshold(threshold,
\r
1524 viewport.getIgnoreGapsConsensus());
\r
1526 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1530 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1533 if (viewport.getConservationSelected())
\r
1535 Conservation c = new Conservation("Group",
\r
1536 ResidueProperties.propHash, 3,
\r
1538 viewport.alignment.getWidth() - 1);
\r
1540 c.verdict(false, viewport.ConsPercGaps);
\r
1541 sg.cs.setConservation(c);
\r
1544 sg.cs.setConservation(null);
\r
1548 if (alignPanel.getOverviewPanel() != null)
\r
1550 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1553 alignPanel.repaint();
\r
1559 * @param e DOCUMENT ME!
\r
1561 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1563 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1565 SliderPanel.setPIDSliderSource(alignPanel,
\r
1566 viewport.getGlobalColourScheme(),
\r
1568 SliderPanel.showPIDSlider();
\r
1575 * @param e DOCUMENT ME!
\r
1577 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1579 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1581 SliderPanel.setConservationSlider(alignPanel,
\r
1582 viewport.globalColourScheme,
\r
1584 SliderPanel.showConservationSlider();
\r
1591 * @param e DOCUMENT ME!
\r
1593 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1595 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1597 viewport.setAbovePIDThreshold(false);
\r
1598 abovePIDThreshold.setSelected(false);
\r
1600 changeColour(viewport.getGlobalColourScheme());
\r
1602 modifyConservation_actionPerformed(null);
\r
1608 * @param e DOCUMENT ME!
\r
1610 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1612 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1614 conservationMenuItem.setSelected(false);
\r
1615 viewport.setConservationSelected(false);
\r
1617 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1619 changeColour(viewport.getGlobalColourScheme());
\r
1621 modifyPID_actionPerformed(null);
\r
1627 * @param e DOCUMENT ME!
\r
1629 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1631 if (e.getActionCommand().equals("User Defined..."))
\r
1633 new UserDefinedColours(alignPanel, null);
\r
1637 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1638 getUserColourSchemes().get(e.getActionCommand());
\r
1640 changeColour(udc);
\r
1644 public void updateUserColourMenu()
\r
1647 Component[] menuItems = colourMenu.getMenuComponents();
\r
1648 int i, iSize = menuItems.length;
\r
1649 for (i = 0; i < iSize; i++)
\r
1651 if (menuItems[i].getName() != null &&
\r
1652 menuItems[i].getName().equals("USER_DEFINED"))
\r
1654 colourMenu.remove(menuItems[i]);
\r
1658 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1660 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1661 getUserColourSchemes().keys();
\r
1663 while (userColours.hasMoreElements())
\r
1665 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1666 nextElement().toString());
\r
1667 radioItem.setName("USER_DEFINED");
\r
1668 radioItem.addMouseListener(new MouseAdapter()
\r
1670 public void mousePressed(MouseEvent evt)
\r
1672 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1674 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1676 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1677 "Remove from default list?",
\r
1678 "Remove user defined colour",
\r
1679 JOptionPane.YES_NO_OPTION);
\r
1680 if(option == JOptionPane.YES_OPTION)
\r
1682 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1683 colourMenu.remove(radioItem);
\r
1686 radioItem.addActionListener(new ActionListener()
\r
1688 public void actionPerformed(ActionEvent evt)
\r
1690 userDefinedColour_actionPerformed(evt);
\r
1696 radioItem.addActionListener(new ActionListener()
\r
1698 public void actionPerformed(ActionEvent evt)
\r
1700 userDefinedColour_actionPerformed(evt);
\r
1704 colourMenu.insert(radioItem, 15);
\r
1705 colours.add(radioItem);
\r
1713 * @param e DOCUMENT ME!
\r
1715 public void PIDColour_actionPerformed(ActionEvent e)
\r
1717 changeColour(new PIDColourScheme());
\r
1723 * @param e DOCUMENT ME!
\r
1725 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1727 changeColour(new Blosum62ColourScheme());
\r
1733 * @param e DOCUMENT ME!
\r
1735 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1737 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1738 HistoryItem.SORT));
\r
1739 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1740 viewport.getAlignment().getSequenceAt(0));
\r
1741 alignPanel.repaint();
\r
1747 * @param e DOCUMENT ME!
\r
1749 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1751 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1752 HistoryItem.SORT));
\r
1753 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1754 alignPanel.repaint();
\r
1760 * @param e DOCUMENT ME!
\r
1762 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1764 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1765 HistoryItem.SORT));
\r
1767 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1768 alignPanel.repaint();
\r
1774 * @param e DOCUMENT ME!
\r
1776 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1778 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1779 JInternalFrame frame = new JInternalFrame();
\r
1780 frame.setContentPane(sp);
\r
1781 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1788 * @param e DOCUMENT ME!
\r
1790 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1792 if ( (viewport.getSelectionGroup() == null) ||
\r
1793 (viewport.getSelectionGroup().getSize() < 2))
\r
1795 JOptionPane.showInternalMessageDialog(this,
\r
1796 "You must select at least 2 sequences.",
\r
1797 "Invalid Selection",
\r
1798 JOptionPane.WARNING_MESSAGE);
\r
1802 JInternalFrame frame = new JInternalFrame();
\r
1803 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1804 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1811 * @param e DOCUMENT ME!
\r
1813 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1815 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1816 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1817 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1818 (viewport.getAlignment().getHeight() < 4))
\r
1820 JOptionPane.showInternalMessageDialog(this,
\r
1821 "Principal component analysis must take\n" +
\r
1822 "at least 4 input sequences.",
\r
1823 "Sequence selection insufficient",
\r
1824 JOptionPane.WARNING_MESSAGE);
\r
1831 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1832 JInternalFrame frame = new JInternalFrame();
\r
1833 frame.setContentPane(pcaPanel);
\r
1834 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1837 catch (java.lang.OutOfMemoryError ex)
\r
1839 JOptionPane.showInternalMessageDialog(this,
\r
1840 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1842 JOptionPane.WARNING_MESSAGE);
\r
1849 * @param e DOCUMENT ME!
\r
1851 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1853 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1859 * @param e DOCUMENT ME!
\r
1861 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1863 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1869 * @param e DOCUMENT ME!
\r
1871 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1873 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1879 * @param e DOCUMENT ME!
\r
1881 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1883 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1889 * @param type DOCUMENT ME!
\r
1890 * @param pwType DOCUMENT ME!
\r
1891 * @param title DOCUMENT ME!
\r
1893 void NewTreePanel(String type, String pwType, String title)
\r
1895 final TreePanel tp;
\r
1897 if ( (viewport.getSelectionGroup() != null) &&
\r
1898 (viewport.getSelectionGroup().getSize() > 3))
\r
1901 SequenceGroup sg = viewport.getSelectionGroup();
\r
1903 /* Decide if the selection is a column region */
\r
1904 while (s < sg.sequences.size())
\r
1906 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1909 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1910 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1911 "Try using the Pad function in the edit menu,\n" +
\r
1912 "or one of the multiple sequence alignment web services.",
\r
1913 "Sequences in selection are not aligned",
\r
1914 JOptionPane.WARNING_MESSAGE);
\r
1920 title = title + " on region";
\r
1921 tp = new TreePanel(viewport,
\r
1922 viewport.getSelectionGroup().sequences, type, pwType,
\r
1923 sg.getStartRes(), sg.getEndRes());
\r
1927 //are the sequences aligned?
\r
1928 if (!viewport.alignment.isAligned())
\r
1930 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1931 "The sequences must be aligned before creating a tree.\n" +
\r
1932 "Try using the Pad function in the edit menu,\n" +
\r
1933 "or one of the multiple sequence alignment web services.",
\r
1934 "Sequences not aligned",
\r
1935 JOptionPane.WARNING_MESSAGE);
\r
1940 tp = new TreePanel(viewport,
\r
1941 viewport.getAlignment().getSequences(), type, pwType,
\r
1943 viewport.alignment.getWidth());
\r
1946 addTreeMenuItem(tp, title);
\r
1947 viewport.setCurrentTree(tp.getTree());
\r
1949 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1955 * @param title DOCUMENT ME!
\r
1956 * @param order DOCUMENT ME!
\r
1958 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1960 final JMenuItem item = new JMenuItem("by " + title);
\r
1962 item.addActionListener(new java.awt.event.ActionListener()
\r
1964 public void actionPerformed(ActionEvent e)
\r
1966 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1967 HistoryItem.SORT));
\r
1969 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1970 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1971 alignPanel.repaint();
\r
1977 * Maintain the Order by->Displayed Tree menu.
\r
1978 * Creates a new menu item for a TreePanel with an appropriate
\r
1979 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1980 * to remove the menu item when the treePanel is closed, and adjust
\r
1981 * the tree leaf to sequence mapping when the alignment is modified.
\r
1982 * @param treePanel Displayed tree window.
\r
1983 * @param title SortBy menu item title.
\r
1985 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1987 final JMenuItem item = new JMenuItem(title);
\r
1991 if (treeCount == 1)
\r
1993 sort.add(sortByTreeMenu);
\r
1996 sortByTreeMenu.add(item);
\r
1997 item.addActionListener(new java.awt.event.ActionListener()
\r
1999 public void actionPerformed(ActionEvent e)
\r
2001 addHistoryItem(new HistoryItem("Tree Sort",
\r
2002 viewport.alignment, HistoryItem.SORT));
\r
2003 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2004 treePanel.getTree());
\r
2005 alignPanel.repaint();
\r
2009 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2010 InternalFrameAdapter()
\r
2012 public void internalFrameClosed(
\r
2013 javax.swing.event.InternalFrameEvent evt)
\r
2016 sortByTreeMenu.remove(item);
\r
2018 if (treeCount == 0)
\r
2020 sort.remove(sortByTreeMenu);
\r
2025 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
2027 public void propertyChange(PropertyChangeEvent evt)
\r
2029 if (evt.getPropertyName().equals("alignment"))
\r
2031 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
2032 treePanel.repaint();
\r
2039 * Work out whether the whole set of sequences
\r
2040 * or just the selected set will be submitted for multiple alignment.
\r
2043 private SequenceI[] gatherSequencesForAlignment()
\r
2045 // Now, check we have enough sequences
\r
2046 SequenceI[] msa = null;
\r
2048 if ( (viewport.getSelectionGroup() != null) &&
\r
2049 (viewport.getSelectionGroup().getSize() > 1))
\r
2051 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2052 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2054 msa = new SequenceI[sz = seqs.getSize()];
\r
2056 for (int i = 0; i < sz; i++)
\r
2058 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2063 Vector seqs = viewport.getAlignment().getSequences();
\r
2065 if (seqs.size() > 1)
\r
2067 msa = new SequenceI[seqs.size()];
\r
2069 for (int i = 0; i < seqs.size(); i++)
\r
2071 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2079 * Decides what is submitted to a secondary structure prediction service,
\r
2080 * the currently selected sequence, or the currently selected alignment
\r
2081 * (where the first sequence in the set is the one that the prediction
\r
2084 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2086 SequenceI seq = null;
\r
2087 SequenceI[] msa = null;
\r
2089 if ( (viewport.getSelectionGroup() != null) &&
\r
2090 (viewport.getSelectionGroup().getSize() > 0))
\r
2092 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2093 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2095 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2097 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2102 msa = new SequenceI[sz = seqs.getSize()];
\r
2104 for (int i = 0; i < sz; i++)
\r
2106 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2112 Vector seqs = viewport.getAlignment().getSequences();
\r
2114 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2116 seq = (SequenceI) seqs.elementAt(0);
\r
2120 msa = new SequenceI[seqs.size()];
\r
2122 for (int i = 0; i < seqs.size(); i++)
\r
2124 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2136 return new SequenceI[]
\r
2146 * @param e DOCUMENT ME!
\r
2148 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2150 // Pick the tree file
\r
2151 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2153 "LAST_DIRECTORY"));
\r
2154 chooser.setFileView(new JalviewFileView());
\r
2155 chooser.setDialogTitle("Select a newick-like tree file");
\r
2156 chooser.setToolTipText("Load a tree file");
\r
2158 int value = chooser.showOpenDialog(null);
\r
2160 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2162 String choice = chooser.getSelectedFile().getPath();
\r
2163 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2167 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2169 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2171 catch (Exception ex)
\r
2173 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2174 "Problem reading tree file",
\r
2176 JOptionPane.WARNING_MESSAGE);
\r
2177 ex.printStackTrace();
\r
2183 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2185 return ShowNewickTree(nf,title,600,500,4,5);
\r
2190 * @param nf DOCUMENT ME!
\r
2191 * @param title DOCUMENT ME!
\r
2193 * @return DOCUMENT ME!
\r
2195 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2197 TreePanel tp = null;
\r
2203 if (nf.getTree() != null)
\r
2205 tp = new TreePanel(viewport,
\r
2206 viewport.getAlignment().getSequences(), nf,
\r
2213 tp.setLocation(x,y);
\r
2216 Desktop.addInternalFrame(tp, title, w, h);
\r
2217 addTreeMenuItem(tp, title);
\r
2220 catch (Exception ex)
\r
2222 ex.printStackTrace();
\r
2233 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2234 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2235 printJob.setPrintable(alignPanel, pf);
\r
2237 if (printJob.printDialog())
\r
2243 catch (Exception PrintException)
\r
2245 PrintException.printStackTrace();
\r
2252 * Generates menu items and listener event actions for web service clients
\r
2255 public void BuildWebServiceMenu()
\r
2257 if ( (Desktop.discoverer.services != null)
\r
2258 && (Desktop.discoverer.services.size() > 0))
\r
2260 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2261 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2262 Vector wsmenu = new Vector();
\r
2263 if (msaws != null)
\r
2265 // Add any Multiple Sequence Alignment Services
\r
2266 final JMenu msawsmenu = new JMenu("Alignment");
\r
2267 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2269 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2271 final JMenuItem method = new JMenuItem(sh.getName());
\r
2272 method.addActionListener(new ActionListener()
\r
2274 public void actionPerformed(ActionEvent e)
\r
2276 SequenceI[] msa = gatherSequencesForAlignment();
\r
2277 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2283 msawsmenu.add(method);
\r
2284 // Deal with services that we know accept partial alignments.
\r
2285 if (sh.getName().indexOf("lustal") > -1)
\r
2287 // We know that ClustalWS can accept partial alignments for refinement.
\r
2288 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2289 methodR.addActionListener(new ActionListener()
\r
2291 public void actionPerformed(ActionEvent e)
\r
2293 SequenceI[] msa = gatherSequencesForAlignment();
\r
2294 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2300 msawsmenu.add(methodR);
\r
2304 wsmenu.add(msawsmenu);
\r
2306 if (secstrpr != null)
\r
2308 // Add any secondary structure prediction services
\r
2309 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2310 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2312 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2314 final JMenuItem method = new JMenuItem(sh.getName());
\r
2315 method.addActionListener(new ActionListener()
\r
2317 public void actionPerformed(ActionEvent e)
\r
2319 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2320 if (msa.length == 1)
\r
2322 // Single Sequence prediction
\r
2323 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2328 if (msa.length > 1)
\r
2330 // Single Sequence prediction
\r
2331 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2337 secstrmenu.add(method);
\r
2339 wsmenu.add(secstrmenu);
\r
2341 this.webService.removeAll();
\r
2342 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2344 webService.add( (JMenu) wsmenu.get(i));
\r
2349 this.webService.removeAll();
\r
2350 this.webService.add(this.webServiceNoServices);
\r
2352 // TODO: add in rediscovery function
\r
2353 // TODO: reduce code redundancy.
\r
2354 // TODO: group services by location as well as function.
\r