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 Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import jalview.analysis.*;
\r
23 import jalview.datamodel.*;
\r
25 import jalview.io.*;
\r
27 import jalview.jbgui.*;
\r
29 import jalview.schemes.*;
\r
31 import jalview.ws.*;
\r
34 import java.awt.datatransfer.*;
\r
35 import java.awt.event.*;
\r
36 import java.awt.print.*;
\r
40 import java.beans.*;
\r
44 import javax.swing.*;
\r
45 import javax.swing.event.*;
\r
52 * @version $Revision$
\r
54 public class AlignFrame extends GAlignFrame
\r
56 /** DOCUMENT ME!! */
\r
57 public static final int NEW_WINDOW_WIDTH = 700;
\r
59 /** DOCUMENT ME!! */
\r
60 public static final int NEW_WINDOW_HEIGHT = 500;
\r
61 final AlignmentPanel alignPanel;
\r
62 final AlignViewport viewport;
\r
64 /** DOCUMENT ME!! */
\r
65 public String currentFileFormat = null;
\r
66 Stack historyList = new Stack();
\r
67 Stack redoList = new Stack();
\r
68 private int treeCount = 0;
\r
71 * Creates a new AlignFrame object.
\r
73 * @param al DOCUMENT ME!
\r
75 public AlignFrame(AlignmentI al)
\r
77 viewport = new AlignViewport(al);
\r
79 alignPanel = new AlignmentPanel(this, viewport);
\r
80 alignPanel.annotationPanel.adjustPanelHeight();
\r
81 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
\r
82 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
\r
83 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
\r
85 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
\r
87 addInternalFrameListener(new InternalFrameAdapter()
\r
89 public void internalFrameActivated(InternalFrameEvent evt)
\r
91 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
95 alignPanel.requestFocus();
\r
106 * @param e DOCUMENT ME!
\r
108 public void parseGroupsFile(String file)
\r
111 BufferedReader in = new BufferedReader(new FileReader(file));
\r
112 SequenceI seq=null;
\r
113 String line, text, token;
\r
114 UserColourScheme ucs;
\r
115 int index, start, end;
\r
116 StringTokenizer st;
\r
118 while( (line = in.readLine())!=null)
\r
120 st = new StringTokenizer(line, "\t");
\r
121 if(st.countTokens()!=6)
\r
123 System.out.println("Groups file "+file+" is invalid. Read help file.");
\r
127 while(st.hasMoreElements())
\r
129 text = st.nextToken();
\r
130 token = st.nextToken();
\r
131 if(!token.equals("ID_NOT_SPECIFIED"))
\r
133 index = viewport.alignment.findIndex(viewport.alignment.findName(
\r
138 index = Integer.parseInt( st.nextToken() );
\r
140 start=Integer.parseInt( st.nextToken() );
\r
141 end = Integer.parseInt( st.nextToken() );
\r
142 ucs = new UserColourScheme(st.nextToken());
\r
144 seq = viewport.alignment.getSequenceAt(index);
\r
145 start = seq.findIndex(start)-1;
\r
146 end = seq.findIndex(end)-1;
\r
148 sg = new SequenceGroup(text,ucs,true,true,false,start,end);
\r
149 sg.addSequence( seq,true);
\r
151 viewport.alignment.addGroup(sg);
\r
155 }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}
\r
161 * @param e DOCUMENT ME!
\r
163 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
165 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
169 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
\r
174 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
\r
175 }, currentFileFormat);
\r
177 chooser.setAcceptAllFileFilterUsed(false);
\r
178 chooser.setFileView(new JalviewFileView());
\r
179 chooser.setDialogTitle("Save Alignment to file");
\r
180 chooser.setToolTipText("Save");
\r
182 int value = chooser.showSaveDialog(this);
\r
184 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
186 currentFileFormat = chooser.getSelectedFormat();
\r
187 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
\r
188 currentFileFormat);
\r
190 String choice = chooser.getSelectedFile().getPath();
\r
191 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
193 saveAlignment(choice, currentFileFormat);
\r
197 public boolean saveAlignment(String file, String format)
\r
199 if (format.equalsIgnoreCase("Jalview"))
\r
201 String shortName = title;
\r
203 if (shortName.indexOf(java.io.File.separatorChar) > -1)
\r
205 shortName = shortName.substring(shortName.lastIndexOf(
\r
206 java.io.File.separatorChar) + 1);
\r
209 Jalview2XML.SaveAlignment(this, file, shortName);
\r
211 // USE Jalview2XML to save this file
\r
216 String output = FormatAdapter.formatSequences(format,
\r
217 viewport.getAlignment().
\r
224 java.io.PrintWriter out = new java.io.PrintWriter(
\r
225 new java.io.FileWriter(file));
\r
226 out.println(output);
\r
230 catch (Exception ex)
\r
232 ex.printStackTrace();
\r
242 * @param e DOCUMENT ME!
\r
244 protected void outputText_actionPerformed(ActionEvent e)
\r
246 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
247 Desktop.addInternalFrame(cap,
\r
248 "Alignment output - " + e.getActionCommand(), 600, 500);
\r
249 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
\r
250 viewport.getAlignment().getSequences()));
\r
256 * @param e DOCUMENT ME!
\r
258 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
260 new HTMLOutput(viewport);
\r
263 public void createImageMap(File file, String image)
\r
265 alignPanel.makePNGImageMap(file, image);
\r
271 * @param e DOCUMENT ME!
\r
273 public void createPNG(File f)
\r
275 alignPanel.makePNG(f);
\r
281 * @param e DOCUMENT ME!
\r
283 public void createEPS(File f)
\r
285 alignPanel.makeEPS(f);
\r
291 * @param e DOCUMENT ME!
\r
293 public void printMenuItem_actionPerformed(ActionEvent e)
\r
295 //Putting in a thread avoids Swing painting problems
\r
296 PrintThread thread = new PrintThread();
\r
303 * @param e DOCUMENT ME!
\r
305 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
309 this.setClosed(true);
\r
311 catch (Exception ex)
\r
319 void updateEditMenuBar()
\r
321 if (historyList.size() > 0)
\r
323 undoMenuItem.setEnabled(true);
\r
325 HistoryItem hi = (HistoryItem) historyList.peek();
\r
326 undoMenuItem.setText("Undo " + hi.getDescription());
\r
330 undoMenuItem.setEnabled(false);
\r
331 undoMenuItem.setText("Undo");
\r
334 if (redoList.size() > 0)
\r
336 redoMenuItem.setEnabled(true);
\r
338 HistoryItem hi = (HistoryItem) redoList.peek();
\r
339 redoMenuItem.setText("Redo " + hi.getDescription());
\r
343 redoMenuItem.setEnabled(false);
\r
344 redoMenuItem.setText("Redo");
\r
351 * @param hi DOCUMENT ME!
\r
353 public void addHistoryItem(HistoryItem hi)
\r
355 historyList.push(hi);
\r
356 updateEditMenuBar();
\r
362 * @param e DOCUMENT ME!
\r
364 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
366 HistoryItem hi = (HistoryItem) historyList.pop();
\r
367 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
368 HistoryItem.HIDE));
\r
369 restoreHistoryItem(hi);
\r
375 * @param e DOCUMENT ME!
\r
377 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
379 HistoryItem hi = (HistoryItem) redoList.pop();
\r
380 restoreHistoryItem(hi);
\r
381 updateEditMenuBar();
\r
382 viewport.updateConsensus();
\r
383 alignPanel.repaint();
\r
384 alignPanel.repaint();
\r
387 // used by undo and redo
\r
388 void restoreHistoryItem(HistoryItem hi)
\r
390 if (hi.getType() == HistoryItem.SORT)
\r
392 for (int i = 0; i < hi.getSequences().size(); i++)
\r
394 viewport.alignment.getSequences().setElementAt(hi.getSequences()
\r
401 for (int i = 0; i < hi.getSequences().size(); i++)
\r
403 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
\r
405 if (restore.getLength() == 0)
\r
407 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
408 viewport.alignment.getSequences().insertElementAt(restore,
\r
409 hi.getAlignIndex(i));
\r
413 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
417 if (hi.getType() == HistoryItem.PASTE)
\r
419 for (int i = viewport.alignment.getHeight() - 1;
\r
420 i > (hi.getSequences().size() - 1); i--)
\r
422 viewport.alignment.deleteSequence(i);
\r
427 updateEditMenuBar();
\r
429 viewport.updateConsensus();
\r
430 viewport.updateConservation();
\r
431 alignPanel.repaint();
\r
432 viewport.firePropertyChange("alignment", null,
\r
433 viewport.getAlignment().getSequences());
\r
439 * @param up DOCUMENT ME!
\r
441 public void moveSelectedSequences(boolean up)
\r
443 SequenceGroup sg = viewport.getSelectionGroup();
\r
452 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
454 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
456 if (!sg.sequences.contains(seq))
\r
461 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
463 if (sg.sequences.contains(temp))
\r
468 viewport.alignment.getSequences().setElementAt(temp, i);
\r
469 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
474 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
476 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
478 if (!sg.sequences.contains(seq))
\r
483 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
485 if (sg.sequences.contains(temp))
\r
490 viewport.alignment.getSequences().setElementAt(temp, i);
\r
491 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
495 alignPanel.repaint();
\r
501 * @param e DOCUMENT ME!
\r
503 protected void copy_actionPerformed(ActionEvent e)
\r
505 if (viewport.getSelectionGroup() == null)
\r
510 SequenceGroup sg = viewport.getSelectionGroup();
\r
512 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
513 StringBuffer buffer = new StringBuffer();
\r
515 Hashtable orderedSeqs = new Hashtable();
\r
517 for (int i = 0; i < sg.getSize(); i++)
\r
519 SequenceI seq = sg.getSequenceAt(i);
\r
520 int index = viewport.alignment.findIndex(seq);
\r
521 orderedSeqs.put(index + "", seq);
\r
526 for (int i = 0; i < sg.getSize(); i++)
\r
528 SequenceI seq = null;
\r
530 while (seq == null)
\r
532 if (orderedSeqs.containsKey(index + ""))
\r
534 seq = (SequenceI) orderedSeqs.get(index + "");
\r
545 buffer.append(seq.getName() + "\t" +
\r
546 seq.findPosition(sg.getStartRes()) + "\t" +
\r
547 seq.findPosition(sg.getEndRes()) + "\t" +
\r
548 sg.getSequenceAt(i).getSequence(sg.getStartRes(),
\r
549 sg.getEndRes() + 1) + "\n");
\r
552 c.setContents(new StringSelection(buffer.toString()), null);
\r
558 * @param e DOCUMENT ME!
\r
560 protected void pasteNew_actionPerformed(ActionEvent e)
\r
568 * @param e DOCUMENT ME!
\r
570 protected void pasteThis_actionPerformed(ActionEvent e)
\r
572 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
573 HistoryItem.PASTE));
\r
580 * @param newAlignment DOCUMENT ME!
\r
582 void paste(boolean newAlignment)
\r
586 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
587 Transferable contents = c.getContents(this);
\r
589 if (contents == null)
\r
594 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
\r
595 StringTokenizer st = new StringTokenizer(str);
\r
596 ArrayList seqs = new ArrayList();
\r
598 while (st.hasMoreElements())
\r
600 String name = st.nextToken();
\r
601 int start = Integer.parseInt(st.nextToken());
\r
602 int end = Integer.parseInt(st.nextToken());
\r
603 Sequence sequence = new Sequence(name, st.nextToken(), start,
\r
608 viewport.alignment.addSequence(sequence);
\r
612 seqs.add(sequence);
\r
618 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
619 seqs.toArray(newSeqs);
\r
621 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
\r
622 String newtitle = new String("Copied sequences");
\r
624 if (title.startsWith("Copied sequences"))
\r
630 newtitle = newtitle.concat("- from " + title);
\r
633 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
634 NEW_WINDOW_HEIGHT);
\r
638 viewport.firePropertyChange("alignment", null,
\r
639 viewport.getAlignment().getSequences());
\r
640 viewport.setEndSeq(viewport.alignment.getHeight());
\r
641 viewport.alignment.getWidth();
\r
642 viewport.updateConservation();
\r
643 viewport.updateConsensus();
\r
644 alignPanel.repaint();
\r
647 catch (Exception ex)
\r
651 // could be anything being pasted in here
\r
657 * @param e DOCUMENT ME!
\r
659 protected void cut_actionPerformed(ActionEvent e)
\r
661 copy_actionPerformed(null);
\r
662 delete_actionPerformed(null);
\r
668 * @param e DOCUMENT ME!
\r
670 protected void delete_actionPerformed(ActionEvent e)
\r
672 boolean seqsdeleted = false;
\r
674 if (viewport.getSelectionGroup() == null)
\r
679 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
680 HistoryItem.HIDE));
\r
682 SequenceGroup sg = viewport.getSelectionGroup();
\r
683 boolean allSequences = false;
\r
684 if(sg.sequences.size()==viewport.alignment.getHeight())
\r
685 allSequences = true;
\r
687 for (int i = 0; i < sg.sequences.size(); i++)
\r
689 SequenceI seq = sg.getSequenceAt(i);
\r
690 int index = viewport.getAlignment().findIndex(seq);
\r
691 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
693 // If the cut affects all sequences, remove highlighted columns
\r
696 viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);
\r
700 if (seq.getSequence().length() < 1)
\r
702 seqsdeleted = true;
\r
703 viewport.getAlignment().deleteSequence(seq);
\r
707 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
711 viewport.setSelectionGroup(null);
\r
712 viewport.alignment.deleteGroup(sg);
\r
716 viewport.firePropertyChange("alignment", null,
\r
717 viewport.getAlignment().getSequences());
\r
720 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
\r
722 if (viewport.getAlignment().getHeight() < 1)
\r
726 this.setClosed(true);
\r
728 catch (Exception ex)
\r
733 viewport.updateConservation();
\r
734 viewport.updateConsensus();
\r
735 alignPanel.repaint();
\r
741 * @param e DOCUMENT ME!
\r
743 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
745 viewport.alignment.deleteAllGroups();
\r
746 viewport.setSelectionGroup(null);
\r
747 alignPanel.repaint();
\r
753 * @param e DOCUMENT ME!
\r
755 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
757 SequenceGroup sg = new SequenceGroup();
\r
759 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
762 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
765 sg.setEndRes(viewport.alignment.getWidth());
\r
766 viewport.setSelectionGroup(sg);
\r
767 PaintRefresher.Refresh(null, viewport.alignment);
\r
773 * @param e DOCUMENT ME!
\r
775 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
777 viewport.setSelectionGroup(null);
\r
778 viewport.getColumnSelection().clear();
\r
779 viewport.setSelectionGroup(null);
\r
780 alignPanel.annotationPanel.activeRes = null;
\r
781 PaintRefresher.Refresh(null, viewport.alignment);
\r
787 * @param e DOCUMENT ME!
\r
789 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
791 SequenceGroup sg = viewport.getSelectionGroup();
\r
795 selectAllSequenceMenuItem_actionPerformed(null);
\r
800 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
803 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
806 PaintRefresher.Refresh(null, viewport.alignment);
\r
812 * @param e DOCUMENT ME!
\r
814 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
816 ColumnSelection colSel = viewport.getColumnSelection();
\r
818 if (colSel.size() > 0)
\r
820 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
821 HistoryItem.HIDE));
\r
823 int min = colSel.getMin();
\r
824 viewport.getAlignment().trimLeft(min);
\r
825 colSel.compensateForEdit(0, min);
\r
827 if (viewport.getSelectionGroup() != null)
\r
829 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
832 Vector groups = viewport.alignment.getGroups();
\r
834 for (int i = 0; i < groups.size(); i++)
\r
836 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
838 if (!sg.adjustForRemoveLeft(min))
\r
840 viewport.alignment.deleteGroup(sg);
\r
844 alignPanel.repaint();
\r
851 * @param e DOCUMENT ME!
\r
853 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
855 ColumnSelection colSel = viewport.getColumnSelection();
\r
857 if (colSel.size() > 0)
\r
859 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
860 HistoryItem.HIDE));
\r
862 int max = colSel.getMax();
\r
863 viewport.getAlignment().trimRight(max);
\r
865 if (viewport.getSelectionGroup() != null)
\r
867 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
870 Vector groups = viewport.alignment.getGroups();
\r
872 for (int i = 0; i < groups.size(); i++)
\r
874 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
876 if (!sg.adjustForRemoveRight(max))
\r
878 viewport.alignment.deleteGroup(sg);
\r
882 alignPanel.repaint();
\r
889 * @param e DOCUMENT ME!
\r
891 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
893 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
894 viewport.alignment, HistoryItem.HIDE));
\r
896 viewport.getAlignment().removeGaps();
\r
897 viewport.updateConservation();
\r
898 viewport.updateConsensus();
\r
899 alignPanel.repaint();
\r
905 * @param e DOCUMENT ME!
\r
907 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
909 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
910 HistoryItem.HIDE));
\r
915 Vector seqs = null;
\r
918 int end = viewport.alignment.getWidth();
\r
920 if (viewport.getSelectionGroup() != null
\r
921 || viewport.getSelectionGroup().sequences.size()<1)
\r
923 seqs = viewport.getSelectionGroup().sequences;
\r
924 start = viewport.getSelectionGroup().getStartRes();
\r
925 end = viewport.getSelectionGroup().getEndRes();
\r
929 seqs = viewport.alignment.getSequences();
\r
932 for (int i = 0; i < seqs.size(); i++)
\r
934 current = (SequenceI) seqs.elementAt(i);
\r
935 jSize = current.getLength();
\r
941 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
943 current.deleteCharAt(j);
\r
950 while (j < end && j < jSize);
\r
953 viewport.updateConservation();
\r
954 viewport.updateConsensus();
\r
955 alignPanel.repaint();
\r
961 * @param e DOCUMENT ME!
\r
963 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
965 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
966 HistoryItem.HIDE));
\r
969 int Width = viewport.getAlignment().getWidth();
\r
971 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
974 current = viewport.getAlignment().getSequenceAt(i);
\r
976 if (current.getLength() < Width)
\r
978 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
982 viewport.updateConservation();
\r
983 viewport.updateConsensus();
\r
984 alignPanel.repaint();
\r
990 * @param e DOCUMENT ME!
\r
992 public void findMenuItem_actionPerformed(ActionEvent e)
\r
994 JInternalFrame frame = new JInternalFrame();
\r
995 Finder finder = new Finder(viewport, alignPanel, frame);
\r
996 frame.setContentPane(finder);
\r
997 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
998 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1004 * @param e DOCUMENT ME!
\r
1006 public void font_actionPerformed(ActionEvent e)
\r
1008 FontChooser fc = new FontChooser(alignPanel);
\r
1014 * @param e DOCUMENT ME!
\r
1016 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1018 viewport.setShowFullId(fullSeqId.isSelected());
\r
1020 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1021 alignPanel.repaint();
\r
1027 * @param e DOCUMENT ME!
\r
1029 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1031 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1032 alignPanel.repaint();
\r
1038 * @param e DOCUMENT ME!
\r
1040 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1042 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1043 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1044 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1045 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1046 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1047 alignPanel.repaint();
\r
1053 * @param e DOCUMENT ME!
\r
1055 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1057 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1058 alignPanel.repaint();
\r
1064 * @param e DOCUMENT ME!
\r
1066 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1068 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1069 alignPanel.repaint();
\r
1075 * @param e DOCUMENT ME!
\r
1077 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1079 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1080 alignPanel.repaint();
\r
1086 * @param e DOCUMENT ME!
\r
1088 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1090 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1091 alignPanel.repaint();
\r
1097 * @param e DOCUMENT ME!
\r
1099 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1101 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1102 alignPanel.repaint();
\r
1108 * @param e DOCUMENT ME!
\r
1110 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1112 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1113 alignPanel.repaint();
\r
1119 * @param evt DOCUMENT ME!
\r
1121 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1123 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1125 if (viewport.showSequenceFeatures &&
\r
1126 !((Alignment) viewport.alignment).featuresAdded)
\r
1128 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,
\r
1130 ((Alignment) viewport.alignment).featuresAdded = true;
\r
1133 alignPanel.repaint();
\r
1139 * @param e DOCUMENT ME!
\r
1141 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1143 if (annotationPanelMenuItem.isSelected() &&
\r
1144 viewport.getWrapAlignment())
\r
1146 annotationPanelMenuItem.setSelected(false);
\r
1151 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1152 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1158 * @param e DOCUMENT ME!
\r
1160 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1162 if (alignPanel.overviewPanel != null)
\r
1167 JInternalFrame frame = new JInternalFrame();
\r
1168 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1169 frame.setContentPane(overview);
\r
1170 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1171 frame.getWidth(), frame.getHeight());
\r
1173 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1174 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1176 public void internalFrameClosed(
\r
1177 javax.swing.event.InternalFrameEvent evt)
\r
1179 alignPanel.setOverviewPanel(null);
\r
1184 alignPanel.setOverviewPanel(overview);
\r
1190 * @param e DOCUMENT ME!
\r
1192 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1194 changeColour(null);
\r
1200 * @param e DOCUMENT ME!
\r
1202 public void clustalColour_actionPerformed(ActionEvent e)
\r
1204 changeColour(new ClustalxColourScheme(
\r
1205 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1211 * @param e DOCUMENT ME!
\r
1213 public void zappoColour_actionPerformed(ActionEvent e)
\r
1215 changeColour(new ZappoColourScheme());
\r
1221 * @param e DOCUMENT ME!
\r
1223 public void taylorColour_actionPerformed(ActionEvent e)
\r
1225 changeColour(new TaylorColourScheme());
\r
1231 * @param e DOCUMENT ME!
\r
1233 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1235 changeColour(new HydrophobicColourScheme());
\r
1241 * @param e DOCUMENT ME!
\r
1243 public void helixColour_actionPerformed(ActionEvent e)
\r
1245 changeColour(new HelixColourScheme());
\r
1251 * @param e DOCUMENT ME!
\r
1253 public void strandColour_actionPerformed(ActionEvent e)
\r
1255 changeColour(new StrandColourScheme());
\r
1261 * @param e DOCUMENT ME!
\r
1263 public void turnColour_actionPerformed(ActionEvent e)
\r
1265 changeColour(new TurnColourScheme());
\r
1271 * @param e DOCUMENT ME!
\r
1273 public void buriedColour_actionPerformed(ActionEvent e)
\r
1275 changeColour(new BuriedColourScheme());
\r
1281 * @param e DOCUMENT ME!
\r
1283 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1285 changeColour(new NucleotideColourScheme());
\r
1291 * @param e DOCUMENT ME!
\r
1293 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1295 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1301 * @param cs DOCUMENT ME!
\r
1303 void changeColour(ColourSchemeI cs)
\r
1305 int threshold = 0;
\r
1307 if (viewport.getAbovePIDThreshold())
\r
1309 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1312 if (cs instanceof ResidueColourScheme)
\r
1314 ((ResidueColourScheme) cs).setThreshold(threshold);
\r
1316 else if (cs instanceof ScoreColourScheme)
\r
1318 ((ScoreColourScheme) cs).setThreshold(threshold);
\r
1321 viewport.setGlobalColourScheme(cs);
\r
1323 else if (cs instanceof ResidueColourScheme)
\r
1325 ((ResidueColourScheme) cs).setThreshold(0);
\r
1327 else if (cs instanceof ScoreColourScheme)
\r
1329 ((ScoreColourScheme) cs).setThreshold(0);
\r
1332 if (viewport.getConservationSelected())
\r
1334 ConservationColourScheme ccs = null;
\r
1336 Alignment al = (Alignment) viewport.alignment;
\r
1337 Conservation c = new Conservation("All",
\r
1338 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
1339 al.getWidth() - 1);
\r
1342 c.verdict(false, viewport.ConsPercGaps);
\r
1344 ccs = new ConservationColourScheme(c, cs);
\r
1346 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1347 ccs.setConsensus(viewport.vconsensus);
\r
1348 viewport.setGlobalColourScheme(ccs);
\r
1350 ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
\r
1355 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1358 cs.setConsensus(viewport.vconsensus);
\r
1361 viewport.setGlobalColourScheme(cs);
\r
1364 if (viewport.getColourAppliesToAllGroups())
\r
1366 Vector groups = viewport.alignment.getGroups();
\r
1368 for (int i = 0; i < groups.size(); i++)
\r
1370 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1376 else if (cs instanceof ClustalxColourScheme)
\r
1378 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1380 else if (cs instanceof UserColourScheme)
\r
1382 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
\r
1388 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1390 catch (Exception ex)
\r
1395 if (viewport.getAbovePIDThreshold())
\r
1397 if (sg.cs instanceof ResidueColourScheme)
\r
1399 ((ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
1401 else if (sg.cs instanceof ScoreColourScheme)
\r
1403 ((ScoreColourScheme) sg.cs).setThreshold(threshold);
\r
1406 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1410 if (viewport.getConservationSelected())
\r
1412 Conservation c = new Conservation("Group",
\r
1413 ResidueProperties.propHash, 3, sg.sequences, 0,
\r
1414 viewport.alignment.getWidth() - 1);
\r
1416 c.verdict(false, viewport.ConsPercGaps);
\r
1418 ConservationColourScheme ccs = new ConservationColourScheme(c,
\r
1421 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1422 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1426 else if (cs != null)
\r
1428 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1429 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1435 if (alignPanel.getOverviewPanel() != null)
\r
1437 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1440 alignPanel.repaint();
\r
1446 * @param e DOCUMENT ME!
\r
1448 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1450 if (viewport.getAbovePIDThreshold())
\r
1452 SliderPanel.setPIDSliderSource(alignPanel,
\r
1453 viewport.getGlobalColourScheme(), "Background");
\r
1454 SliderPanel.showPIDSlider();
\r
1461 * @param e DOCUMENT ME!
\r
1463 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1465 if (viewport.getConservationSelected())
\r
1467 SliderPanel.setConservationSlider(alignPanel,
\r
1468 viewport.globalColourScheme, "Background");
\r
1469 SliderPanel.showConservationSlider();
\r
1476 * @param e DOCUMENT ME!
\r
1478 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1480 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1482 viewport.setAbovePIDThreshold(false);
\r
1483 abovePIDThreshold.setSelected(false);
\r
1485 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1487 if (cs instanceof ConservationColourScheme)
\r
1489 changeColour(((ConservationColourScheme) cs).cs);
\r
1496 modifyConservation_actionPerformed(null);
\r
1502 * @param e DOCUMENT ME!
\r
1504 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1506 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1508 conservationMenuItem.setSelected(false);
\r
1509 viewport.setConservationSelected(false);
\r
1511 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1513 if (cs instanceof ConservationColourScheme)
\r
1515 changeColour(((ConservationColourScheme) cs).cs);
\r
1522 modifyPID_actionPerformed(null);
\r
1528 * @param e DOCUMENT ME!
\r
1530 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1532 new UserDefinedColours(alignPanel, null);
\r
1538 * @param e DOCUMENT ME!
\r
1540 public void PIDColour_actionPerformed(ActionEvent e)
\r
1542 changeColour(new PIDColourScheme());
\r
1548 * @param e DOCUMENT ME!
\r
1550 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1552 changeColour(new Blosum62ColourScheme());
\r
1558 * @param e DOCUMENT ME!
\r
1560 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1562 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1563 HistoryItem.SORT));
\r
1564 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1565 viewport.getAlignment().getSequenceAt(0));
\r
1566 alignPanel.repaint();
\r
1572 * @param e DOCUMENT ME!
\r
1574 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1576 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1577 HistoryItem.SORT));
\r
1578 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1579 alignPanel.repaint();
\r
1585 * @param e DOCUMENT ME!
\r
1587 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1589 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1590 HistoryItem.SORT));
\r
1592 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1593 alignPanel.repaint();
\r
1599 * @param e DOCUMENT ME!
\r
1601 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1603 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1604 JInternalFrame frame = new JInternalFrame();
\r
1605 frame.setContentPane(sp);
\r
1606 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1613 * @param e DOCUMENT ME!
\r
1615 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1617 if ((viewport.getSelectionGroup() == null) ||
\r
1618 (viewport.getSelectionGroup().getSize() < 2))
\r
1620 JOptionPane.showInternalMessageDialog(this,
\r
1621 "You must select at least 2 sequences.", "Invalid Selection",
\r
1622 JOptionPane.WARNING_MESSAGE);
\r
1626 JInternalFrame frame = new JInternalFrame();
\r
1627 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1628 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1635 * @param e DOCUMENT ME!
\r
1637 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1639 if (((viewport.getSelectionGroup() != null) &&
\r
1640 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1641 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1642 (viewport.getAlignment().getHeight() < 4))
\r
1644 JOptionPane.showInternalMessageDialog(this,
\r
1645 "Principal component analysis must take\n" +
\r
1646 "at least 4 input sequences.",
\r
1647 "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);
\r
1654 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1655 JInternalFrame frame = new JInternalFrame();
\r
1656 frame.setContentPane(pcaPanel);
\r
1657 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1660 catch (java.lang.OutOfMemoryError ex)
\r
1662 JOptionPane.showInternalMessageDialog(this,
\r
1663 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1664 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
1671 * @param e DOCUMENT ME!
\r
1673 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1675 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1681 * @param e DOCUMENT ME!
\r
1683 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1685 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1691 * @param e DOCUMENT ME!
\r
1693 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1695 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1701 * @param e DOCUMENT ME!
\r
1703 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1705 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1711 * @param type DOCUMENT ME!
\r
1712 * @param pwType DOCUMENT ME!
\r
1713 * @param title DOCUMENT ME!
\r
1715 void NewTreePanel(String type, String pwType, String title)
\r
1717 final TreePanel tp;
\r
1719 if ((viewport.getSelectionGroup() != null) &&
\r
1720 (viewport.getSelectionGroup().getSize() > 3))
\r
1723 SequenceGroup sg = viewport.getSelectionGroup();
\r
1725 /* Decide if the selection is a column region */
\r
1726 while (s < sg.sequences.size())
\r
1728 if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())
\r
1730 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1731 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1732 "Try using the Pad function in the edit menu,\n" +
\r
1733 "or one of the multiple sequence alignment web services.",
\r
1734 "Sequences in selection are not aligned",
\r
1735 JOptionPane.WARNING_MESSAGE);
\r
1741 title = title + " on region";
\r
1742 tp = new TreePanel(viewport,
\r
1743 viewport.getSelectionGroup().sequences, type, pwType,
\r
1744 sg.getStartRes(), sg.getEndRes());
\r
1748 //are the sequences aligned?
\r
1749 if (!viewport.alignment.isAligned())
\r
1751 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1752 "The sequences must be aligned before creating a tree.\n" +
\r
1753 "Try using the Pad function in the edit menu,\n" +
\r
1754 "or one of the multiple sequence alignment web services.",
\r
1755 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1760 tp = new TreePanel(viewport,
\r
1761 viewport.getAlignment().getSequences(), type, pwType, 0,
\r
1762 viewport.alignment.getWidth());
\r
1765 addTreeMenuItem(tp, title);
\r
1766 viewport.setCurrentTree(tp.getTree());
\r
1768 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1774 * @param title DOCUMENT ME!
\r
1775 * @param order DOCUMENT ME!
\r
1777 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1779 final JMenuItem item = new JMenuItem("by " + title);
\r
1781 item.addActionListener(new java.awt.event.ActionListener()
\r
1783 public void actionPerformed(ActionEvent e)
\r
1785 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1786 HistoryItem.SORT));
\r
1788 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1789 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1790 alignPanel.repaint();
\r
1798 * @param treePanel DOCUMENT ME!
\r
1799 * @param title DOCUMENT ME!
\r
1801 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1803 final JMenuItem item = new JMenuItem(title);
\r
1807 if (treeCount == 1)
\r
1809 sort.add(sortByTreeMenu);
\r
1812 sortByTreeMenu.add(item);
\r
1813 item.addActionListener(new java.awt.event.ActionListener()
\r
1815 public void actionPerformed(ActionEvent e)
\r
1817 addHistoryItem(new HistoryItem("Tree Sort",
\r
1818 viewport.alignment, HistoryItem.SORT));
\r
1819 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1820 treePanel.getTree());
\r
1821 alignPanel.repaint();
\r
1825 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1827 public void internalFrameClosed(
\r
1828 javax.swing.event.InternalFrameEvent evt)
\r
1831 sortByTreeMenu.remove(item);
\r
1833 if (treeCount == 0)
\r
1835 sort.remove(sortByTreeMenu);
\r
1840 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
1842 public void propertyChange(PropertyChangeEvent evt)
\r
1844 if (evt.getPropertyName().equals("alignment"))
\r
1846 treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());
\r
1847 treePanel.repaint();
\r
1856 * @param e DOCUMENT ME!
\r
1858 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1860 // TODO:resolve which menu item was actually selected
\r
1861 // Now, check we have enough sequences
\r
1862 SequenceI[] msa = null;
\r
1864 if ((viewport.getSelectionGroup() != null) &&
\r
1865 (viewport.getSelectionGroup().getSize() > 1))
\r
1867 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1868 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1870 msa = new SequenceI[sz = seqs.getSize()];
\r
1872 for (int i = 0; i < sz; i++)
\r
1874 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1879 Vector seqs = viewport.getAlignment().getSequences();
\r
1881 if (seqs.size() > 1)
\r
1883 msa = new SequenceI[seqs.size()];
\r
1885 for (int i = 0; i < seqs.size(); i++)
\r
1887 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1894 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1895 title, msa, false, true);
\r
1902 * @param e DOCUMENT ME!
\r
1904 public void ClustalRealign_actionPerformed(ActionEvent e)
\r
1906 // TODO:resolve which menu item was actually selected
\r
1907 // Now, check we have enough sequences
\r
1908 SequenceI[] msa = null;
\r
1910 if ((viewport.getSelectionGroup() != null) &&
\r
1911 (viewport.getSelectionGroup().getSize() > 1))
\r
1913 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1914 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1916 msa = new SequenceI[sz = seqs.getSize()];
\r
1918 for (int i = 0; i < sz; i++)
\r
1920 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1925 Vector seqs = viewport.getAlignment().getSequences();
\r
1927 if (seqs.size() > 1)
\r
1929 msa = new SequenceI[seqs.size()];
\r
1931 for (int i = 0; i < seqs.size(); i++)
\r
1933 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1940 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1941 title, msa, true, true);
\r
1948 * @param e DOCUMENT ME!
\r
1950 protected void jpred_actionPerformed(ActionEvent e)
\r
1952 SequenceI seq = null;
\r
1953 SequenceI[] msa = null;
\r
1955 if ((viewport.getSelectionGroup() != null) &&
\r
1956 (viewport.getSelectionGroup().getSize() > 0))
\r
1958 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1959 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1961 if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
1963 seq = (SequenceI) seqs.getSequenceAt(0);
\r
1968 msa = new SequenceI[sz = seqs.getSize()];
\r
1970 for (int i = 0; i < sz; i++)
\r
1972 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1978 Vector seqs = viewport.getAlignment().getSequences();
\r
1980 if ((seqs.size() == 1) || !viewport.alignment.isAligned())
\r
1982 seq = (SequenceI) seqs.elementAt(0);
\r
1986 msa = new SequenceI[seqs.size()];
\r
1988 for (int i = 0; i < seqs.size(); i++)
\r
1990 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1997 JPredClient ct = new JPredClient(title, msa);
\r
1999 else if (seq != null)
\r
2001 JPredClient ct = new JPredClient(title, seq);
\r
2006 "JALVIEW ERROR! - Unexpected JPred selection state!\n");
\r
2013 * @param e DOCUMENT ME!
\r
2015 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
2017 // TODO:resolve which menu item was actually selected
\r
2018 // Now, check we have enough sequences
\r
2019 SequenceI[] msa = null;
\r
2021 if ((viewport.getSelectionGroup() != null) &&
\r
2022 (viewport.getSelectionGroup().getSize() > 1))
\r
2024 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2025 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2027 msa = new SequenceI[sz = seqs.getSize()];
\r
2029 for (int i = 0; i < sz; i++)
\r
2031 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2036 Vector seqs = viewport.getAlignment().getSequences();
\r
2038 if (seqs.size() > 1)
\r
2040 msa = new SequenceI[seqs.size()];
\r
2042 for (int i = 0; i < seqs.size(); i++)
\r
2044 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2051 MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
\r
2059 * @param e DOCUMENT ME!
\r
2061 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2063 // Pick the tree file
\r
2064 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
2065 "LAST_DIRECTORY"));
\r
2066 chooser.setFileView(new JalviewFileView());
\r
2067 chooser.setDialogTitle("Select a newick-like tree file");
\r
2068 chooser.setToolTipText("Load a tree file");
\r
2070 int value = chooser.showOpenDialog(null);
\r
2072 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2074 String choice = chooser.getSelectedFile().getPath();
\r
2075 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2079 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2081 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2083 catch (Exception ex)
\r
2085 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2086 "Problem reading tree file", ex.getMessage(),
\r
2087 JOptionPane.WARNING_MESSAGE);
\r
2088 ex.printStackTrace();
\r
2096 * @param nf DOCUMENT ME!
\r
2097 * @param title DOCUMENT ME!
\r
2099 * @return DOCUMENT ME!
\r
2101 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2103 TreePanel tp = null;
\r
2109 if (nf.getTree() != null)
\r
2111 tp = new TreePanel(viewport,
\r
2112 viewport.getAlignment().getSequences(), nf, "FromFile",
\r
2114 Desktop.addInternalFrame(tp, title, 600, 500);
\r
2115 addTreeMenuItem(tp, title);
\r
2118 catch (Exception ex)
\r
2120 ex.printStackTrace();
\r
2126 class PrintThread extends Thread
\r
2130 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2131 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2132 printJob.setPrintable(alignPanel, pf);
\r
2134 if (printJob.printDialog())
\r
2140 catch (Exception PrintException)
\r
2142 PrintException.printStackTrace();
\r