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
20 package jalview.appletgui;
\r
22 import jalview.jbappletgui.GAlignFrame;
\r
23 import jalview.schemes.*;
\r
24 import jalview.datamodel.*;
\r
25 import jalview.analysis.*;
\r
26 import jalview.io.*;
\r
28 import java.awt.event.*;
\r
30 import java.io.InputStreamReader;
\r
31 import java.io.BufferedReader;
\r
32 import java.net.URL;
\r
34 public class AlignFrame
\r
37 final AlignmentPanel alignPanel;
\r
38 public final AlignViewport viewport;
\r
39 int NEW_WINDOW_WIDTH = 700;
\r
40 int NEW_WINDOW_HEIGHT = 500;
\r
41 jalview.bin.JalviewLite applet;
\r
44 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
\r
46 this.applet = applet;
\r
47 viewport = new AlignViewport(al, applet);
\r
48 alignPanel = new AlignmentPanel(this, viewport);
\r
50 alignPanel.validate();
\r
54 String treeFile = applet.getParameter("treeFile");
\r
55 if (treeFile != null)
\r
59 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
\r
60 getCodeBase() + treeFile, "URL");
\r
63 if (fin.getTree() != null)
\r
65 TreePanel tp = null;
\r
66 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
67 fin, "FromFile", applet.getCodeBase() + treeFile);
\r
68 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
\r
69 addTreeMenuItem(tp, treeFile);
\r
72 catch (Exception ex)
\r
74 ex.printStackTrace();
\r
78 String param = applet.getParameter("sortBy");
\r
81 if (param.equalsIgnoreCase("Id"))
\r
82 sortIDMenuItem_actionPerformed(null);
\r
83 else if (param.equalsIgnoreCase("Pairwise Identity"))
\r
84 sortPairwiseMenuItem_actionPerformed(null);
\r
87 param = applet.getParameter("wrap");
\r
90 if (param.equalsIgnoreCase("true"))
\r
92 wrapMenuItem.setState(true);
\r
93 wrapMenuItem_actionPerformed(null);
\r
99 param = applet.getParameter("windowWidth");
\r
102 int width = Integer.parseInt(param);
\r
103 NEW_WINDOW_WIDTH = width;
\r
105 param = applet.getParameter("windowHeight");
\r
108 int height = Integer.parseInt(param);
\r
109 NEW_WINDOW_HEIGHT = height;
\r
112 catch (Exception ex)
\r
117 this.addWindowListener(new WindowAdapter()
\r
119 public void windowClosing(WindowEvent e)
\r
121 closeMenuItem_actionPerformed(null);
\r
125 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
127 public void propertyChange(java.beans.PropertyChangeEvent evt)
\r
129 if (evt.getPropertyName().equals("alignment"))
\r
131 alignmentChanged();
\r
136 jalview.bin.JalviewLite.addFrame(this, title,
\r
138 NEW_WINDOW_HEIGHT);
\r
147 * @param String DOCUMENT ME!
\r
150 public void parseFeaturesFile(String file)
\r
154 URL url = new URL(file);
\r
156 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
\r
157 SequenceI seq = null;
\r
158 String line, type, desc, token;
\r
160 int index, start, end;
\r
161 StringTokenizer st;
\r
162 SequenceFeature sf;
\r
163 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
\r
165 while ( (line = in.readLine()) != null)
\r
168 st = new StringTokenizer(line, "\t");
\r
169 if (st.countTokens() == 2)
\r
171 type = st.nextToken();
\r
172 UserColourScheme ucs = new UserColourScheme(st.nextToken());
\r
173 fr.setColour(type, ucs.findColour("A"));
\r
177 while (st.hasMoreElements())
\r
179 desc = st.nextToken();
\r
180 token = st.nextToken();
\r
181 if (!token.equals("ID_NOT_SPECIFIED"))
\r
183 index = viewport.alignment.findIndex(viewport.alignment.findName(
\r
189 index = Integer.parseInt(st.nextToken());
\r
192 start = Integer.parseInt(st.nextToken());
\r
193 end = Integer.parseInt(st.nextToken());
\r
195 seq = viewport.alignment.getSequenceAt(index);
\r
196 start = seq.findIndex(start) - 1;
\r
197 end = seq.findIndex(end) - 1;
\r
199 type = st.nextToken();
\r
201 if(fr.getColour(type)==null)
\r
203 // Probably the old style groups file
\r
204 UserColourScheme ucs = new UserColourScheme(type);
\r
205 fr.setColour(type, ucs.findColour("A"));
\r
208 sf = new SequenceFeature(type, desc, "", start, end);
\r
210 seq.addSequenceFeature(sf);
\r
214 viewport.showSequenceFeatures = true;
\r
215 ((Alignment)viewport.alignment).featuresAdded = true;
\r
217 alignPanel.repaint();
\r
220 catch (Exception ex)
\r
222 System.out.println("Error parsing groups file: " + ex);
\r
227 public void inputText_actionPerformed(ActionEvent e)
\r
229 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
\r
230 Frame frame = new Frame();
\r
232 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
\r
235 protected void outputText_actionPerformed(ActionEvent e)
\r
237 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
\r
238 Frame frame = new Frame();
\r
240 jalview.bin.JalviewLite.addFrame(frame,
\r
241 "Alignment output - " + e.getActionCommand(),
\r
243 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
\r
244 viewport.getAlignment().getSequences(),
\r
245 viewport.showDBPrefix,
\r
246 viewport.showJVSuffix));
\r
249 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
251 PaintRefresher.components.remove(viewport.alignment);
\r
252 if(PaintRefresher.components.size()==0 && applet==null)
\r
256 Stack historyList = new Stack();
\r
257 Stack redoList = new Stack();
\r
259 void updateEditMenuBar()
\r
261 if (historyList.size() > 0)
\r
263 undoMenuItem.setEnabled(true);
\r
264 HistoryItem hi = (HistoryItem) historyList.peek();
\r
265 undoMenuItem.setLabel("Undo " + hi.getDescription());
\r
269 undoMenuItem.setEnabled(false);
\r
270 undoMenuItem.setLabel("Undo");
\r
273 if (redoList.size() > 0)
\r
275 redoMenuItem.setEnabled(true);
\r
276 HistoryItem hi = (HistoryItem) redoList.peek();
\r
277 redoMenuItem.setLabel("Redo " + hi.getDescription());
\r
281 redoMenuItem.setEnabled(false);
\r
282 redoMenuItem.setLabel("Redo");
\r
286 public void addHistoryItem(HistoryItem hi)
\r
288 historyList.push(hi);
\r
289 updateEditMenuBar();
\r
292 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
294 HistoryItem hi = (HistoryItem) historyList.pop();
\r
295 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
296 HistoryItem.HIDE));
\r
297 restoreHistoryItem(hi);
\r
298 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
301 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
303 HistoryItem hi = (HistoryItem) redoList.pop();
\r
304 restoreHistoryItem(hi);
\r
305 updateEditMenuBar();
\r
306 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
309 // used by undo and redo
\r
310 void restoreHistoryItem(HistoryItem hi)
\r
312 if (hi.getType() == HistoryItem.SORT)
\r
314 for (int i = 0; i < hi.getSequences().size(); i++)
\r
316 viewport.alignment.getSequences().setElementAt(hi.getSequences().
\r
322 for (int i = 0; i < hi.getSequences().size(); i++)
\r
324 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
\r
325 if (restore.getLength() == 0)
\r
327 // log.System.out.println(hi.getHidden().elementAt(i));
\r
328 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
329 viewport.alignment.getSequences().insertElementAt(
\r
331 hi.getAlignIndex(i));
\r
335 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
338 if (hi.getType() == HistoryItem.PASTE)
\r
340 for (int i = viewport.alignment.getHeight() - 1;
\r
341 i > hi.getSequences().size() - 1; i--)
\r
343 viewport.alignment.deleteSequence(i);
\r
348 updateEditMenuBar();
\r
350 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
353 public void moveSelectedSequences(boolean up)
\r
355 SequenceGroup sg = viewport.getSelectionGroup();
\r
363 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
365 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
366 if (!sg.sequences.contains(seq))
\r
371 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
372 if (sg.sequences.contains(temp))
\r
377 viewport.alignment.getSequences().setElementAt(temp, i);
\r
378 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
383 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
385 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
386 if (!sg.sequences.contains(seq))
\r
391 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
392 if (sg.sequences.contains(temp))
\r
397 viewport.alignment.getSequences().setElementAt(temp, i);
\r
398 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
402 alignPanel.repaint();
\r
405 StringBuffer copiedSequences;
\r
406 protected void copy_actionPerformed(ActionEvent e)
\r
408 if (viewport.getSelectionGroup() == null)
\r
413 SequenceGroup sg = viewport.getSelectionGroup();
\r
414 copiedSequences = new StringBuffer();
\r
415 Hashtable orderedSeqs = new Hashtable();
\r
416 for (int i = 0; i < sg.getSize(); i++)
\r
418 SequenceI seq = sg.getSequenceAt(i);
\r
419 int index = viewport.alignment.findIndex(seq);
\r
420 orderedSeqs.put(index + "", seq);
\r
423 int index = 0, startRes, endRes;
\r
426 for (int i = 0; i < sg.getSize(); i++)
\r
428 SequenceI seq = null;
\r
430 while (seq == null)
\r
432 if (orderedSeqs.containsKey(index + ""))
\r
434 seq = (SequenceI) orderedSeqs.get(index + "");
\r
446 //Returns residue following index if gap
\r
447 startRes = seq.findPosition(sg.getStartRes());
\r
450 //Need to find the residue preceeding index if gap
\r
453 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
\r
455 ch = seq.getCharAt(j);
\r
456 if (!jalview.util.Comparison.isGap( (ch)))
\r
464 endRes += seq.getStart() -1;
\r
467 copiedSequences.append(seq.getName() + "\t" +
\r
470 seq.getSequence(sg.getStartRes(),
\r
471 sg.getEndRes() + 1) + "\n");
\r
476 protected void pasteNew_actionPerformed(ActionEvent e)
\r
481 protected void pasteThis_actionPerformed(ActionEvent e)
\r
483 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
484 HistoryItem.PASTE));
\r
488 void paste(boolean newAlignment)
\r
492 if (copiedSequences == null)
\r
497 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
\r
498 Vector seqs = new Vector();
\r
499 while (st.hasMoreElements())
\r
501 String name = st.nextToken();
\r
502 int start = Integer.parseInt(st.nextToken());
\r
503 int end = Integer.parseInt(st.nextToken());
\r
504 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
\r
508 viewport.alignment.addSequence(sequence);
\r
512 seqs.addElement(sequence);
\r
518 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
519 for (int i = 0; i < seqs.size(); i++)
\r
521 newSeqs[i] = (SequenceI) seqs.elementAt(i);
\r
524 String newtitle = new String("Copied sequences");
\r
525 if (getTitle().startsWith("Copied sequences"))
\r
527 newtitle = getTitle();
\r
531 newtitle = newtitle.concat("- from " + getTitle());
\r
533 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
\r
535 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
536 NEW_WINDOW_HEIGHT);
\r
540 viewport.setEndSeq(viewport.alignment.getHeight());
\r
541 viewport.alignment.getWidth();
\r
542 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
546 catch (Exception ex)
\r
547 {} // could be anything being pasted in here
\r
551 protected void cut_actionPerformed(ActionEvent e)
\r
553 copy_actionPerformed(null);
\r
554 delete_actionPerformed(null);
\r
557 protected void delete_actionPerformed(ActionEvent e)
\r
559 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
560 HistoryItem.HIDE));
\r
561 if (viewport.getSelectionGroup() == null)
\r
567 SequenceGroup sg = viewport.getSelectionGroup();
\r
568 boolean allSequences = false;
\r
569 if(sg.sequences.size()==viewport.alignment.getHeight())
\r
570 allSequences = true;
\r
572 for (int i = 0; i < sg.sequences.size(); i++)
\r
574 SequenceI seq = sg.getSequenceAt(i);
\r
575 int index = viewport.getAlignment().findIndex(seq);
\r
576 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
578 // If the cut affects all sequences, remove highlighted columns
\r
581 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
582 sg.getEndRes() + 1);
\r
586 if (seq.getSequence().length() < 1)
\r
588 viewport.getAlignment().deleteSequence(seq);
\r
592 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
596 viewport.setSelectionGroup(null);
\r
597 viewport.alignment.deleteGroup(sg);
\r
598 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
\r
599 if (viewport.getAlignment().getHeight() < 1)
\r
603 this.setVisible(false);
\r
605 catch (Exception ex)
\r
608 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
612 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
614 viewport.alignment.deleteAllGroups();
\r
615 viewport.setSelectionGroup(null);
\r
617 alignPanel.repaint();
\r
620 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
622 SequenceGroup sg = new SequenceGroup();
\r
623 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
625 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
627 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
628 viewport.setSelectionGroup(sg);
\r
629 alignPanel.repaint();
\r
630 PaintRefresher.Refresh(null, viewport.alignment);
\r
633 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
635 viewport.setSelectionGroup(null);
\r
636 viewport.getColumnSelection().clear();
\r
637 viewport.setSelectionGroup(null);
\r
638 alignPanel.repaint();
\r
639 PaintRefresher.Refresh(null, viewport.alignment);
\r
642 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
644 SequenceGroup sg = viewport.getSelectionGroup();
\r
645 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
647 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
650 PaintRefresher.Refresh(null, viewport.alignment);
\r
653 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
655 ColumnSelection colSel = viewport.getColumnSelection();
\r
656 if (colSel.size() > 0)
\r
658 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
659 HistoryItem.HIDE));
\r
660 int min = colSel.getMin();
\r
661 viewport.getAlignment().trimLeft(min);
\r
662 colSel.compensateForEdit(0, min);
\r
664 if (viewport.getSelectionGroup() != null)
\r
666 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
669 Vector groups = viewport.alignment.getGroups();
\r
670 for (int i = 0; i < groups.size(); i++)
\r
672 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
673 if (!sg.adjustForRemoveLeft(min))
\r
675 viewport.alignment.deleteGroup(sg);
\r
678 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
682 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
684 ColumnSelection colSel = viewport.getColumnSelection();
\r
685 if (colSel.size() > 0)
\r
687 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
688 HistoryItem.HIDE));
\r
689 int max = colSel.getMax();
\r
690 viewport.getAlignment().trimRight(max);
\r
691 if (viewport.getSelectionGroup() != null)
\r
693 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
696 Vector groups = viewport.alignment.getGroups();
\r
697 for (int i = 0; i < groups.size(); i++)
\r
699 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
700 if (!sg.adjustForRemoveRight(max))
\r
702 viewport.alignment.deleteGroup(sg);
\r
705 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
710 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
712 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
713 viewport.alignment,
\r
714 HistoryItem.HIDE));
\r
716 //This is to maintain viewport position on first residue
\r
717 //of first sequence
\r
718 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
719 int startRes = seq.findPosition(viewport.startRes);
\r
721 viewport.getAlignment().removeGaps();
\r
723 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
725 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
728 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
730 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
731 HistoryItem.HIDE));
\r
733 //This is to maintain viewport position on first residue
\r
734 //of first sequence
\r
735 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
736 int startRes = seq.findPosition(viewport.startRes);
\r
743 int start=0, end = viewport.alignment.getWidth();
\r
745 if (viewport.getSelectionGroup() != null
\r
746 && viewport.getSelectionGroup().sequences != null
\r
747 && viewport.getSelectionGroup().sequences.size()>0)
\r
749 seqs = viewport.getSelectionGroup().sequences;
\r
750 start = viewport.getSelectionGroup().getStartRes();
\r
751 end = viewport.getSelectionGroup().getEndRes()+1;
\r
754 seqs = viewport.alignment.getSequences();
\r
756 for (int i = 0; i < seqs.size(); i++)
\r
758 current = (SequenceI) seqs.elementAt(i);
\r
759 jSize = current.getLength();
\r
761 // Removing a range is much quicker than removing gaps
\r
762 // one by one for long sequences
\r
764 int rangeStart=-1, rangeEnd=-1;
\r
768 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
785 current.deleteChars(rangeStart, rangeEnd);
\r
786 j-=rangeEnd-rangeStart;
\r
787 jSize-=rangeEnd-rangeStart;
\r
795 while (j < end && j < jSize);
\r
798 current.deleteChars(rangeStart, rangeEnd);
\r
801 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
802 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
805 public void alignmentChanged()
\r
807 viewport.updateConsensus();
\r
808 viewport.updateConservation ();
\r
809 resetAllColourSchemes();
\r
810 if(alignPanel.overviewPanel!=null)
\r
811 alignPanel.overviewPanel.updateOverviewImage();
\r
812 alignPanel.repaint();
\r
815 void resetAllColourSchemes()
\r
817 ColourSchemeI cs = viewport.globalColourScheme;
\r
820 if (cs instanceof ClustalxColourScheme)
\r
822 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
823 resetClustalX(viewport.alignment.getSequences(),
\r
824 viewport.alignment.getWidth());
\r
827 cs.setConsensus(viewport.vconsensus);
\r
828 if (cs.conservationApplied())
\r
830 Alignment al = (Alignment) viewport.alignment;
\r
831 Conservation c = new Conservation("All",
\r
832 ResidueProperties.propHash, 3,
\r
833 al.getSequences(), 0,
\r
834 al.getWidth() - 1);
\r
836 c.verdict(false, viewport.ConsPercGaps);
\r
838 cs.setConservation(c);
\r
842 int s, sSize = viewport.alignment.getGroups().size();
\r
843 for(s=0; s<sSize; s++)
\r
845 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
846 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
848 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
850 sg.recalcConservation();
\r
856 public void findMenuItem_actionPerformed(ActionEvent e)
\r
858 new Finder(alignPanel);
\r
861 public void font_actionPerformed(ActionEvent e)
\r
863 new FontChooser(alignPanel);
\r
866 public void dbref_actionPerformed(ItemEvent e)
\r
868 viewport.showDBPrefix = dbref.getState();
\r
869 alignPanel.fontChanged();
\r
870 alignPanel.repaint();
\r
873 public void seqLimits_itemStateChanged(ItemEvent e)
\r
875 viewport.setShowJVSuffix(seqLimits.getState());
\r
876 alignPanel.fontChanged();
\r
877 alignPanel.repaint();
\r
881 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
883 viewport.setColourText(colourTextMenuItem.getState());
\r
884 alignPanel.repaint();
\r
887 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
889 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
890 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
891 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
892 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
893 scaleRight.setEnabled(wrapMenuItem.getState());
\r
894 alignPanel.repaint();
\r
897 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
899 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
900 alignPanel.repaint();
\r
903 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
905 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
906 alignPanel.repaint();
\r
909 protected void scaleRight_actionPerformed(ActionEvent e)
\r
911 viewport.setScaleRightWrapped(scaleRight.getState());
\r
912 alignPanel.repaint();
\r
915 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
917 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
918 alignPanel.repaint();
\r
921 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
923 viewport.setShowText(viewTextMenuItem.getState());
\r
924 alignPanel.repaint();
\r
927 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
929 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
930 alignPanel.repaint();
\r
933 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
935 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
936 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
939 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
941 if (alignPanel.overviewPanel != null)
\r
946 Frame frame = new Frame();
\r
947 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
948 frame.add(overview);
\r
949 // +50 must allow for applet frame window
\r
950 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
951 overview.preferredSize().width,
\r
952 overview.preferredSize().height + 50);
\r
955 frame.addWindowListener(new WindowAdapter()
\r
957 public void windowClosing(WindowEvent e)
\r
959 alignPanel.setOverviewPanel(null);
\r
963 alignPanel.setOverviewPanel(overview);
\r
967 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
969 changeColour(null);
\r
972 public void clustalColour_actionPerformed(ActionEvent e)
\r
974 abovePIDThreshold.setState(false);
\r
975 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
976 viewport.alignment.getWidth()));
\r
979 public void zappoColour_actionPerformed(ActionEvent e)
\r
981 changeColour(new ZappoColourScheme());
\r
984 public void taylorColour_actionPerformed(ActionEvent e)
\r
986 changeColour(new TaylorColourScheme());
\r
989 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
991 changeColour(new HydrophobicColourScheme());
\r
994 public void helixColour_actionPerformed(ActionEvent e)
\r
996 changeColour(new HelixColourScheme());
\r
999 public void strandColour_actionPerformed(ActionEvent e)
\r
1001 changeColour(new StrandColourScheme());
\r
1004 public void turnColour_actionPerformed(ActionEvent e)
\r
1006 changeColour(new TurnColourScheme());
\r
1009 public void buriedColour_actionPerformed(ActionEvent e)
\r
1011 changeColour(new BuriedColourScheme());
\r
1014 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1016 changeColour(new NucleotideColourScheme());
\r
1019 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1021 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1024 void changeColour(ColourSchemeI cs)
\r
1026 int threshold = 0;
\r
1030 if (viewport.getAbovePIDThreshold())
\r
1032 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1034 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1036 viewport.setGlobalColourScheme(cs);
\r
1040 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1043 if (viewport.getConservationSelected())
\r
1046 Alignment al = (Alignment) viewport.alignment;
\r
1047 Conservation c = new Conservation("All",
\r
1048 ResidueProperties.propHash, 3,
\r
1049 al.getSequences(), 0,
\r
1050 al.getWidth() - 1);
\r
1053 c.verdict(false, viewport.ConsPercGaps);
\r
1055 cs.setConservation(c);
\r
1057 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1063 cs.setConservation(null);
\r
1066 cs.setConsensus(viewport.vconsensus);
\r
1069 viewport.setGlobalColourScheme(cs);
\r
1071 if (viewport.getColourAppliesToAllGroups())
\r
1073 Vector groups = viewport.alignment.getGroups();
\r
1074 for (int i = 0; i < groups.size(); i++)
\r
1076 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1083 if (cs instanceof ClustalxColourScheme)
\r
1085 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1091 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1093 catch (Exception ex)
\r
1095 ex.printStackTrace();
\r
1100 if (viewport.getAbovePIDThreshold()
\r
1101 || cs instanceof PIDColourScheme
\r
1102 || cs instanceof Blosum62ColourScheme)
\r
1104 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1105 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1108 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1110 if (viewport.getConservationSelected())
\r
1112 Conservation c = new Conservation("Group",
\r
1113 ResidueProperties.propHash, 3,
\r
1115 viewport.alignment.getWidth() - 1);
\r
1117 c.verdict(false, viewport.ConsPercGaps);
\r
1118 sg.cs.setConservation(c);
\r
1122 sg.cs.setConservation(null);
\r
1123 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1130 if (alignPanel.getOverviewPanel() != null)
\r
1132 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1135 alignPanel.repaint();
\r
1140 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1142 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1144 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1146 SliderPanel.showPIDSlider();
\r
1150 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1152 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1154 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1156 SliderPanel.showConservationSlider();
\r
1160 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1162 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1164 viewport.setAbovePIDThreshold(false);
\r
1165 abovePIDThreshold.setState(false);
\r
1167 changeColour(viewport.getGlobalColourScheme());
\r
1169 modifyConservation_actionPerformed(null);
\r
1172 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1174 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1176 conservationMenuItem.setState(false);
\r
1177 viewport.setConservationSelected(false);
\r
1179 changeColour(viewport.getGlobalColourScheme());
\r
1181 modifyPID_actionPerformed(null);
\r
1184 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1186 new UserDefinedColours(alignPanel, null);
\r
1189 public void PIDColour_actionPerformed(ActionEvent e)
\r
1191 changeColour(new PIDColourScheme());
\r
1194 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1196 changeColour(new Blosum62ColourScheme());
\r
1199 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1201 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1202 HistoryItem.SORT));
\r
1203 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1204 viewport.getAlignment().getSequenceAt(0));
\r
1205 alignPanel.repaint();
\r
1208 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1210 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1211 HistoryItem.SORT));
\r
1212 AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
\r
1213 alignPanel.repaint();
\r
1216 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1218 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1219 HistoryItem.SORT));
\r
1220 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1221 alignPanel.repaint();
\r
1225 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1227 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1228 Frame frame = new Frame();
\r
1230 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1235 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1237 if (viewport.getSelectionGroup().getSize() > 1)
\r
1239 Frame frame = new Frame();
\r
1240 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1241 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1245 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1247 //are the sequences aligned?
\r
1248 if (!viewport.alignment.isAligned())
\r
1250 SequenceI current;
\r
1251 int Width = viewport.getAlignment().getWidth();
\r
1253 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1256 current = viewport.getAlignment().getSequenceAt(i);
\r
1258 if (current.getLength() < Width)
\r
1260 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1263 alignPanel.repaint();
\r
1266 if ( (viewport.getSelectionGroup() != null &&
\r
1267 viewport.getSelectionGroup().getSize() < 4 &&
\r
1268 viewport.getSelectionGroup().getSize() > 0)
\r
1269 || viewport.getAlignment().getHeight() < 4)
\r
1276 new PCAPanel(viewport);
\r
1278 catch (java.lang.OutOfMemoryError ex)
\r
1284 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1286 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1289 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1291 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1294 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1296 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1299 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1301 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1304 void NewTreePanel(String type, String pwType, String title)
\r
1306 //are the sequences aligned?
\r
1307 if (!viewport.alignment.isAligned())
\r
1309 SequenceI current;
\r
1310 int Width = viewport.getAlignment().getWidth();
\r
1312 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1315 current = viewport.getAlignment().getSequenceAt(i);
\r
1317 if (current.getLength() < Width)
\r
1319 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1322 alignPanel.repaint();
\r
1326 final TreePanel tp;
\r
1327 if (viewport.getSelectionGroup() != null &&
\r
1328 viewport.getSelectionGroup().getSize() > 3)
\r
1330 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1332 0, viewport.alignment.getWidth());
\r
1336 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1337 type, pwType, 0, viewport.alignment.getWidth());
\r
1340 addTreeMenuItem(tp, title);
\r
1342 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1345 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1347 final MenuItem item = new MenuItem(title);
\r
1348 sortByTreeMenu.add(item);
\r
1349 item.addActionListener(new java.awt.event.ActionListener()
\r
1351 public void actionPerformed(ActionEvent e)
\r
1353 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1354 HistoryItem.SORT));
\r
1355 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1356 alignPanel.repaint();
\r
1360 treePanel.addWindowListener(new WindowAdapter()
\r
1362 public void windowClosing(WindowEvent e)
\r
1364 sortByTreeMenu.remove(item);
\r
1369 protected void documentation_actionPerformed(ActionEvent e)
\r
1371 showURL("http://www.jalview.org/help.html");
\r
1374 protected void about_actionPerformed(ActionEvent e)
\r
1377 class AboutPanel extends Canvas
\r
1380 public AboutPanel(String version)
\r
1381 { this.version = version; }
\r
1383 public void paint(Graphics g)
\r
1385 g.setColor(Color.white);
\r
1386 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1387 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1388 FontMetrics fm = g.getFontMetrics();
\r
1389 int fh = fm.getHeight();
\r
1391 g.setColor(Color.black);
\r
1392 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1393 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1394 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1395 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1397 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1400 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1402 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1403 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1405 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1409 String version = "test";
\r
1410 java.net.URL url = getClass().getResource("/.build_properties");
\r
1415 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1416 url.openStream()));
\r
1418 while ( (line = reader.readLine()) != null)
\r
1420 if (line.indexOf("VERSION") > -1)
\r
1422 version = line.substring(line.indexOf("=") + 1);
\r
1426 catch (Exception ex)
\r
1428 ex.printStackTrace();
\r
1433 Frame frame = new Frame();
\r
1434 frame.add(new AboutPanel(version));
\r
1435 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1440 * Displays the given URL in a new browser window
\r
1442 * @param url URL to display in browser window.
\r
1443 * <br>New window will be named "HELP_WINDOW"
\r
1445 public void showURL(String url)
\r
1447 showURL(url, "HELP");
\r
1450 public void showURL(String url, String target)
\r
1452 if (applet == null)
\r
1454 System.out.println("Not running as applet - no browser available.");
\r
1460 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1463 catch (Exception ex)
\r
1465 ex.printStackTrace();
\r