2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.appletgui;
26 import java.awt.event.*;
28 import jalview.analysis.*;
29 import jalview.commands.*;
30 import jalview.datamodel.*;
32 import jalview.schemes.*;
34 public class AlignFrame extends EmbmenuFrame implements ActionListener,
35 ItemListener, KeyListener
37 public AlignmentPanel alignPanel;
39 public AlignViewport viewport;
41 int DEFAULT_WIDTH = 700;
43 int DEFAULT_HEIGHT = 500;
45 String jalviewServletURL;
47 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
48 String title, boolean embedded)
53 jalviewServletURL = applet.getParameter("APPLICATION_URL");
59 } catch (Exception ex)
64 viewport = new AlignViewport(al, applet);
65 alignPanel = new AlignmentPanel(this, viewport);
67 viewport.updateConservation(alignPanel);
68 viewport.updateConsensus(alignPanel);
70 annotationPanelMenuItem.setState(viewport.showAnnotation);
72 seqLimits.setState(viewport.showJVSuffix);
76 String param = applet.getParameter("sortBy");
79 if (param.equalsIgnoreCase("Id"))
81 sortIDMenuItem_actionPerformed();
83 else if (param.equalsIgnoreCase("Pairwise Identity"))
85 sortPairwiseMenuItem_actionPerformed();
89 param = applet.getParameter("wrap");
92 if (param.equalsIgnoreCase("true"))
94 wrapMenuItem.setState(true);
95 wrapMenuItem_actionPerformed();
98 param = applet.getParameter("centrecolumnlabels");
101 centreColumnLabelFlag.setState(true);
102 centreColumnLabelFlag_stateChanged();
107 param = applet.getParameter("windowWidth");
110 int width = Integer.parseInt(param);
111 DEFAULT_WIDTH = width;
113 param = applet.getParameter("windowHeight");
116 int height = Integer.parseInt(param);
117 DEFAULT_HEIGHT = height;
119 } catch (Exception ex)
125 // Some JVMS send keyevents to Top frame or lowest panel,
126 // Havent worked out why yet. So add to both this frame and seqCanvas for
128 this.addKeyListener(this);
129 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
130 alignPanel.idPanel.idCanvas.addKeyListener(this);
131 alignPanel.scalePanel.addKeyListener(this);
132 alignPanel.annotationPanel.addKeyListener(this);
133 createAlignFrameWindow(embedded, title);
134 alignPanel.validate();
135 alignPanel.paintAlignment(true);
138 public AlignViewport getAlignViewport()
143 public SeqCanvas getSeqcanvas()
145 return alignPanel.seqPanel.seqCanvas;
155 public void parseFeaturesFile(String file, String type)
157 Hashtable featureLinks = new Hashtable();
158 boolean featuresFile = false;
161 featuresFile = new jalview.io.FeaturesFile(file, type).parse(
162 viewport.alignment, alignPanel.seqPanel.seqCanvas
163 .getFeatureRenderer().featureColours, featureLinks,
165 } catch (Exception ex)
167 ex.printStackTrace();
172 if (featureLinks.size() > 0)
174 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
176 viewport.showSequenceFeatures = true;
177 sequenceFeatures.setState(true);
178 alignPanel.paintAlignment(true);
183 public void keyPressed(KeyEvent evt)
185 if (viewport.cursorMode
186 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
187 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
188 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
189 && Character.isDigit(evt.getKeyChar()))
190 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
192 switch (evt.getKeyCode())
194 case 27: // escape key
195 deselectAllSequenceMenuItem_actionPerformed();
198 if (evt.isControlDown() || evt.isMetaDown())
200 cut_actionPerformed();
204 if (viewport.cursorMode && !evt.isControlDown())
206 alignPanel.seqPanel.setCursorColumn();
208 if (evt.isControlDown() || evt.isMetaDown())
210 copy_actionPerformed();
214 if (evt.isControlDown())
216 paste(evt.isShiftDown());
220 if (evt.isControlDown() || evt.isMetaDown())
222 selectAllSequenceMenuItem_actionPerformed();
225 case KeyEvent.VK_DOWN:
226 if (viewport.cursorMode)
228 alignPanel.seqPanel.moveCursor(0, 1);
232 moveSelectedSequences(false);
237 if (viewport.cursorMode)
239 alignPanel.seqPanel.moveCursor(0, -1);
243 moveSelectedSequences(true);
247 case KeyEvent.VK_LEFT:
248 if (evt.isAltDown() || !viewport.cursorMode)
249 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
251 alignPanel.seqPanel.moveCursor(-1, 0);
254 case KeyEvent.VK_RIGHT:
255 if (evt.isAltDown() || !viewport.cursorMode)
256 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
258 alignPanel.seqPanel.moveCursor(1, 0);
261 case KeyEvent.VK_SPACE:
262 if (viewport.cursorMode)
264 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
265 || evt.isShiftDown() || evt.isAltDown());
269 case KeyEvent.VK_DELETE:
270 case KeyEvent.VK_BACK_SPACE:
271 if (viewport.cursorMode)
273 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
274 || evt.isShiftDown() || evt.isAltDown());
278 cut_actionPerformed();
279 alignPanel.seqPanel.seqCanvas.repaint();
284 if (viewport.cursorMode)
286 alignPanel.seqPanel.setCursorRow();
290 if (viewport.cursorMode)
292 alignPanel.seqPanel.setCursorPosition();
296 case KeyEvent.VK_ENTER:
297 case KeyEvent.VK_COMMA:
298 if (viewport.cursorMode)
300 alignPanel.seqPanel.setCursorRowAndColumn();
305 if (viewport.cursorMode)
307 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
311 if (viewport.cursorMode)
313 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
318 viewport.cursorMode = !viewport.cursorMode;
319 statusBar.setText("Keyboard editing mode is "
320 + (viewport.cursorMode ? "on" : "off"));
321 if (viewport.cursorMode)
323 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
324 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
329 if (evt.isControlDown())
331 findMenuItem_actionPerformed();
337 boolean toggleSeqs = !evt.isControlDown();
338 boolean toggleCols = !evt.isShiftDown();
339 boolean hide = false;
340 SequenceGroup sg = viewport.getSelectionGroup();
344 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
347 viewport.hideAllSelectedSeqs();
349 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
351 viewport.showAllHiddenSeqs();
357 if (viewport.colSel.getSelected().size() > 0)
359 viewport.hideSelectedColumns();
362 viewport.selectionGroup = sg;
367 viewport.showAllHiddenColumns();
373 case KeyEvent.VK_PAGE_UP:
374 if (viewport.wrapAlignment)
376 alignPanel.scrollUp(true);
380 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
381 - viewport.endSeq + viewport.startSeq);
385 case KeyEvent.VK_PAGE_DOWN:
386 if (viewport.wrapAlignment)
388 alignPanel.scrollUp(false);
392 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
393 + viewport.endSeq - viewport.startSeq);
398 if (evt.isControlDown())
400 undoMenuItem_actionPerformed();
405 if (evt.isControlDown())
407 redoMenuItem_actionPerformed();
412 if (evt.isControlDown())
419 if (evt.isControlDown())
421 trimAlignment(false);
426 if (evt.isControlDown())
428 if (evt.isShiftDown())
430 this.removeAllGapsMenuItem_actionPerformed();
434 removeGappedColumnMenuItem_actionPerformed();
439 if (evt.isControlDown())
443 viewport.invertColumnSelection();
447 this.invertSequenceMenuItem_actionPerformed();
453 if (evt.isControlDown())
455 this.deleteGroups_actionPerformed();
460 if (evt.isControlDown())
467 alignPanel.paintAlignment(true);
470 public void keyReleased(KeyEvent evt)
474 public void keyTyped(KeyEvent evt)
478 public void itemStateChanged(ItemEvent evt)
480 if (evt.getSource() == colourTextMenuItem)
482 colourTextMenuItem_actionPerformed();
484 else if (evt.getSource() == wrapMenuItem)
486 wrapMenuItem_actionPerformed();
488 else if (evt.getSource() == scaleAbove)
490 viewport.setScaleAboveWrapped(scaleAbove.getState());
492 else if (evt.getSource() == scaleLeft)
494 viewport.setScaleLeftWrapped(scaleLeft.getState());
496 else if (evt.getSource() == scaleRight)
498 viewport.setScaleRightWrapped(scaleRight.getState());
500 else if (evt.getSource() == seqLimits)
502 seqLimits_itemStateChanged();
504 else if (evt.getSource() == viewBoxesMenuItem)
506 viewport.setShowBoxes(viewBoxesMenuItem.getState());
508 else if (evt.getSource() == viewTextMenuItem)
510 viewport.setShowText(viewTextMenuItem.getState());
512 else if (evt.getSource() == renderGapsMenuItem)
514 viewport.setRenderGaps(renderGapsMenuItem.getState());
516 else if (evt.getSource() == annotationPanelMenuItem)
518 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
519 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
521 else if (evt.getSource() == sequenceFeatures)
523 viewport.showSequenceFeatures(sequenceFeatures.getState());
524 alignPanel.seqPanel.seqCanvas.repaint();
526 else if (evt.getSource() == conservationMenuItem)
528 conservationMenuItem_actionPerformed();
530 else if (evt.getSource() == abovePIDThreshold)
532 abovePIDThreshold_actionPerformed();
534 else if (evt.getSource() == applyToAllGroups)
536 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
538 else if (evt.getSource() == autoCalculate)
540 viewport.autocalculateConsensus = autoCalculate.getState();
542 else if (evt.getSource() == this.centreColumnLabelFlag)
544 centreColumnLabelFlag_stateChanged();
545 } else if (evt.getSource() == this.followMouseOverFlag)
547 mouseOverFlag_stateChanged();
550 alignPanel.paintAlignment(true);
553 private void mouseOverFlag_stateChanged()
555 viewport.followHighlight = followMouseOverFlag.getState();
556 // TODO: could kick the scrollTo mechanism to reset view for current searchresults.
559 private void centreColumnLabelFlag_stateChanged()
561 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
562 this.alignPanel.annotationPanel.repaint();
565 public void actionPerformed(ActionEvent evt)
567 Object source = evt.getSource();
569 if (source == inputText)
571 inputText_actionPerformed();
573 else if (source == loadTree)
575 loadTree_actionPerformed();
577 else if (source == loadApplication)
579 launchFullApplication();
581 else if (source == loadAnnotations)
585 else if (source == outputAnnotations)
587 outputAnnotations(true);
589 else if (source == outputFeatures)
591 outputFeatures(true, "Jalview");
593 else if (source == closeMenuItem)
595 closeMenuItem_actionPerformed();
597 else if (source == copy)
599 copy_actionPerformed();
601 else if (source == undoMenuItem)
603 undoMenuItem_actionPerformed();
605 else if (source == redoMenuItem)
607 redoMenuItem_actionPerformed();
609 else if (source == inputText)
611 inputText_actionPerformed();
613 else if (source == closeMenuItem)
615 closeMenuItem_actionPerformed();
617 else if (source == undoMenuItem)
619 undoMenuItem_actionPerformed();
621 else if (source == redoMenuItem)
623 redoMenuItem_actionPerformed();
625 else if (source == copy)
627 copy_actionPerformed();
629 else if (source == pasteNew)
631 pasteNew_actionPerformed();
633 else if (source == pasteThis)
635 pasteThis_actionPerformed();
637 else if (source == cut)
639 cut_actionPerformed();
641 else if (source == delete)
643 delete_actionPerformed();
645 else if (source == deleteGroups)
647 deleteGroups_actionPerformed();
649 else if (source == selectAllSequenceMenuItem)
651 selectAllSequenceMenuItem_actionPerformed();
653 else if (source == deselectAllSequenceMenuItem)
655 deselectAllSequenceMenuItem_actionPerformed();
657 else if (source == invertSequenceMenuItem)
659 invertSequenceMenuItem_actionPerformed();
661 else if (source == invertColSel)
663 viewport.invertColumnSelection();
664 alignPanel.paintAlignment(true);
666 else if (source == remove2LeftMenuItem)
670 else if (source == remove2RightMenuItem)
672 trimAlignment(false);
674 else if (source == removeGappedColumnMenuItem)
676 removeGappedColumnMenuItem_actionPerformed();
678 else if (source == removeAllGapsMenuItem)
680 removeAllGapsMenuItem_actionPerformed();
682 else if (source == findMenuItem)
684 findMenuItem_actionPerformed();
686 else if (source == font)
688 new FontChooser(alignPanel);
690 else if (source == newView)
694 else if (source == showColumns)
696 viewport.showAllHiddenColumns();
697 alignPanel.paintAlignment(true);
699 else if (source == showSeqs)
701 viewport.showAllHiddenSeqs();
703 else if (source == hideColumns)
705 viewport.hideSelectedColumns();
706 alignPanel.paintAlignment(true);
708 else if (source == hideSequences
709 && viewport.getSelectionGroup() != null)
711 viewport.hideAllSelectedSeqs();
713 else if (source == featureSettings)
715 new FeatureSettings(alignPanel);
717 else if (source == alProperties)
719 StringBuffer contents = new StringBuffer();
722 int min = Integer.MAX_VALUE, max = 0;
723 for (int i = 0; i < viewport.alignment.getHeight(); i++)
725 int size = viewport.alignment.getSequenceAt(i).getEnd()
726 - viewport.alignment.getSequenceAt(i).getStart();
733 avg = avg / (float) viewport.alignment.getHeight();
735 contents.append("\nSequences: " + viewport.alignment.getHeight());
736 contents.append("\nMinimum Sequence Length: " + min);
737 contents.append("\nMaximum Sequence Length: " + max);
738 contents.append("\nAverage Length: " + (int) avg);
740 if (((Alignment) viewport.alignment).alignmentProperties != null)
742 Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
743 Enumeration en = props.keys();
744 while (en.hasMoreElements())
746 String key = en.nextElement().toString();
747 contents.append("\n" + key + "\t" + props.get(key));
751 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
752 cap.setText(contents.toString());
753 Frame frame = new Frame();
755 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
756 + getTitle(), 400, 250);
758 else if (source == overviewMenuItem)
760 overviewMenuItem_actionPerformed();
762 else if (source == noColourmenuItem)
766 else if (source == clustalColour)
768 abovePIDThreshold.setState(false);
769 changeColour(new ClustalxColourScheme(viewport.alignment
770 .getSequences(), viewport.alignment.getWidth()));
772 else if (source == zappoColour)
774 changeColour(new ZappoColourScheme());
776 else if (source == taylorColour)
778 changeColour(new TaylorColourScheme());
780 else if (source == hydrophobicityColour)
782 changeColour(new HydrophobicColourScheme());
784 else if (source == helixColour)
786 changeColour(new HelixColourScheme());
788 else if (source == strandColour)
790 changeColour(new StrandColourScheme());
792 else if (source == turnColour)
794 changeColour(new TurnColourScheme());
796 else if (source == buriedColour)
798 changeColour(new BuriedColourScheme());
800 else if (source == nucleotideColour)
802 changeColour(new NucleotideColourScheme());
804 else if (source == modifyPID)
806 modifyPID_actionPerformed();
808 else if (source == modifyConservation)
810 modifyConservation_actionPerformed();
812 else if (source == userDefinedColour)
814 new UserDefinedColours(alignPanel, null);
816 else if (source == PIDColour)
818 changeColour(new PIDColourScheme());
820 else if (source == BLOSUM62Colour)
822 changeColour(new Blosum62ColourScheme());
824 else if (source == annotationColour)
826 new AnnotationColourChooser(viewport, alignPanel);
828 else if (source == sortPairwiseMenuItem)
830 sortPairwiseMenuItem_actionPerformed();
832 else if (source == sortIDMenuItem)
834 sortIDMenuItem_actionPerformed();
836 else if (source == sortGroupMenuItem)
838 sortGroupMenuItem_actionPerformed();
840 else if (source == removeRedundancyMenuItem)
842 removeRedundancyMenuItem_actionPerformed();
844 else if (source == pairwiseAlignmentMenuItem)
846 pairwiseAlignmentMenuItem_actionPerformed();
848 else if (source == PCAMenuItem)
850 PCAMenuItem_actionPerformed();
852 else if (source == averageDistanceTreeMenuItem)
854 averageDistanceTreeMenuItem_actionPerformed();
856 else if (source == neighbourTreeMenuItem)
858 neighbourTreeMenuItem_actionPerformed();
860 else if (source == njTreeBlosumMenuItem)
862 njTreeBlosumMenuItem_actionPerformed();
864 else if (source == avDistanceTreeBlosumMenuItem)
866 avTreeBlosumMenuItem_actionPerformed();
868 else if (source == documentation)
870 documentation_actionPerformed();
872 else if (source == about)
874 about_actionPerformed();
879 public void inputText_actionPerformed()
881 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
882 Frame frame = new Frame();
884 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
887 protected void outputText_actionPerformed(ActionEvent e)
889 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
890 Frame frame = new Frame();
892 jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
893 + e.getActionCommand(), 600, 500);
894 cap.setText(new AppletFormatAdapter().formatSequences(e
895 .getActionCommand(), viewport.getAlignment(),
896 viewport.showJVSuffix));
899 public void loadAnnotations()
901 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
902 cap.setText("Paste your features / annotations file here.");
903 cap.setAnnotationImport();
904 Frame frame = new Frame();
906 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
910 public String outputAnnotations(boolean displayTextbox)
912 String annotation = new AnnotationFile().printAnnotations(
913 viewport.showAnnotation ? viewport.alignment
914 .getAlignmentAnnotation() : null, viewport.alignment
916 ((Alignment) viewport.alignment).alignmentProperties);
920 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
921 Frame frame = new Frame();
923 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
924 cap.setText(annotation);
930 public String outputFeatures(boolean displayTextbox, String format)
933 if (format.equalsIgnoreCase("Jalview"))
935 features = new FeaturesFile().printJalviewFormat(viewport.alignment
936 .getSequencesArray(), viewport.featuresDisplayed);
940 features = new FeaturesFile().printGFFFormat(viewport.alignment
941 .getSequencesArray(), viewport.featuresDisplayed);
946 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
947 Frame frame = new Frame();
949 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
951 cap.setText(features);
957 void launchFullApplication()
959 StringBuffer url = new StringBuffer(jalviewServletURL);
962 + appendProtocol(viewport.applet.getParameter("file")));
964 if (viewport.applet.getParameter("features") != null)
966 url.append("&features=");
967 url.append(appendProtocol(viewport.applet.getParameter("features")));
970 if (viewport.applet.getParameter("annotations") != null)
972 url.append("&annotations=");
974 .append(appendProtocol(viewport.applet
975 .getParameter("annotations")));
978 if (viewport.applet.getParameter("jnetfile") != null)
980 url.append("&annotations=");
981 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
984 if (viewport.applet.getParameter("defaultColour") != null)
986 url.append("&colour="
987 + removeWhiteSpace(viewport.applet
988 .getParameter("defaultColour")));
991 if (viewport.applet.getParameter("userDefinedColour") != null)
993 url.append("&colour="
994 + removeWhiteSpace(viewport.applet
995 .getParameter("userDefinedColour")));
997 if (viewport.applet.getParameter("tree") != null)
1000 + appendProtocol(viewport.applet.getParameter("tree")));
1002 if (viewport.applet.getParameter("treeFile") != null)
1005 + appendProtocol(viewport.applet.getParameter("treeFile")));
1008 showURL(url.toString(), "FULL_APP");
1011 String removeWhiteSpace(String colour)
1013 StringBuffer sb = new StringBuffer();
1014 for (int i = 0; i < colour.length(); i++)
1016 if (Character.isWhitespace(colour.charAt(i)))
1022 sb.append(colour.charAt(i));
1026 return sb.toString();
1029 String appendProtocol(String url)
1034 url = URLEncoder.encode(url);
1037 * When we finally deprecate 1.1 compatibility, we can start to use
1038 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1039 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1040 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1041 * ex.printStackTrace(); }
1043 catch (java.net.MalformedURLException ex)
1045 url = viewport.applet.getCodeBase() + url;
1050 public void closeMenuItem_actionPerformed()
1052 PaintRefresher.RemoveComponent(alignPanel);
1053 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1054 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1056 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1067 void updateEditMenuBar()
1070 if (viewport.historyList.size() > 0)
1072 undoMenuItem.setEnabled(true);
1073 CommandI command = (CommandI) viewport.historyList.peek();
1074 undoMenuItem.setLabel("Undo " + command.getDescription());
1078 undoMenuItem.setEnabled(false);
1079 undoMenuItem.setLabel("Undo");
1082 if (viewport.redoList.size() > 0)
1084 redoMenuItem.setEnabled(true);
1086 CommandI command = (CommandI) viewport.redoList.peek();
1087 redoMenuItem.setLabel("Redo " + command.getDescription());
1091 redoMenuItem.setEnabled(false);
1092 redoMenuItem.setLabel("Redo");
1096 public void addHistoryItem(CommandI command)
1098 if (command.getSize() > 0)
1100 viewport.historyList.push(command);
1101 viewport.redoList.removeAllElements();
1102 updateEditMenuBar();
1103 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1113 protected void undoMenuItem_actionPerformed()
1115 if (viewport.historyList.size() < 1)
1120 CommandI command = (CommandI) viewport.historyList.pop();
1121 viewport.redoList.push(command);
1122 command.undoCommand(null);
1124 AlignViewport originalSource = getOriginatingSource(command);
1126 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1127 updateEditMenuBar();
1128 originalSource.firePropertyChange("alignment", null,
1129 originalSource.alignment.getSequences());
1138 protected void redoMenuItem_actionPerformed()
1140 if (viewport.redoList.size() < 1)
1145 CommandI command = (CommandI) viewport.redoList.pop();
1146 viewport.historyList.push(command);
1147 command.doCommand(null);
1149 AlignViewport originalSource = getOriginatingSource(command);
1150 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1152 updateEditMenuBar();
1153 originalSource.firePropertyChange("alignment", null,
1154 originalSource.alignment.getSequences());
1157 AlignViewport getOriginatingSource(CommandI command)
1159 AlignViewport originalSource = null;
1160 // For sequence removal and addition, we need to fire
1161 // the property change event FROM the viewport where the
1162 // original alignment was altered
1163 AlignmentI al = null;
1164 if (command instanceof EditCommand)
1166 EditCommand editCommand = (EditCommand) command;
1167 al = editCommand.getAlignment();
1168 Vector comps = (Vector) PaintRefresher.components.get(viewport
1169 .getSequenceSetId());
1170 for (int i = 0; i < comps.size(); i++)
1172 if (comps.elementAt(i) instanceof AlignmentPanel)
1174 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1176 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1183 if (originalSource == null)
1185 // The original view is closed, we must validate
1186 // the current view against the closed view first
1189 PaintRefresher.validateSequences(al, viewport.alignment);
1192 originalSource = viewport;
1195 return originalSource;
1198 public void moveSelectedSequences(boolean up)
1200 SequenceGroup sg = viewport.getSelectionGroup();
1208 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1210 SequenceI seq = viewport.alignment.getSequenceAt(i);
1211 if (!sg.getSequences(null).contains(seq))
1216 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1217 if (sg.getSequences(null).contains(temp))
1222 viewport.alignment.getSequences().setElementAt(temp, i);
1223 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1228 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1230 SequenceI seq = viewport.alignment.getSequenceAt(i);
1231 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1236 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1237 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1242 viewport.alignment.getSequences().setElementAt(temp, i);
1243 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1247 alignPanel.paintAlignment(true);
1250 synchronized void slideSequences(boolean right, int size)
1252 Vector sg = new Vector();
1253 if (viewport.cursorMode)
1255 sg.addElement(viewport.alignment
1256 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1258 else if (viewport.getSelectionGroup() != null
1259 && viewport.getSelectionGroup().getSize() != viewport.alignment
1262 sg = viewport.getSelectionGroup().getSequences(
1263 viewport.hiddenRepSequences);
1271 Vector invertGroup = new Vector();
1273 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1275 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1276 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1279 SequenceI[] seqs1 = new SequenceI[sg.size()];
1280 for (int i = 0; i < sg.size(); i++)
1281 seqs1[i] = (SequenceI) sg.elementAt(i);
1283 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1284 for (int i = 0; i < invertGroup.size(); i++)
1285 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1287 SlideSequencesCommand ssc;
1289 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1290 size, viewport.getGapCharacter());
1292 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1293 size, viewport.getGapCharacter());
1295 int groupAdjustment = 0;
1296 if (ssc.getGapsInsertedBegin() && right)
1298 if (viewport.cursorMode)
1299 alignPanel.seqPanel.moveCursor(size, 0);
1301 groupAdjustment = size;
1303 else if (!ssc.getGapsInsertedBegin() && !right)
1305 if (viewport.cursorMode)
1306 alignPanel.seqPanel.moveCursor(-size, 0);
1308 groupAdjustment = -size;
1311 if (groupAdjustment != 0)
1313 viewport.getSelectionGroup().setStartRes(
1314 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1315 viewport.getSelectionGroup().setEndRes(
1316 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1319 boolean appendHistoryItem = false;
1320 if (viewport.historyList != null && viewport.historyList.size() > 0
1321 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1323 appendHistoryItem = ssc
1324 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1328 if (!appendHistoryItem)
1329 addHistoryItem(ssc);
1334 static StringBuffer copiedSequences;
1336 static Vector copiedHiddenColumns;
1338 protected void copy_actionPerformed()
1340 if (viewport.getSelectionGroup() == null)
1345 SequenceGroup sg = viewport.getSelectionGroup();
1346 copiedSequences = new StringBuffer();
1347 Hashtable orderedSeqs = new Hashtable();
1348 for (int i = 0; i < sg.getSize(); i++)
1350 SequenceI seq = sg.getSequenceAt(i);
1351 int index = viewport.alignment.findIndex(seq);
1352 orderedSeqs.put(index + "", seq);
1355 int index = 0, startRes, endRes;
1358 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1360 copiedHiddenColumns = new Vector();
1361 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1362 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1365 int[] region = (int[]) viewport.getColumnSelection()
1366 .getHiddenColumns().elementAt(i);
1368 copiedHiddenColumns.addElement(new int[]
1369 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1374 copiedHiddenColumns = null;
1377 for (int i = 0; i < sg.getSize(); i++)
1379 SequenceI seq = null;
1383 if (orderedSeqs.containsKey(index + ""))
1385 seq = (SequenceI) orderedSeqs.get(index + "");
1397 // Returns residue following index if gap
1398 startRes = seq.findPosition(sg.getStartRes());
1401 // Need to find the residue preceeding index if gap
1404 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1406 ch = seq.getCharAt(j);
1407 if (!jalview.util.Comparison.isGap((ch)))
1415 endRes += seq.getStart() - 1;
1418 copiedSequences.append(seq.getName()
1424 + seq.getSequenceAsString(sg.getStartRes(),
1425 sg.getEndRes() + 1) + "\n");
1430 protected void pasteNew_actionPerformed()
1435 protected void pasteThis_actionPerformed()
1440 void paste(boolean newAlignment)
1445 if (copiedSequences == null)
1450 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1451 Vector seqs = new Vector();
1452 while (st.hasMoreElements())
1454 String name = st.nextToken();
1455 int start = Integer.parseInt(st.nextToken());
1456 int end = Integer.parseInt(st.nextToken());
1457 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1459 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1460 for (int i = 0; i < seqs.size(); i++)
1462 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1467 String newtitle = new String("Copied sequences");
1468 if (getTitle().startsWith("Copied sequences"))
1470 newtitle = getTitle();
1474 newtitle = newtitle.concat("- from " + getTitle());
1476 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1477 viewport.applet, newtitle, false);
1478 if (copiedHiddenColumns != null)
1480 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1482 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1483 af.viewport.hideColumns(region[0], region[1]);
1487 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1492 addSequences(newSeqs);
1495 } catch (Exception ex)
1497 } // could be anything being pasted in here
1501 void addSequences(SequenceI[] seqs)
1503 for (int i = 0; i < seqs.length; i++)
1505 viewport.alignment.addSequence(seqs[i]);
1509 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1510 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1512 viewport.setEndSeq(viewport.alignment.getHeight());
1513 viewport.alignment.getWidth();
1514 viewport.firePropertyChange("alignment", null, viewport.alignment
1519 protected void cut_actionPerformed()
1521 copy_actionPerformed();
1522 delete_actionPerformed();
1525 protected void delete_actionPerformed()
1528 SequenceGroup sg = viewport.getSelectionGroup();
1534 Vector seqs = new Vector();
1536 for (int i = 0; i < sg.getSize(); i++)
1538 seq = sg.getSequenceAt(i);
1539 seqs.addElement(seq);
1542 // If the cut affects all sequences, remove highlighted columns
1543 if (sg.getSize() == viewport.alignment.getHeight())
1545 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1546 sg.getEndRes() + 1);
1549 SequenceI[] cut = new SequenceI[seqs.size()];
1550 for (int i = 0; i < seqs.size(); i++)
1552 cut[i] = (SequenceI) seqs.elementAt(i);
1556 * //ADD HISTORY ITEM
1558 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1559 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1560 viewport.alignment));
1562 viewport.setSelectionGroup(null);
1563 viewport.alignment.deleteGroup(sg);
1565 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1568 if (viewport.getAlignment().getHeight() < 1)
1570 this.setVisible(false);
1574 protected void deleteGroups_actionPerformed()
1576 viewport.alignment.deleteAllGroups();
1577 viewport.sequenceColours = null;
1578 viewport.setSelectionGroup(null);
1580 alignPanel.paintAlignment(true);
1583 public void selectAllSequenceMenuItem_actionPerformed()
1585 SequenceGroup sg = new SequenceGroup();
1586 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1588 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1590 sg.setEndRes(viewport.alignment.getWidth() - 1);
1591 viewport.setSelectionGroup(sg);
1592 alignPanel.paintAlignment(true);
1593 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1596 public void deselectAllSequenceMenuItem_actionPerformed()
1598 if (viewport.cursorMode)
1600 alignPanel.seqPanel.keyboardNo1 = null;
1601 alignPanel.seqPanel.keyboardNo2 = null;
1603 viewport.setSelectionGroup(null);
1604 viewport.getColumnSelection().clear();
1605 viewport.setSelectionGroup(null);
1606 alignPanel.idPanel.idCanvas.searchResults = null;
1607 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1608 alignPanel.paintAlignment(true);
1609 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1612 public void invertSequenceMenuItem_actionPerformed()
1614 SequenceGroup sg = viewport.getSelectionGroup();
1615 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1617 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1620 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1623 void trimAlignment(boolean trimLeft)
1625 ColumnSelection colSel = viewport.getColumnSelection();
1628 if (colSel.size() > 0)
1632 column = colSel.getMin();
1636 column = colSel.getMax();
1640 if (viewport.getSelectionGroup() != null)
1642 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1643 viewport.hiddenRepSequences);
1647 seqs = viewport.alignment.getSequencesArray();
1650 TrimRegionCommand trimRegion;
1653 trimRegion = new TrimRegionCommand("Remove Left",
1654 TrimRegionCommand.TRIM_LEFT, seqs, column,
1655 viewport.alignment, viewport.colSel,
1656 viewport.selectionGroup);
1657 viewport.setStartRes(0);
1661 trimRegion = new TrimRegionCommand("Remove Right",
1662 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1663 viewport.alignment, viewport.colSel,
1664 viewport.selectionGroup);
1667 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1669 addHistoryItem(trimRegion);
1671 Vector groups = viewport.alignment.getGroups();
1673 for (int i = 0; i < groups.size(); i++)
1675 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1677 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1678 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1680 viewport.alignment.deleteGroup(sg);
1684 viewport.firePropertyChange("alignment", null, viewport
1685 .getAlignment().getSequences());
1689 public void removeGappedColumnMenuItem_actionPerformed()
1691 int start = 0, end = viewport.alignment.getWidth() - 1;
1694 if (viewport.getSelectionGroup() != null)
1696 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1697 viewport.hiddenRepSequences);
1698 start = viewport.getSelectionGroup().getStartRes();
1699 end = viewport.getSelectionGroup().getEndRes();
1703 seqs = viewport.alignment.getSequencesArray();
1706 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1707 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1709 addHistoryItem(removeGapCols);
1711 statusBar.setText("Removed " + removeGapCols.getSize()
1712 + " empty columns.");
1714 // This is to maintain viewport position on first residue
1715 // of first sequence
1716 SequenceI seq = viewport.alignment.getSequenceAt(0);
1717 int startRes = seq.findPosition(viewport.startRes);
1718 // ShiftList shifts;
1719 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1720 // edit.alColumnChanges=shifts.getInverse();
1721 // if (viewport.hasHiddenColumns)
1722 // viewport.getColumnSelection().compensateForEdits(shifts);
1723 viewport.setStartRes(seq.findIndex(startRes) - 1);
1724 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1729 public void removeAllGapsMenuItem_actionPerformed()
1731 int start = 0, end = viewport.alignment.getWidth() - 1;
1734 if (viewport.getSelectionGroup() != null)
1736 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1737 viewport.hiddenRepSequences);
1738 start = viewport.getSelectionGroup().getStartRes();
1739 end = viewport.getSelectionGroup().getEndRes();
1743 seqs = viewport.alignment.getSequencesArray();
1746 // This is to maintain viewport position on first residue
1747 // of first sequence
1748 SequenceI seq = viewport.alignment.getSequenceAt(0);
1749 int startRes = seq.findPosition(viewport.startRes);
1751 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1752 viewport.alignment));
1754 viewport.setStartRes(seq.findIndex(startRes) - 1);
1756 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1761 public void findMenuItem_actionPerformed()
1763 new Finder(alignPanel);
1767 * create a new view derived from the current view
1770 * @return frame for the new view
1772 public AlignFrame newView(String viewtitle)
1775 if (viewport.hasHiddenRows)
1777 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1778 .getFullAlignment().getSequencesArray());
1782 newal = new Alignment(viewport.alignment.getSequencesArray());
1785 if (viewport.alignment.getAlignmentAnnotation() != null)
1787 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
1789 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
1792 .addAnnotation(viewport.alignment
1793 .getAlignmentAnnotation()[i]);
1798 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
1800 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
1801 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
1802 PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
1803 .getSequenceSetId());
1805 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
1806 newaf.alignPanel.av.getSequenceSetId());
1807 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
1808 newaf.alignPanel.av.getSequenceSetId());
1810 Vector comps = (Vector) PaintRefresher.components.get(viewport
1811 .getSequenceSetId());
1813 for (int i = 0; i < comps.size(); i++)
1815 if (comps.elementAt(i) instanceof AlignmentPanel)
1821 String title = new String(this.getTitle());
1822 if (viewtitle != null)
1824 title = viewtitle + " ( " + title + ")";
1828 if (title.indexOf("(View") > -1)
1830 title = title.substring(0, title.indexOf("(View"));
1832 title += "(View " + viewSize + ")";
1835 newaf.setTitle(title.toString());
1837 newaf.viewport.historyList = viewport.historyList;
1838 newaf.viewport.redoList = viewport.redoList;
1844 * @return list of feature groups on the view
1846 public String[] getFeatureGroups()
1848 FeatureRenderer fr = null;
1849 if (alignPanel != null
1850 && (fr = alignPanel.getFeatureRenderer()) != null)
1852 return fr.getGroups();
1858 * get sequence feature groups that are hidden or shown
1864 public String[] getFeatureGroupsOfState(boolean visible)
1866 FeatureRenderer fr = null;
1867 if (alignPanel != null
1868 && (fr = alignPanel.getFeatureRenderer()) != null)
1870 return fr.getGroups(visible);
1876 * Change the display state for the given feature groups
1879 * list of group strings
1881 * visible or invisible
1883 public void setFeatureGroupState(String[] groups, boolean state)
1885 FeatureRenderer fr = null;
1886 this.sequenceFeatures.setState(true);
1887 viewport.showSequenceFeatures(true);
1888 if (alignPanel != null
1889 && (fr = alignPanel.getFeatureRenderer()) != null)
1891 fr.setGroupState(groups, state);
1892 alignPanel.seqPanel.seqCanvas.repaint();
1893 if (alignPanel.overviewPanel != null)
1895 alignPanel.overviewPanel.updateOverviewImage();
1900 public void seqLimits_itemStateChanged()
1902 viewport.setShowJVSuffix(seqLimits.getState());
1903 alignPanel.fontChanged();
1904 alignPanel.paintAlignment(true);
1907 protected void colourTextMenuItem_actionPerformed()
1909 viewport.setColourText(colourTextMenuItem.getState());
1910 alignPanel.paintAlignment(true);
1913 protected void wrapMenuItem_actionPerformed()
1915 viewport.setWrapAlignment(wrapMenuItem.getState());
1916 alignPanel.setWrapAlignment(wrapMenuItem.getState());
1917 scaleAbove.setEnabled(wrapMenuItem.getState());
1918 scaleLeft.setEnabled(wrapMenuItem.getState());
1919 scaleRight.setEnabled(wrapMenuItem.getState());
1920 alignPanel.paintAlignment(true);
1923 public void overviewMenuItem_actionPerformed()
1925 if (alignPanel.overviewPanel != null)
1930 Frame frame = new Frame();
1931 OverviewPanel overview = new OverviewPanel(alignPanel);
1932 frame.add(overview);
1933 // +50 must allow for applet frame window
1934 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
1935 overview.getPreferredSize().width,
1936 overview.getPreferredSize().height + 50);
1939 frame.addWindowListener(new WindowAdapter()
1941 public void windowClosing(WindowEvent e)
1943 alignPanel.setOverviewPanel(null);
1947 alignPanel.setOverviewPanel(overview);
1951 void changeColour(ColourSchemeI cs)
1957 if (viewport.getAbovePIDThreshold())
1959 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
1962 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1964 viewport.setGlobalColourScheme(cs);
1968 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1971 if (viewport.getConservationSelected())
1974 Alignment al = (Alignment) viewport.alignment;
1975 Conservation c = new Conservation("All",
1976 ResidueProperties.propHash, 3, al.getSequences(), 0, al
1980 c.verdict(false, viewport.ConsPercGaps);
1982 cs.setConservation(c);
1984 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
1990 cs.setConservation(null);
1993 cs.setConsensus(viewport.hconsensus);
1996 viewport.setGlobalColourScheme(cs);
1998 if (viewport.getColourAppliesToAllGroups())
2000 Vector groups = viewport.alignment.getGroups();
2001 for (int i = 0; i < groups.size(); i++)
2003 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2010 if (cs instanceof ClustalxColourScheme)
2012 sg.cs = new ClustalxColourScheme(sg
2013 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2019 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2020 } catch (Exception ex)
2022 ex.printStackTrace();
2027 if (viewport.getAbovePIDThreshold()
2028 || cs instanceof PIDColourScheme
2029 || cs instanceof Blosum62ColourScheme)
2031 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2032 sg.cs.setConsensus(AAFrequency.calculate(sg
2033 .getSequences(viewport.hiddenRepSequences), 0, sg
2038 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2041 if (viewport.getConservationSelected())
2043 Conservation c = new Conservation("Group",
2044 ResidueProperties.propHash, 3, sg
2045 .getSequences(viewport.hiddenRepSequences), 0,
2046 viewport.alignment.getWidth() - 1);
2048 c.verdict(false, viewport.ConsPercGaps);
2049 sg.cs.setConservation(c);
2053 sg.cs.setConservation(null);
2054 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2060 if (alignPanel.getOverviewPanel() != null)
2062 alignPanel.getOverviewPanel().updateOverviewImage();
2065 jalview.structure.StructureSelectionManager
2066 .getStructureSelectionManager().sequenceColoursChanged(
2069 alignPanel.paintAlignment(true);
2072 protected void modifyPID_actionPerformed()
2074 if (viewport.getAbovePIDThreshold()
2075 && viewport.globalColourScheme != null)
2077 SliderPanel.setPIDSliderSource(alignPanel, viewport
2078 .getGlobalColourScheme(), "Background");
2079 SliderPanel.showPIDSlider();
2083 protected void modifyConservation_actionPerformed()
2085 if (viewport.getConservationSelected()
2086 && viewport.globalColourScheme != null)
2088 SliderPanel.setConservationSlider(alignPanel,
2089 viewport.globalColourScheme, "Background");
2090 SliderPanel.showConservationSlider();
2094 protected void conservationMenuItem_actionPerformed()
2096 viewport.setConservationSelected(conservationMenuItem.getState());
2098 viewport.setAbovePIDThreshold(false);
2099 abovePIDThreshold.setState(false);
2101 changeColour(viewport.getGlobalColourScheme());
2103 modifyConservation_actionPerformed();
2106 public void abovePIDThreshold_actionPerformed()
2108 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2110 conservationMenuItem.setState(false);
2111 viewport.setConservationSelected(false);
2113 changeColour(viewport.getGlobalColourScheme());
2115 modifyPID_actionPerformed();
2118 public void sortPairwiseMenuItem_actionPerformed()
2120 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2121 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2122 .getAlignment().getSequenceAt(0), null);
2123 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2124 viewport.alignment));
2125 alignPanel.paintAlignment(true);
2128 public void sortIDMenuItem_actionPerformed()
2130 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
2131 // HistoryItem.SORT));
2132 AlignmentSorter.sortByID(viewport.getAlignment());
2133 alignPanel.paintAlignment(true);
2136 public void sortGroupMenuItem_actionPerformed()
2138 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
2139 // HistoryItem.SORT));
2140 AlignmentSorter.sortByGroup(viewport.getAlignment());
2141 alignPanel.paintAlignment(true);
2145 public void removeRedundancyMenuItem_actionPerformed()
2147 new RedundancyPanel(alignPanel);
2150 public void pairwiseAlignmentMenuItem_actionPerformed()
2152 if (viewport.getSelectionGroup() != null
2153 && viewport.getSelectionGroup().getSize() > 1)
2155 Frame frame = new Frame();
2156 frame.add(new PairwiseAlignPanel(alignPanel));
2157 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2162 public void PCAMenuItem_actionPerformed()
2164 // are the sequences aligned?
2165 if (!viewport.alignment.isAligned())
2168 int Width = viewport.getAlignment().getWidth();
2170 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2172 current = viewport.getAlignment().getSequenceAt(i);
2174 if (current.getLength() < Width)
2176 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2179 alignPanel.paintAlignment(true);
2182 if ((viewport.getSelectionGroup() != null
2183 && viewport.getSelectionGroup().getSize() < 4 && viewport
2184 .getSelectionGroup().getSize() > 0)
2185 || viewport.getAlignment().getHeight() < 4)
2192 new PCAPanel(viewport);
2193 } catch (java.lang.OutOfMemoryError ex)
2199 public void averageDistanceTreeMenuItem_actionPerformed()
2201 NewTreePanel("AV", "PID", "Average distance tree using PID");
2204 public void neighbourTreeMenuItem_actionPerformed()
2206 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2209 protected void njTreeBlosumMenuItem_actionPerformed()
2211 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2214 protected void avTreeBlosumMenuItem_actionPerformed()
2216 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2219 void NewTreePanel(String type, String pwType, String title)
2221 // are the sequences aligned?
2222 if (!viewport.alignment.isAligned())
2225 int Width = viewport.getAlignment().getWidth();
2227 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2229 current = viewport.getAlignment().getSequenceAt(i);
2231 if (current.getLength() < Width)
2233 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2236 alignPanel.paintAlignment(true);
2240 if ((viewport.getSelectionGroup() != null && viewport
2241 .getSelectionGroup().getSize() > 1)
2242 || (viewport.getSelectionGroup() == null && viewport.alignment
2245 final TreePanel tp = new TreePanel(viewport, type, pwType);
2247 addTreeMenuItem(tp, title);
2249 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2253 void loadTree_actionPerformed()
2255 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2256 cap.setText("Paste your Newick tree file here.");
2257 cap.setTreeImport();
2258 Frame frame = new Frame();
2260 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2263 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2265 TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
2266 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2267 addTreeMenuItem(tp, treeFile);
2270 void addTreeMenuItem(final TreePanel treePanel, String title)
2272 final MenuItem item = new MenuItem(title);
2273 sortByTreeMenu.add(item);
2274 item.addActionListener(new java.awt.event.ActionListener()
2276 public void actionPerformed(ActionEvent evt)
2278 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2279 // HistoryItem.SORT));
2280 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
2282 alignPanel.paintAlignment(true);
2286 treePanel.addWindowListener(new WindowAdapter()
2288 public void windowClosing(WindowEvent e)
2290 sortByTreeMenu.remove(item);
2295 protected void documentation_actionPerformed()
2297 showURL("http://www.jalview.org/help.html", "HELP");
2300 protected void about_actionPerformed()
2303 class AboutPanel extends Canvas
2307 public AboutPanel(String version)
2309 this.version = version;
2312 public void paint(Graphics g)
2314 g.setColor(Color.white);
2315 g.fillRect(0, 0, getSize().width, getSize().height);
2316 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2317 FontMetrics fm = g.getFontMetrics();
2318 int fh = fm.getHeight();
2320 g.setColor(Color.black);
2321 // TODO: update this text for each release or centrally store it for
2322 // lite and application
2323 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2324 g.drawString("JalviewLite - Release " + version, x, y += fh);
2325 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2328 "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
2330 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2333 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2337 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2339 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2342 "\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
2344 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
2348 String version = "test";
2349 java.net.URL url = getClass().getResource("/.build_properties");
2354 BufferedReader reader = new BufferedReader(new InputStreamReader(
2357 while ((line = reader.readLine()) != null)
2359 if (line.indexOf("VERSION") > -1)
2361 version = line.substring(line.indexOf("=") + 1);
2364 } catch (Exception ex)
2366 ex.printStackTrace();
2370 Frame frame = new Frame();
2371 frame.add(new AboutPanel(version));
2372 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2376 public void showURL(String url, String target)
2378 if (viewport.applet == null)
2380 System.out.println("Not running as applet - no browser available.");
2386 if (url.indexOf(":")==-1)
2388 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
2389 if (url.indexOf("/")==0)
2391 String codebase = viewport.applet.getCodeBase().toString();
2392 url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
2394 url = viewport.applet.getCodeBase()+url;
2396 System.out.println("Show url (prepended codebase): " + url);
2398 System.out.println("Show url: " + url);
2400 viewport.applet.getAppletContext().showDocument(
2401 new java.net.URL(url), target);
2402 } catch (Exception ex)
2404 ex.printStackTrace();
2409 // ////////////////////////////////////////////////////////////////////////////////
2410 // JBuilder Graphics here
2412 MenuBar alignFrameMenuBar = new MenuBar();
2414 Menu fileMenu = new Menu("File");
2416 MenuItem loadApplication = new MenuItem("View in Full Application");
2418 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2420 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2422 MenuItem outputFeatures = new MenuItem("Export Features ...");
2424 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2426 MenuItem closeMenuItem = new MenuItem("Close");
2428 Menu editMenu = new Menu("Edit");
2430 Menu viewMenu = new Menu("View");
2432 Menu colourMenu = new Menu("Colour");
2434 Menu calculateMenu = new Menu("Calculate");
2436 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2438 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2440 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2442 MenuItem remove2LeftMenuItem = new MenuItem();
2444 MenuItem remove2RightMenuItem = new MenuItem();
2446 MenuItem removeGappedColumnMenuItem = new MenuItem();
2448 MenuItem removeAllGapsMenuItem = new MenuItem();
2450 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2452 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2454 MenuItem sortPairwiseMenuItem = new MenuItem();
2456 MenuItem sortIDMenuItem = new MenuItem();
2458 MenuItem sortGroupMenuItem = new MenuItem();
2460 MenuItem removeRedundancyMenuItem = new MenuItem();
2462 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2464 MenuItem PCAMenuItem = new MenuItem();
2466 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2468 MenuItem neighbourTreeMenuItem = new MenuItem();
2470 BorderLayout borderLayout1 = new BorderLayout();
2472 public Label statusBar = new Label();
2474 Menu outputTextboxMenu = new Menu();
2476 MenuItem clustalColour = new MenuItem();
2478 MenuItem zappoColour = new MenuItem();
2480 MenuItem taylorColour = new MenuItem();
2482 MenuItem hydrophobicityColour = new MenuItem();
2484 MenuItem helixColour = new MenuItem();
2486 MenuItem strandColour = new MenuItem();
2488 MenuItem turnColour = new MenuItem();
2490 MenuItem buriedColour = new MenuItem();
2492 MenuItem userDefinedColour = new MenuItem();
2494 MenuItem PIDColour = new MenuItem();
2496 MenuItem BLOSUM62Colour = new MenuItem();
2498 MenuItem njTreeBlosumMenuItem = new MenuItem();
2500 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2502 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2504 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2506 MenuItem alProperties = new MenuItem("Alignment Properties...");
2508 MenuItem overviewMenuItem = new MenuItem();
2510 MenuItem undoMenuItem = new MenuItem();
2512 MenuItem redoMenuItem = new MenuItem();
2514 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2516 MenuItem noColourmenuItem = new MenuItem();
2518 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2520 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2522 MenuItem findMenuItem = new MenuItem();
2524 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2526 MenuItem nucleotideColour = new MenuItem();
2528 MenuItem deleteGroups = new MenuItem();
2530 MenuItem delete = new MenuItem();
2532 MenuItem copy = new MenuItem();
2534 MenuItem cut = new MenuItem();
2536 Menu pasteMenu = new Menu();
2538 MenuItem pasteNew = new MenuItem();
2540 MenuItem pasteThis = new MenuItem();
2542 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2544 MenuItem font = new MenuItem();
2546 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2548 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2550 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2552 MenuItem modifyPID = new MenuItem();
2554 MenuItem modifyConservation = new MenuItem();
2556 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2557 "Autocalculate Consensus", true);
2559 Menu sortByTreeMenu = new Menu();
2561 Menu sort = new Menu();
2563 Menu calculate = new Menu();
2565 MenuItem inputText = new MenuItem();
2567 Menu helpMenu = new Menu();
2569 MenuItem documentation = new MenuItem();
2571 MenuItem about = new MenuItem();
2573 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2575 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2577 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2579 private void jbInit() throws Exception
2582 setMenuBar(alignFrameMenuBar);
2586 // dynamically fill save as menu with available formats
2587 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2590 item = new MenuItem(
2591 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2593 item.addActionListener(new java.awt.event.ActionListener()
2595 public void actionPerformed(ActionEvent e)
2597 outputText_actionPerformed(e);
2601 outputTextboxMenu.add(item);
2603 closeMenuItem.addActionListener(this);
2604 loadApplication.addActionListener(this);
2606 loadTree.addActionListener(this);
2607 loadAnnotations.addActionListener(this);
2608 outputFeatures.addActionListener(this);
2609 outputAnnotations.addActionListener(this);
2610 selectAllSequenceMenuItem.addActionListener(this);
2611 deselectAllSequenceMenuItem.addActionListener(this);
2612 invertSequenceMenuItem.addActionListener(this);
2613 remove2LeftMenuItem.setLabel("Remove Left");
2614 remove2LeftMenuItem.addActionListener(this);
2615 remove2RightMenuItem.setLabel("Remove Right");
2616 remove2RightMenuItem.addActionListener(this);
2617 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2618 removeGappedColumnMenuItem.addActionListener(this);
2619 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2620 removeAllGapsMenuItem.addActionListener(this);
2621 viewBoxesMenuItem.setLabel("Boxes");
2622 viewBoxesMenuItem.setState(true);
2623 viewBoxesMenuItem.addItemListener(this);
2624 viewTextMenuItem.setLabel("Text");
2625 viewTextMenuItem.setState(true);
2626 viewTextMenuItem.addItemListener(this);
2627 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2628 sortPairwiseMenuItem.addActionListener(this);
2629 sortIDMenuItem.setLabel("by ID");
2630 sortIDMenuItem.addActionListener(this);
2631 sortGroupMenuItem.setLabel("by Group");
2632 sortGroupMenuItem.addActionListener(this);
2633 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2634 removeRedundancyMenuItem.addActionListener(this);
2635 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2636 pairwiseAlignmentMenuItem.addActionListener(this);
2637 PCAMenuItem.setLabel("Principal Component Analysis");
2638 PCAMenuItem.addActionListener(this);
2639 averageDistanceTreeMenuItem
2640 .setLabel("Average Distance Using % Identity");
2641 averageDistanceTreeMenuItem.addActionListener(this);
2642 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2643 neighbourTreeMenuItem.addActionListener(this);
2644 statusBar.setBackground(Color.white);
2645 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2646 statusBar.setText("Status bar");
2647 outputTextboxMenu.setLabel("Output to Textbox");
2648 clustalColour.setLabel("Clustalx");
2650 clustalColour.addActionListener(this);
2651 zappoColour.setLabel("Zappo");
2652 zappoColour.addActionListener(this);
2653 taylorColour.setLabel("Taylor");
2654 taylorColour.addActionListener(this);
2655 hydrophobicityColour.setLabel("Hydrophobicity");
2656 hydrophobicityColour.addActionListener(this);
2657 helixColour.setLabel("Helix Propensity");
2658 helixColour.addActionListener(this);
2659 strandColour.setLabel("Strand Propensity");
2660 strandColour.addActionListener(this);
2661 turnColour.setLabel("Turn Propensity");
2662 turnColour.addActionListener(this);
2663 buriedColour.setLabel("Buried Index");
2664 buriedColour.addActionListener(this);
2665 userDefinedColour.setLabel("User Defined...");
2666 userDefinedColour.addActionListener(this);
2667 PIDColour.setLabel("Percentage Identity");
2668 PIDColour.addActionListener(this);
2669 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2670 BLOSUM62Colour.addActionListener(this);
2671 avDistanceTreeBlosumMenuItem
2672 .setLabel("Average Distance Using BLOSUM62");
2673 avDistanceTreeBlosumMenuItem.addActionListener(this);
2674 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2675 njTreeBlosumMenuItem.addActionListener(this);
2676 annotationPanelMenuItem.setLabel("Show Annotations");
2677 annotationPanelMenuItem.addItemListener(this);
2678 colourTextMenuItem.setLabel("Colour Text");
2679 colourTextMenuItem.addItemListener(this);
2680 alProperties.addActionListener(this);
2681 overviewMenuItem.setLabel("Overview Window");
2682 overviewMenuItem.addActionListener(this);
2683 undoMenuItem.setEnabled(false);
2684 undoMenuItem.setLabel("Undo");
2685 undoMenuItem.addActionListener(this);
2686 redoMenuItem.setEnabled(false);
2687 redoMenuItem.setLabel("Redo");
2688 redoMenuItem.addActionListener(this);
2689 conservationMenuItem.setLabel("by Conservation");
2690 conservationMenuItem.addItemListener(this);
2691 noColourmenuItem.setLabel("None");
2692 noColourmenuItem.addActionListener(this);
2693 wrapMenuItem.setLabel("Wrap");
2694 wrapMenuItem.addItemListener(this);
2695 renderGapsMenuItem.setLabel("Show Gaps");
2696 renderGapsMenuItem.setState(true);
2697 renderGapsMenuItem.addItemListener(this);
2698 findMenuItem.setLabel("Find...");
2699 findMenuItem.addActionListener(this);
2700 abovePIDThreshold.setLabel("Above Identity Threshold");
2701 abovePIDThreshold.addItemListener(this);
2702 nucleotideColour.setLabel("Nucleotide");
2703 nucleotideColour.addActionListener(this);
2704 deleteGroups.setLabel("Undefine Groups");
2705 deleteGroups.addActionListener(this);
2706 copy.setLabel("Copy");
2707 copy.addActionListener(this);
2708 cut.setLabel("Cut");
2709 cut.addActionListener(this);
2710 delete.setLabel("Delete");
2711 delete.addActionListener(this);
2712 pasteMenu.setLabel("Paste");
2713 pasteNew.setLabel("To New Alignment");
2714 pasteNew.addActionListener(this);
2715 pasteThis.setLabel("Add To This Alignment");
2716 pasteThis.addActionListener(this);
2717 applyToAllGroups.setLabel("Apply Colour To All Groups");
2718 applyToAllGroups.setState(true);
2719 applyToAllGroups.addItemListener(this);
2720 font.setLabel("Font...");
2721 font.addActionListener(this);
2722 scaleAbove.setLabel("Scale Above");
2723 scaleAbove.setState(true);
2724 scaleAbove.setEnabled(false);
2725 scaleAbove.addItemListener(this);
2726 scaleLeft.setEnabled(false);
2727 scaleLeft.setState(true);
2728 scaleLeft.setLabel("Scale Left");
2729 scaleLeft.addItemListener(this);
2730 scaleRight.setEnabled(false);
2731 scaleRight.setState(true);
2732 scaleRight.setLabel("Scale Right");
2733 scaleRight.addItemListener(this);
2734 modifyPID.setLabel("Modify Identity Threshold...");
2735 modifyPID.addActionListener(this);
2736 modifyConservation.setLabel("Modify Conservation Threshold...");
2737 modifyConservation.addActionListener(this);
2738 sortByTreeMenu.setLabel("By Tree Order");
2739 sort.setLabel("Sort");
2740 calculate.setLabel("Calculate Tree");
2741 autoCalculate.addItemListener(this);
2742 inputText.setLabel("Input from textbox");
2743 inputText.addActionListener(this);
2744 centreColumnLabelFlag.setLabel("Centre column labels");
2745 centreColumnLabelFlag.addItemListener(this);
2746 followMouseOverFlag.setLabel("Automatic Scrolling");
2747 followMouseOverFlag.addItemListener(this);
2748 helpMenu.setLabel("Help");
2749 documentation.setLabel("Documentation");
2750 documentation.addActionListener(this);
2752 about.setLabel("About...");
2753 about.addActionListener(this);
2754 seqLimits.setState(true);
2755 seqLimits.setLabel("Show Sequence Limits");
2756 seqLimits.addItemListener(this);
2757 featureSettings.setLabel("Feature Settings...");
2758 featureSettings.addActionListener(this);
2759 sequenceFeatures.setLabel("Sequence Features");
2760 sequenceFeatures.addItemListener(this);
2761 sequenceFeatures.setState(false);
2762 annotationColour.setLabel("by Annotation...");
2763 annotationColour.addActionListener(this);
2764 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2765 invertColSel.setLabel("Invert Column Selection");
2766 menu1.setLabel("Show");
2767 showColumns.setLabel("All Columns ");
2768 showSeqs.setLabel("All Sequences");
2769 menu2.setLabel("Hide");
2770 hideColumns.setLabel("Selected Columns");
2771 hideSequences.setLabel("Selected Sequences");
2772 invertColSel.addActionListener(this);
2773 showColumns.addActionListener(this);
2774 showSeqs.addActionListener(this);
2775 hideColumns.addActionListener(this);
2776 hideSequences.addActionListener(this);
2777 formatMenu.setLabel("Format");
2778 selectMenu.setLabel("Select");
2779 newView.setLabel("New View");
2780 newView.addActionListener(this);
2781 alignFrameMenuBar.add(fileMenu);
2782 alignFrameMenuBar.add(editMenu);
2783 alignFrameMenuBar.add(selectMenu);
2784 alignFrameMenuBar.add(viewMenu);
2785 alignFrameMenuBar.add(formatMenu);
2786 alignFrameMenuBar.add(colourMenu);
2787 alignFrameMenuBar.add(calculateMenu);
2788 alignFrameMenuBar.add(helpMenu);
2790 fileMenu.add(inputText);
2791 fileMenu.add(loadTree);
2792 fileMenu.add(loadAnnotations);
2794 fileMenu.addSeparator();
2795 fileMenu.add(outputTextboxMenu);
2796 fileMenu.add(outputFeatures);
2797 fileMenu.add(outputAnnotations);
2799 if (jalviewServletURL != null)
2801 fileMenu.add(loadApplication);
2804 fileMenu.addSeparator();
2805 fileMenu.add(closeMenuItem);
2807 editMenu.add(undoMenuItem);
2808 editMenu.add(redoMenuItem);
2811 editMenu.add(pasteMenu);
2812 editMenu.add(delete);
2813 editMenu.addSeparator();
2814 editMenu.add(remove2LeftMenuItem);
2815 editMenu.add(remove2RightMenuItem);
2816 editMenu.add(removeGappedColumnMenuItem);
2817 editMenu.add(removeAllGapsMenuItem);
2818 editMenu.add(removeRedundancyMenuItem);
2819 viewMenu.add(newView);
2820 viewMenu.addSeparator();
2821 viewMenu.add(menu1);
2822 viewMenu.add(menu2);
2823 viewMenu.addSeparator();
2824 viewMenu.add(followMouseOverFlag);
2825 viewMenu.add(annotationPanelMenuItem);
2826 viewMenu.addSeparator();
2827 viewMenu.add(sequenceFeatures);
2828 viewMenu.add(featureSettings);
2829 viewMenu.addSeparator();
2830 viewMenu.add(alProperties);
2831 viewMenu.addSeparator();
2832 viewMenu.add(overviewMenuItem);
2833 colourMenu.add(applyToAllGroups);
2834 colourMenu.addSeparator();
2835 colourMenu.add(noColourmenuItem);
2836 colourMenu.add(clustalColour);
2837 colourMenu.add(BLOSUM62Colour);
2838 colourMenu.add(PIDColour);
2839 colourMenu.add(zappoColour);
2840 colourMenu.add(taylorColour);
2841 colourMenu.add(hydrophobicityColour);
2842 colourMenu.add(helixColour);
2843 colourMenu.add(strandColour);
2844 colourMenu.add(turnColour);
2845 colourMenu.add(buriedColour);
2846 colourMenu.add(nucleotideColour);
2847 colourMenu.add(userDefinedColour);
2848 colourMenu.addSeparator();
2849 colourMenu.add(conservationMenuItem);
2850 colourMenu.add(modifyConservation);
2851 colourMenu.add(abovePIDThreshold);
2852 colourMenu.add(modifyPID);
2853 colourMenu.add(annotationColour);
2854 calculateMenu.add(sort);
2855 calculateMenu.add(calculate);
2856 calculateMenu.addSeparator();
2857 calculateMenu.add(pairwiseAlignmentMenuItem);
2858 calculateMenu.add(PCAMenuItem);
2859 calculateMenu.add(autoCalculate);
2860 this.add(statusBar, BorderLayout.SOUTH);
2861 pasteMenu.add(pasteNew);
2862 pasteMenu.add(pasteThis);
2863 sort.add(sortIDMenuItem);
2864 sort.add(sortByTreeMenu);
2865 sort.add(sortGroupMenuItem);
2866 sort.add(sortPairwiseMenuItem);
2867 calculate.add(averageDistanceTreeMenuItem);
2868 calculate.add(neighbourTreeMenuItem);
2869 calculate.add(avDistanceTreeBlosumMenuItem);
2870 calculate.add(njTreeBlosumMenuItem);
2871 helpMenu.add(documentation);
2872 helpMenu.add(about);
2873 menu1.add(showColumns);
2874 menu1.add(showSeqs);
2875 menu2.add(hideColumns);
2876 menu2.add(hideSequences);
2877 formatMenu.add(font);
2878 formatMenu.add(seqLimits);
2879 formatMenu.add(wrapMenuItem);
2880 formatMenu.add(scaleAbove);
2881 formatMenu.add(scaleLeft);
2882 formatMenu.add(scaleRight);
2883 formatMenu.add(viewBoxesMenuItem);
2884 formatMenu.add(viewTextMenuItem);
2885 formatMenu.add(colourTextMenuItem);
2886 formatMenu.add(renderGapsMenuItem);
2887 formatMenu.add(centreColumnLabelFlag);
2888 selectMenu.add(findMenuItem);
2889 selectMenu.addSeparator();
2890 selectMenu.add(selectAllSequenceMenuItem);
2891 selectMenu.add(deselectAllSequenceMenuItem);
2892 selectMenu.add(invertSequenceMenuItem);
2893 selectMenu.add(invertColSel);
2894 selectMenu.add(deleteGroups);
2897 MenuItem featureSettings = new MenuItem();
2899 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
2901 MenuItem annotationColour = new MenuItem();
2903 MenuItem invertColSel = new MenuItem();
2905 Menu menu1 = new Menu();
2907 MenuItem showColumns = new MenuItem();
2909 MenuItem showSeqs = new MenuItem();
2911 Menu menu2 = new Menu();
2913 MenuItem hideColumns = new MenuItem();
2915 MenuItem hideSequences = new MenuItem();
2917 Menu formatMenu = new Menu();
2919 Menu selectMenu = new Menu();
2921 MenuItem newView = new MenuItem();
2924 * Attach the alignFrame panels after embedding menus, if necessary. This used
2925 * to be called setEmbedded, but is now creates the dropdown menus in a
2926 * platform independent manner to avoid OSX/Mac menu appendage daftness.
2928 * @param reallyEmbedded
2929 * true to attach the view to the applet area on the page
2930 * rather than in a new window
2932 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
2937 // Explicly build the embedded menu panel for the on-page applet
2939 // view cannot be closed if its actually on the page
2940 fileMenu.remove(closeMenuItem);
2941 fileMenu.remove(3); // Remove Seperator
2942 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
2943 Font.PLAIN, 10, false); // use our own fonts.
2944 // and actually add the components to the applet area
2945 viewport.applet.setLayout(new BorderLayout());
2946 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
2947 viewport.applet.add(statusBar, BorderLayout.SOUTH);
2948 alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
2950 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
2951 viewport.applet.add(alignPanel, BorderLayout.CENTER);
2952 viewport.applet.validate();
2957 // test and embed menu bar if necessary.
2959 if (embedMenuIfNeeded(alignPanel))
2961 // adjust for status bar height too
2962 alignPanel.setSize(getSize().width, getSize().height
2963 - statusBar.HEIGHT);
2965 add(statusBar, BorderLayout.SOUTH);
2966 add(alignPanel, BorderLayout.CENTER);
2967 // and register with the applet so it can pass external API calls to us
2968 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,