2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.appletgui;
25 import java.awt.event.*;
27 import jalview.analysis.*;
28 import jalview.api.SequenceStructureBinding;
29 import jalview.bin.JalviewLite;
30 import jalview.commands.*;
31 import jalview.datamodel.*;
33 import jalview.schemes.*;
35 public class AlignFrame extends EmbmenuFrame implements ActionListener,
36 ItemListener, KeyListener
38 public AlignmentPanel alignPanel;
40 public AlignViewport viewport;
42 int DEFAULT_WIDTH = 700;
44 int DEFAULT_HEIGHT = 500;
46 String jalviewServletURL;
48 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
49 String title, boolean embedded)
54 jalviewServletURL = applet.getParameter("APPLICATION_URL");
60 } catch (Exception ex)
65 viewport = new AlignViewport(al, applet);
66 alignPanel = new AlignmentPanel(this, viewport);
68 viewport.updateConservation(alignPanel);
69 viewport.updateConsensus(alignPanel);
71 annotationPanelMenuItem.setState(viewport.showAnnotation);
72 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
73 followMouseOverFlag.setState(viewport.getFollowHighlight());
75 seqLimits.setState(viewport.showJVSuffix);
79 String param = applet.getParameter("sortBy");
82 if (param.equalsIgnoreCase("Id"))
84 sortIDMenuItem_actionPerformed();
86 else if (param.equalsIgnoreCase("Pairwise Identity"))
88 sortPairwiseMenuItem_actionPerformed();
90 else if (param.equalsIgnoreCase("Length"))
92 sortLengthMenuItem_actionPerformed();
96 param = applet.getParameter("wrap");
99 if (param.equalsIgnoreCase("true"))
101 wrapMenuItem.setState(true);
102 wrapMenuItem_actionPerformed();
105 param = applet.getParameter("centrecolumnlabels");
108 centreColumnLabelFlag.setState(true);
109 centreColumnLabelFlag_stateChanged();
113 param = applet.getParameter("windowWidth");
116 int width = Integer.parseInt(param);
117 DEFAULT_WIDTH = width;
119 param = applet.getParameter("windowHeight");
122 int height = Integer.parseInt(param);
123 DEFAULT_HEIGHT = height;
125 } catch (Exception ex)
131 // Some JVMS send keyevents to Top frame or lowest panel,
132 // Havent worked out why yet. So add to both this frame and seqCanvas for
134 this.addKeyListener(this);
135 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
136 alignPanel.idPanel.idCanvas.addKeyListener(this);
137 alignPanel.scalePanel.addKeyListener(this);
138 alignPanel.annotationPanel.addKeyListener(this);
139 createAlignFrameWindow(embedded, title);
140 alignPanel.validate();
141 alignPanel.paintAlignment(true);
144 public AlignViewport getAlignViewport()
149 public SeqCanvas getSeqcanvas()
151 return alignPanel.seqPanel.seqCanvas;
161 public void parseFeaturesFile(String file, String type)
163 Hashtable featureLinks = new Hashtable();
164 boolean featuresFile = false;
167 featuresFile = new jalview.io.FeaturesFile(file, type)
168 .parse(viewport.alignment,
169 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
171 } catch (Exception ex)
173 ex.printStackTrace();
178 if (featureLinks.size() > 0)
180 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
182 viewport.showSequenceFeatures = true;
183 sequenceFeatures.setState(true);
184 if (viewport.featureSettings != null)
186 viewport.featureSettings.refreshTable();
188 alignPanel.paintAlignment(true);
193 public void keyPressed(KeyEvent evt)
195 if (viewport.cursorMode
196 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
197 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
198 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
199 && Character.isDigit(evt.getKeyChar()))
200 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
202 switch (evt.getKeyCode())
204 case 27: // escape key
205 deselectAllSequenceMenuItem_actionPerformed();
208 if (evt.isControlDown() || evt.isMetaDown())
210 cut_actionPerformed();
214 if (viewport.cursorMode && !evt.isControlDown())
216 alignPanel.seqPanel.setCursorColumn();
218 if (evt.isControlDown() || evt.isMetaDown())
220 copy_actionPerformed();
224 if (evt.isControlDown())
226 paste(evt.isShiftDown());
230 if (evt.isControlDown() || evt.isMetaDown())
232 selectAllSequenceMenuItem_actionPerformed();
235 case KeyEvent.VK_DOWN:
236 if (viewport.cursorMode)
238 alignPanel.seqPanel.moveCursor(0, 1);
242 moveSelectedSequences(false);
247 if (viewport.cursorMode)
249 alignPanel.seqPanel.moveCursor(0, -1);
253 moveSelectedSequences(true);
257 case KeyEvent.VK_LEFT:
258 if (evt.isAltDown() || !viewport.cursorMode)
259 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
261 alignPanel.seqPanel.moveCursor(-1, 0);
264 case KeyEvent.VK_RIGHT:
265 if (evt.isAltDown() || !viewport.cursorMode)
266 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
268 alignPanel.seqPanel.moveCursor(1, 0);
271 case KeyEvent.VK_SPACE:
272 if (viewport.cursorMode)
274 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
275 || evt.isShiftDown() || evt.isAltDown());
279 case KeyEvent.VK_DELETE:
280 case KeyEvent.VK_BACK_SPACE:
281 if (viewport.cursorMode)
283 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
284 || evt.isShiftDown() || evt.isAltDown());
288 cut_actionPerformed();
289 alignPanel.seqPanel.seqCanvas.repaint();
294 if (viewport.cursorMode)
296 alignPanel.seqPanel.setCursorRow();
300 if (viewport.cursorMode)
302 alignPanel.seqPanel.setCursorPosition();
306 case KeyEvent.VK_ENTER:
307 case KeyEvent.VK_COMMA:
308 if (viewport.cursorMode)
310 alignPanel.seqPanel.setCursorRowAndColumn();
315 if (viewport.cursorMode)
317 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
321 if (viewport.cursorMode)
323 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
328 viewport.cursorMode = !viewport.cursorMode;
329 statusBar.setText("Keyboard editing mode is "
330 + (viewport.cursorMode ? "on" : "off"));
331 if (viewport.cursorMode)
333 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
334 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
339 if (evt.isControlDown())
341 findMenuItem_actionPerformed();
347 boolean toggleSeqs = !evt.isControlDown();
348 boolean toggleCols = !evt.isShiftDown();
349 toggleHiddenRegions(toggleSeqs, toggleCols);
353 case KeyEvent.VK_PAGE_UP:
354 if (viewport.wrapAlignment)
356 alignPanel.scrollUp(true);
360 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
361 - viewport.endSeq + viewport.startSeq);
365 case KeyEvent.VK_PAGE_DOWN:
366 if (viewport.wrapAlignment)
368 alignPanel.scrollUp(false);
372 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
373 + viewport.endSeq - viewport.startSeq);
378 if (evt.isControlDown())
380 undoMenuItem_actionPerformed();
385 if (evt.isControlDown())
387 redoMenuItem_actionPerformed();
392 if (evt.isControlDown())
399 if (evt.isControlDown())
401 trimAlignment(false);
406 if (evt.isControlDown())
408 if (evt.isShiftDown())
410 this.removeAllGapsMenuItem_actionPerformed();
414 removeGappedColumnMenuItem_actionPerformed();
419 if (evt.isControlDown())
423 invertColSel_actionPerformed();
427 invertSequenceMenuItem_actionPerformed();
433 if (evt.isControlDown())
435 this.deleteGroups_actionPerformed();
440 if (evt.isControlDown())
447 alignPanel.paintAlignment(true);
451 * called by key handler and the hide all/show all menu items
456 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
458 boolean hide = false;
459 SequenceGroup sg = viewport.getSelectionGroup();
460 if (!toggleSeqs && !toggleCols)
462 // Hide everything by the current selection - this is a hack - we do the
463 // invert and then hide
464 // first check that there will be visible columns after the invert.
465 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
466 .getSelected().size() > 0)
467 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
470 // now invert the sequence set, if required - empty selection implies
471 // that no hiding is required.
474 invertSequenceMenuItem_actionPerformed();
475 sg = viewport.getSelectionGroup();
479 viewport.expandColSelection(sg, true);
480 // finally invert the column selection and get the new sequence
481 // selection and indicate it should be hidden.
482 invertColSel_actionPerformed();
489 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
492 viewport.hideAllSelectedSeqs();
494 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
496 viewport.showAllHiddenSeqs();
502 if (viewport.colSel.getSelected().size() > 0)
504 viewport.hideSelectedColumns();
507 viewport.selectionGroup = sg;
512 viewport.showAllHiddenColumns();
517 public void keyReleased(KeyEvent evt)
521 public void keyTyped(KeyEvent evt)
525 public void itemStateChanged(ItemEvent evt)
527 if (evt.getSource() == displayNonconservedMenuItem)
529 displayNonconservedMenuItem_actionPerformed();
531 else if (evt.getSource() == colourTextMenuItem)
533 colourTextMenuItem_actionPerformed();
535 else if (evt.getSource() == wrapMenuItem)
537 wrapMenuItem_actionPerformed();
539 else if (evt.getSource() == scaleAbove)
541 viewport.setScaleAboveWrapped(scaleAbove.getState());
543 else if (evt.getSource() == scaleLeft)
545 viewport.setScaleLeftWrapped(scaleLeft.getState());
547 else if (evt.getSource() == scaleRight)
549 viewport.setScaleRightWrapped(scaleRight.getState());
551 else if (evt.getSource() == seqLimits)
553 seqLimits_itemStateChanged();
555 else if (evt.getSource() == viewBoxesMenuItem)
557 viewport.setShowBoxes(viewBoxesMenuItem.getState());
559 else if (evt.getSource() == viewTextMenuItem)
561 viewport.setShowText(viewTextMenuItem.getState());
563 else if (evt.getSource() == renderGapsMenuItem)
565 viewport.setRenderGaps(renderGapsMenuItem.getState());
567 else if (evt.getSource() == annotationPanelMenuItem)
569 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
570 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
572 else if (evt.getSource() == sequenceFeatures)
574 viewport.showSequenceFeatures(sequenceFeatures.getState());
575 alignPanel.seqPanel.seqCanvas.repaint();
577 else if (evt.getSource() == conservationMenuItem)
579 conservationMenuItem_actionPerformed();
581 else if (evt.getSource() == abovePIDThreshold)
583 abovePIDThreshold_actionPerformed();
585 else if (evt.getSource() == applyToAllGroups)
587 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
589 else if (evt.getSource() == autoCalculate)
591 viewport.autocalculateConsensus = autoCalculate.getState();
593 else if (evt.getSource() == this.centreColumnLabelFlag)
595 centreColumnLabelFlag_stateChanged();
597 else if (evt.getSource() == this.followMouseOverFlag)
599 mouseOverFlag_stateChanged();
602 alignPanel.paintAlignment(true);
605 private void mouseOverFlag_stateChanged()
607 viewport.followHighlight = followMouseOverFlag.getState();
608 // TODO: could kick the scrollTo mechanism to reset view for current
612 private void centreColumnLabelFlag_stateChanged()
614 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
615 this.alignPanel.annotationPanel.repaint();
618 public void actionPerformed(ActionEvent evt)
620 Object source = evt.getSource();
622 if (source == inputText)
624 inputText_actionPerformed();
626 else if (source == loadTree)
628 loadTree_actionPerformed();
630 else if (source == loadApplication)
632 launchFullApplication();
634 else if (source == loadAnnotations)
638 else if (source == outputAnnotations)
640 outputAnnotations(true);
642 else if (source == outputFeatures)
644 outputFeatures(true, "Jalview");
646 else if (source == closeMenuItem)
648 closeMenuItem_actionPerformed();
650 else if (source == copy)
652 copy_actionPerformed();
654 else if (source == undoMenuItem)
656 undoMenuItem_actionPerformed();
658 else if (source == redoMenuItem)
660 redoMenuItem_actionPerformed();
662 else if (source == inputText)
664 inputText_actionPerformed();
666 else if (source == closeMenuItem)
668 closeMenuItem_actionPerformed();
670 else if (source == undoMenuItem)
672 undoMenuItem_actionPerformed();
674 else if (source == redoMenuItem)
676 redoMenuItem_actionPerformed();
678 else if (source == copy)
680 copy_actionPerformed();
682 else if (source == pasteNew)
684 pasteNew_actionPerformed();
686 else if (source == pasteThis)
688 pasteThis_actionPerformed();
690 else if (source == cut)
692 cut_actionPerformed();
694 else if (source == delete)
696 delete_actionPerformed();
698 else if (source == grpsFromSelection)
700 makeGrpsFromSelection_actionPerformed();
702 else if (source == deleteGroups)
704 deleteGroups_actionPerformed();
706 else if (source == selectAllSequenceMenuItem)
708 selectAllSequenceMenuItem_actionPerformed();
710 else if (source == deselectAllSequenceMenuItem)
712 deselectAllSequenceMenuItem_actionPerformed();
714 else if (source == invertSequenceMenuItem)
716 invertSequenceMenuItem_actionPerformed();
718 else if (source == invertColSel)
720 viewport.invertColumnSelection();
721 alignPanel.paintAlignment(true);
723 else if (source == remove2LeftMenuItem)
727 else if (source == remove2RightMenuItem)
729 trimAlignment(false);
731 else if (source == removeGappedColumnMenuItem)
733 removeGappedColumnMenuItem_actionPerformed();
735 else if (source == removeAllGapsMenuItem)
737 removeAllGapsMenuItem_actionPerformed();
739 else if (source == findMenuItem)
741 findMenuItem_actionPerformed();
743 else if (source == font)
745 new FontChooser(alignPanel);
747 else if (source == newView)
751 else if (source == showColumns)
753 viewport.showAllHiddenColumns();
754 alignPanel.paintAlignment(true);
756 else if (source == showSeqs)
758 viewport.showAllHiddenSeqs();
759 alignPanel.paintAlignment(true);
761 else if (source == hideColumns)
763 viewport.hideSelectedColumns();
764 alignPanel.paintAlignment(true);
766 else if (source == hideSequences
767 && viewport.getSelectionGroup() != null)
769 viewport.hideAllSelectedSeqs();
770 alignPanel.paintAlignment(true);
772 else if (source == hideAllButSelection)
774 toggleHiddenRegions(false, false);
775 alignPanel.paintAlignment(true);
777 else if (source == hideAllSelection)
779 SequenceGroup sg = viewport.getSelectionGroup();
780 viewport.expandColSelection(sg, false);
781 viewport.hideAllSelectedSeqs();
782 viewport.hideSelectedColumns();
783 alignPanel.paintAlignment(true);
785 else if (source == showAllHidden)
787 viewport.showAllHiddenColumns();
788 viewport.showAllHiddenSeqs();
789 alignPanel.paintAlignment(true);
791 else if (source == featureSettings)
793 new FeatureSettings(alignPanel);
795 else if (source == alProperties)
797 StringBuffer contents = new jalview.io.AlignmentProperties(
798 viewport.alignment).formatAsString();
799 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
800 cap.setText(contents.toString());
801 Frame frame = new Frame();
803 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
804 + getTitle(), 400, 250);
806 else if (source == overviewMenuItem)
808 overviewMenuItem_actionPerformed();
810 else if (source == noColourmenuItem)
814 else if (source == clustalColour)
816 abovePIDThreshold.setState(false);
817 changeColour(new ClustalxColourScheme(
818 viewport.alignment.getSequences(),
819 viewport.alignment.getWidth()));
821 else if (source == zappoColour)
823 changeColour(new ZappoColourScheme());
825 else if (source == taylorColour)
827 changeColour(new TaylorColourScheme());
829 else if (source == hydrophobicityColour)
831 changeColour(new HydrophobicColourScheme());
833 else if (source == helixColour)
835 changeColour(new HelixColourScheme());
837 else if (source == strandColour)
839 changeColour(new StrandColourScheme());
841 else if (source == turnColour)
843 changeColour(new TurnColourScheme());
845 else if (source == buriedColour)
847 changeColour(new BuriedColourScheme());
849 else if (source == nucleotideColour)
851 changeColour(new NucleotideColourScheme());
853 else if (source == modifyPID)
855 modifyPID_actionPerformed();
857 else if (source == modifyConservation)
859 modifyConservation_actionPerformed();
861 else if (source == userDefinedColour)
863 new UserDefinedColours(alignPanel, null);
865 else if (source == PIDColour)
867 changeColour(new PIDColourScheme());
869 else if (source == BLOSUM62Colour)
871 changeColour(new Blosum62ColourScheme());
873 else if (source == annotationColour)
875 new AnnotationColourChooser(viewport, alignPanel);
877 else if (source == sortPairwiseMenuItem)
879 sortPairwiseMenuItem_actionPerformed();
881 else if (source == sortIDMenuItem)
883 sortIDMenuItem_actionPerformed();
885 else if (source == sortLengthMenuItem)
887 sortLengthMenuItem_actionPerformed();
889 else if (source == sortGroupMenuItem)
891 sortGroupMenuItem_actionPerformed();
893 else if (source == removeRedundancyMenuItem)
895 removeRedundancyMenuItem_actionPerformed();
897 else if (source == pairwiseAlignmentMenuItem)
899 pairwiseAlignmentMenuItem_actionPerformed();
901 else if (source == PCAMenuItem)
903 PCAMenuItem_actionPerformed();
905 else if (source == averageDistanceTreeMenuItem)
907 averageDistanceTreeMenuItem_actionPerformed();
909 else if (source == neighbourTreeMenuItem)
911 neighbourTreeMenuItem_actionPerformed();
913 else if (source == njTreeBlosumMenuItem)
915 njTreeBlosumMenuItem_actionPerformed();
917 else if (source == avDistanceTreeBlosumMenuItem)
919 avTreeBlosumMenuItem_actionPerformed();
921 else if (source == documentation)
923 documentation_actionPerformed();
925 else if (source == about)
927 about_actionPerformed();
932 public void inputText_actionPerformed()
934 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
935 Frame frame = new Frame();
937 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
940 protected void outputText_actionPerformed(ActionEvent e)
942 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
943 Frame frame = new Frame();
945 jalview.bin.JalviewLite.addFrame(frame,
946 "Alignment output - " + e.getActionCommand(), 600, 500);
947 cap.setText(new AppletFormatAdapter().formatSequences(
948 e.getActionCommand(), viewport.getAlignment(),
949 viewport.showJVSuffix));
952 public void loadAnnotations()
954 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
955 cap.setText("Paste your features / annotations file here.");
956 cap.setAnnotationImport();
957 Frame frame = new Frame();
959 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
963 public String outputAnnotations(boolean displayTextbox)
965 String annotation = new AnnotationFile().printAnnotations(
966 viewport.showAnnotation ? viewport.alignment
967 .getAlignmentAnnotation() : null, viewport.alignment
969 ((Alignment) viewport.alignment).alignmentProperties);
973 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
974 Frame frame = new Frame();
976 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
977 cap.setText(annotation);
983 private Hashtable getDisplayedFeatureCols()
985 if (alignPanel.getFeatureRenderer() != null)
987 FeatureRenderer fr = alignPanel.getFeatureRenderer();
988 Hashtable fcols = new Hashtable();
989 Enumeration en = viewport.featuresDisplayed.keys();
990 while (en.hasMoreElements())
992 Object col = en.nextElement();
993 fcols.put(col, fr.featureColours.get(col));
1000 public String outputFeatures(boolean displayTextbox, String format)
1003 if (format.equalsIgnoreCase("Jalview"))
1005 features = new FeaturesFile().printJalviewFormat(
1006 viewport.alignment.getSequencesArray(),
1007 getDisplayedFeatureCols());
1011 features = new FeaturesFile().printGFFFormat(
1012 viewport.alignment.getSequencesArray(),
1013 getDisplayedFeatureCols());
1018 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1019 Frame frame = new Frame();
1021 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1023 cap.setText(features);
1029 void launchFullApplication()
1031 StringBuffer url = new StringBuffer(jalviewServletURL);
1034 + appendProtocol(viewport.applet.getParameter("file")));
1036 if (viewport.applet.getParameter("features") != null)
1038 url.append("&features=");
1039 url.append(appendProtocol(viewport.applet.getParameter("features")));
1042 if (viewport.applet.getParameter("annotations") != null)
1044 url.append("&annotations=");
1045 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1048 if (viewport.applet.getParameter("jnetfile") != null)
1050 url.append("&annotations=");
1051 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1054 if (viewport.applet.getParameter("defaultColour") != null)
1056 url.append("&colour="
1057 + removeWhiteSpace(viewport.applet
1058 .getParameter("defaultColour")));
1061 if (viewport.applet.getParameter("userDefinedColour") != null)
1063 url.append("&colour="
1064 + removeWhiteSpace(viewport.applet
1065 .getParameter("userDefinedColour")));
1067 if (viewport.applet.getParameter("tree") != null)
1070 + appendProtocol(viewport.applet.getParameter("tree")));
1072 if (viewport.applet.getParameter("treeFile") != null)
1075 + appendProtocol(viewport.applet.getParameter("treeFile")));
1078 showURL(url.toString(), "FULL_APP");
1081 String removeWhiteSpace(String colour)
1083 StringBuffer sb = new StringBuffer();
1084 for (int i = 0; i < colour.length(); i++)
1086 if (Character.isWhitespace(colour.charAt(i)))
1092 sb.append(colour.charAt(i));
1096 return sb.toString();
1099 String appendProtocol(String url)
1104 url = URLEncoder.encode(url);
1107 * When we finally deprecate 1.1 compatibility, we can start to use
1108 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1109 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1110 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1111 * ex.printStackTrace(); }
1113 catch (java.net.MalformedURLException ex)
1115 url = viewport.applet.getCodeBase() + url;
1120 public void closeMenuItem_actionPerformed()
1122 PaintRefresher.RemoveComponent(alignPanel);
1123 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1124 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1126 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1137 void updateEditMenuBar()
1140 if (viewport.historyList.size() > 0)
1142 undoMenuItem.setEnabled(true);
1143 CommandI command = (CommandI) viewport.historyList.peek();
1144 undoMenuItem.setLabel("Undo " + command.getDescription());
1148 undoMenuItem.setEnabled(false);
1149 undoMenuItem.setLabel("Undo");
1152 if (viewport.redoList.size() > 0)
1154 redoMenuItem.setEnabled(true);
1156 CommandI command = (CommandI) viewport.redoList.peek();
1157 redoMenuItem.setLabel("Redo " + command.getDescription());
1161 redoMenuItem.setEnabled(false);
1162 redoMenuItem.setLabel("Redo");
1166 public void addHistoryItem(CommandI command)
1168 if (command.getSize() > 0)
1170 viewport.historyList.push(command);
1171 viewport.redoList.removeAllElements();
1172 updateEditMenuBar();
1173 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1183 protected void undoMenuItem_actionPerformed()
1185 if (viewport.historyList.size() < 1)
1190 CommandI command = (CommandI) viewport.historyList.pop();
1191 viewport.redoList.push(command);
1192 command.undoCommand(null);
1194 AlignViewport originalSource = getOriginatingSource(command);
1196 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1197 updateEditMenuBar();
1198 originalSource.firePropertyChange("alignment", null,
1199 originalSource.alignment.getSequences());
1208 protected void redoMenuItem_actionPerformed()
1210 if (viewport.redoList.size() < 1)
1215 CommandI command = (CommandI) viewport.redoList.pop();
1216 viewport.historyList.push(command);
1217 command.doCommand(null);
1219 AlignViewport originalSource = getOriginatingSource(command);
1220 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1222 updateEditMenuBar();
1223 originalSource.firePropertyChange("alignment", null,
1224 originalSource.alignment.getSequences());
1227 AlignViewport getOriginatingSource(CommandI command)
1229 AlignViewport originalSource = null;
1230 // For sequence removal and addition, we need to fire
1231 // the property change event FROM the viewport where the
1232 // original alignment was altered
1233 AlignmentI al = null;
1234 if (command instanceof EditCommand)
1236 EditCommand editCommand = (EditCommand) command;
1237 al = editCommand.getAlignment();
1238 Vector comps = (Vector) PaintRefresher.components.get(viewport
1239 .getSequenceSetId());
1240 for (int i = 0; i < comps.size(); i++)
1242 if (comps.elementAt(i) instanceof AlignmentPanel)
1244 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1246 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1253 if (originalSource == null)
1255 // The original view is closed, we must validate
1256 // the current view against the closed view first
1259 PaintRefresher.validateSequences(al, viewport.alignment);
1262 originalSource = viewport;
1265 return originalSource;
1268 public void moveSelectedSequences(boolean up)
1270 SequenceGroup sg = viewport.getSelectionGroup();
1278 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1280 SequenceI seq = viewport.alignment.getSequenceAt(i);
1281 if (!sg.getSequences(null).contains(seq))
1286 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1287 if (sg.getSequences(null).contains(temp))
1292 viewport.alignment.getSequences().setElementAt(temp, i);
1293 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1298 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1300 SequenceI seq = viewport.alignment.getSequenceAt(i);
1301 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1306 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1307 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1312 viewport.alignment.getSequences().setElementAt(temp, i);
1313 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1317 alignPanel.paintAlignment(true);
1320 synchronized void slideSequences(boolean right, int size)
1322 Vector sg = new Vector();
1323 if (viewport.cursorMode)
1325 sg.addElement(viewport.alignment
1326 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1328 else if (viewport.getSelectionGroup() != null
1329 && viewport.getSelectionGroup().getSize() != viewport.alignment
1332 sg = viewport.getSelectionGroup().getSequences(
1333 viewport.hiddenRepSequences);
1341 Vector invertGroup = new Vector();
1343 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1345 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1346 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1349 SequenceI[] seqs1 = new SequenceI[sg.size()];
1350 for (int i = 0; i < sg.size(); i++)
1351 seqs1[i] = (SequenceI) sg.elementAt(i);
1353 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1354 for (int i = 0; i < invertGroup.size(); i++)
1355 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1357 SlideSequencesCommand ssc;
1359 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1360 size, viewport.getGapCharacter());
1362 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1363 size, viewport.getGapCharacter());
1365 int groupAdjustment = 0;
1366 if (ssc.getGapsInsertedBegin() && right)
1368 if (viewport.cursorMode)
1369 alignPanel.seqPanel.moveCursor(size, 0);
1371 groupAdjustment = size;
1373 else if (!ssc.getGapsInsertedBegin() && !right)
1375 if (viewport.cursorMode)
1376 alignPanel.seqPanel.moveCursor(-size, 0);
1378 groupAdjustment = -size;
1381 if (groupAdjustment != 0)
1383 viewport.getSelectionGroup().setStartRes(
1384 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1385 viewport.getSelectionGroup().setEndRes(
1386 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1389 boolean appendHistoryItem = false;
1390 if (viewport.historyList != null && viewport.historyList.size() > 0
1391 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1393 appendHistoryItem = ssc
1394 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1398 if (!appendHistoryItem)
1399 addHistoryItem(ssc);
1404 static StringBuffer copiedSequences;
1406 static Vector copiedHiddenColumns;
1408 protected void copy_actionPerformed()
1410 if (viewport.getSelectionGroup() == null)
1415 SequenceGroup sg = viewport.getSelectionGroup();
1416 copiedSequences = new StringBuffer();
1417 Hashtable orderedSeqs = new Hashtable();
1418 for (int i = 0; i < sg.getSize(); i++)
1420 SequenceI seq = sg.getSequenceAt(i);
1421 int index = viewport.alignment.findIndex(seq);
1422 orderedSeqs.put(index + "", seq);
1425 int index = 0, startRes, endRes;
1428 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1430 copiedHiddenColumns = new Vector();
1431 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1432 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1435 int[] region = (int[]) viewport.getColumnSelection()
1436 .getHiddenColumns().elementAt(i);
1438 copiedHiddenColumns.addElement(new int[]
1439 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1444 copiedHiddenColumns = null;
1447 for (int i = 0; i < sg.getSize(); i++)
1449 SequenceI seq = null;
1453 if (orderedSeqs.containsKey(index + ""))
1455 seq = (SequenceI) orderedSeqs.get(index + "");
1467 // Returns residue following index if gap
1468 startRes = seq.findPosition(sg.getStartRes());
1471 // Need to find the residue preceeding index if gap
1474 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1476 ch = seq.getCharAt(j);
1477 if (!jalview.util.Comparison.isGap((ch)))
1485 endRes += seq.getStart() - 1;
1488 copiedSequences.append(seq.getName()
1494 + seq.getSequenceAsString(sg.getStartRes(),
1495 sg.getEndRes() + 1) + "\n");
1500 protected void pasteNew_actionPerformed()
1505 protected void pasteThis_actionPerformed()
1510 void paste(boolean newAlignment)
1515 if (copiedSequences == null)
1520 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1521 Vector seqs = new Vector();
1522 while (st.hasMoreElements())
1524 String name = st.nextToken();
1525 int start = Integer.parseInt(st.nextToken());
1526 int end = Integer.parseInt(st.nextToken());
1527 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1529 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1530 for (int i = 0; i < seqs.size(); i++)
1532 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1537 String newtitle = new String("Copied sequences");
1538 if (getTitle().startsWith("Copied sequences"))
1540 newtitle = getTitle();
1544 newtitle = newtitle.concat("- from " + getTitle());
1546 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1547 viewport.applet, newtitle, false);
1548 if (copiedHiddenColumns != null)
1550 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1552 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1553 af.viewport.hideColumns(region[0], region[1]);
1557 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1562 addSequences(newSeqs);
1565 } catch (Exception ex)
1567 } // could be anything being pasted in here
1571 void addSequences(SequenceI[] seqs)
1573 for (int i = 0; i < seqs.length; i++)
1575 viewport.alignment.addSequence(seqs[i]);
1579 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1580 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1582 viewport.setEndSeq(viewport.alignment.getHeight());
1583 viewport.alignment.getWidth();
1584 viewport.firePropertyChange("alignment", null,
1585 viewport.alignment.getSequences());
1589 protected void cut_actionPerformed()
1591 copy_actionPerformed();
1592 delete_actionPerformed();
1595 protected void delete_actionPerformed()
1598 SequenceGroup sg = viewport.getSelectionGroup();
1604 Vector seqs = new Vector();
1606 for (int i = 0; i < sg.getSize(); i++)
1608 seq = sg.getSequenceAt(i);
1609 seqs.addElement(seq);
1612 // If the cut affects all sequences, remove highlighted columns
1613 if (sg.getSize() == viewport.alignment.getHeight())
1615 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1616 sg.getEndRes() + 1);
1619 SequenceI[] cut = new SequenceI[seqs.size()];
1620 for (int i = 0; i < seqs.size(); i++)
1622 cut[i] = (SequenceI) seqs.elementAt(i);
1626 * //ADD HISTORY ITEM
1628 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1629 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1630 viewport.alignment));
1632 viewport.setSelectionGroup(null);
1633 viewport.alignment.deleteGroup(sg);
1635 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1638 if (viewport.getAlignment().getHeight() < 1)
1640 this.setVisible(false);
1642 viewport.sendSelection();
1645 protected void makeGrpsFromSelection_actionPerformed()
1647 if (viewport.getSelectionGroup() != null)
1649 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
1650 viewport.getSequenceSelection(),
1651 viewport.getAlignmentView(true).getSequenceStrings(
1652 viewport.getGapCharacter()),
1653 viewport.alignment.getGroups());
1654 viewport.alignment.deleteAllGroups();
1655 viewport.sequenceColours = null;
1656 viewport.setSelectionGroup(null);
1657 // set view properties for each group
1658 for (int g = 0; g < gps.length; g++)
1660 // gps[g].setShowunconserved(viewport.getShowUnconserved());
1661 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
1662 viewport.alignment.addGroup(gps[g]);
1663 Color col = new Color((int) (Math.random() * 255),
1664 (int) (Math.random() * 255), (int) (Math.random() * 255));
1665 col = col.brighter();
1666 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
1667 .hasMoreElements(); viewport.setSequenceColour(
1668 (SequenceI) sq.nextElement(), col))
1671 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1672 // alignPanel.updateAnnotation();
1673 alignPanel.paintAlignment(true);
1677 protected void deleteGroups_actionPerformed()
1679 viewport.alignment.deleteAllGroups();
1680 viewport.sequenceColours = null;
1681 viewport.setSelectionGroup(null);
1683 alignPanel.paintAlignment(true);
1686 public void selectAllSequenceMenuItem_actionPerformed()
1688 SequenceGroup sg = new SequenceGroup();
1689 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1691 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1693 sg.setEndRes(viewport.alignment.getWidth() - 1);
1694 viewport.setSelectionGroup(sg);
1695 alignPanel.paintAlignment(true);
1696 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1697 viewport.sendSelection();
1700 public void deselectAllSequenceMenuItem_actionPerformed()
1702 if (viewport.cursorMode)
1704 alignPanel.seqPanel.keyboardNo1 = null;
1705 alignPanel.seqPanel.keyboardNo2 = null;
1707 viewport.setSelectionGroup(null);
1708 viewport.getColumnSelection().clear();
1709 viewport.setSelectionGroup(null);
1710 alignPanel.idPanel.idCanvas.searchResults = null;
1711 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1712 alignPanel.paintAlignment(true);
1713 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1714 viewport.sendSelection();
1717 public void invertSequenceMenuItem_actionPerformed()
1719 SequenceGroup sg = viewport.getSelectionGroup();
1720 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1722 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1725 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1726 viewport.sendSelection();
1729 public void invertColSel_actionPerformed()
1731 viewport.invertColumnSelection();
1732 alignPanel.paintAlignment(true);
1733 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1734 viewport.sendSelection();
1737 void trimAlignment(boolean trimLeft)
1739 ColumnSelection colSel = viewport.getColumnSelection();
1742 if (colSel.size() > 0)
1746 column = colSel.getMin();
1750 column = colSel.getMax();
1754 if (viewport.getSelectionGroup() != null)
1756 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1757 viewport.hiddenRepSequences);
1761 seqs = viewport.alignment.getSequencesArray();
1764 TrimRegionCommand trimRegion;
1767 trimRegion = new TrimRegionCommand("Remove Left",
1768 TrimRegionCommand.TRIM_LEFT, seqs, column,
1769 viewport.alignment, viewport.colSel,
1770 viewport.selectionGroup);
1771 viewport.setStartRes(0);
1775 trimRegion = new TrimRegionCommand("Remove Right",
1776 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1777 viewport.alignment, viewport.colSel,
1778 viewport.selectionGroup);
1781 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1783 addHistoryItem(trimRegion);
1785 Vector groups = viewport.alignment.getGroups();
1787 for (int i = 0; i < groups.size(); i++)
1789 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1791 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1792 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1794 viewport.alignment.deleteGroup(sg);
1798 viewport.firePropertyChange("alignment", null, viewport
1799 .getAlignment().getSequences());
1803 public void removeGappedColumnMenuItem_actionPerformed()
1805 int start = 0, end = viewport.alignment.getWidth() - 1;
1808 if (viewport.getSelectionGroup() != null)
1810 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1811 viewport.hiddenRepSequences);
1812 start = viewport.getSelectionGroup().getStartRes();
1813 end = viewport.getSelectionGroup().getEndRes();
1817 seqs = viewport.alignment.getSequencesArray();
1820 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1821 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1823 addHistoryItem(removeGapCols);
1825 statusBar.setText("Removed " + removeGapCols.getSize()
1826 + " empty columns.");
1828 // This is to maintain viewport position on first residue
1829 // of first sequence
1830 SequenceI seq = viewport.alignment.getSequenceAt(0);
1831 int startRes = seq.findPosition(viewport.startRes);
1832 // ShiftList shifts;
1833 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1834 // edit.alColumnChanges=shifts.getInverse();
1835 // if (viewport.hasHiddenColumns)
1836 // viewport.getColumnSelection().compensateForEdits(shifts);
1837 viewport.setStartRes(seq.findIndex(startRes) - 1);
1838 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1843 public void removeAllGapsMenuItem_actionPerformed()
1845 int start = 0, end = viewport.alignment.getWidth() - 1;
1848 if (viewport.getSelectionGroup() != null)
1850 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1851 viewport.hiddenRepSequences);
1852 start = viewport.getSelectionGroup().getStartRes();
1853 end = viewport.getSelectionGroup().getEndRes();
1857 seqs = viewport.alignment.getSequencesArray();
1860 // This is to maintain viewport position on first residue
1861 // of first sequence
1862 SequenceI seq = viewport.alignment.getSequenceAt(0);
1863 int startRes = seq.findPosition(viewport.startRes);
1865 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1866 viewport.alignment));
1868 viewport.setStartRes(seq.findIndex(startRes) - 1);
1870 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1875 public void findMenuItem_actionPerformed()
1877 new Finder(alignPanel);
1881 * create a new view derived from the current view
1884 * @return frame for the new view
1886 public AlignFrame newView(String viewtitle)
1889 if (viewport.hasHiddenRows)
1891 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1892 .getFullAlignment().getSequencesArray());
1896 newal = new Alignment(viewport.alignment.getSequencesArray());
1899 if (viewport.alignment.getAlignmentAnnotation() != null)
1901 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
1903 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
1905 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
1910 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
1912 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
1913 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
1914 PaintRefresher.Register(newaf.alignPanel,
1915 newaf.alignPanel.av.getSequenceSetId());
1917 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
1918 newaf.alignPanel.av.getSequenceSetId());
1919 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
1920 newaf.alignPanel.av.getSequenceSetId());
1922 Vector comps = (Vector) PaintRefresher.components.get(viewport
1923 .getSequenceSetId());
1925 for (int i = 0; i < comps.size(); i++)
1927 if (comps.elementAt(i) instanceof AlignmentPanel)
1933 String title = new String(this.getTitle());
1934 if (viewtitle != null)
1936 title = viewtitle + " ( " + title + ")";
1940 if (title.indexOf("(View") > -1)
1942 title = title.substring(0, title.indexOf("(View"));
1944 title += "(View " + viewSize + ")";
1947 newaf.setTitle(title.toString());
1949 newaf.viewport.historyList = viewport.historyList;
1950 newaf.viewport.redoList = viewport.redoList;
1956 * @return list of feature groups on the view
1958 public String[] getFeatureGroups()
1960 FeatureRenderer fr = null;
1961 if (alignPanel != null
1962 && (fr = alignPanel.getFeatureRenderer()) != null)
1964 return fr.getGroups();
1970 * get sequence feature groups that are hidden or shown
1976 public String[] getFeatureGroupsOfState(boolean visible)
1978 FeatureRenderer fr = null;
1979 if (alignPanel != null
1980 && (fr = alignPanel.getFeatureRenderer()) != null)
1982 return fr.getGroups(visible);
1988 * Change the display state for the given feature groups
1991 * list of group strings
1993 * visible or invisible
1995 public void setFeatureGroupState(String[] groups, boolean state)
1997 FeatureRenderer fr = null;
1998 this.sequenceFeatures.setState(true);
1999 viewport.showSequenceFeatures(true);
2000 if (alignPanel != null
2001 && (fr = alignPanel.getFeatureRenderer()) != null)
2003 fr.setGroupState(groups, state);
2004 alignPanel.seqPanel.seqCanvas.repaint();
2005 if (alignPanel.overviewPanel != null)
2007 alignPanel.overviewPanel.updateOverviewImage();
2012 public void seqLimits_itemStateChanged()
2014 viewport.setShowJVSuffix(seqLimits.getState());
2015 alignPanel.fontChanged();
2016 alignPanel.paintAlignment(true);
2019 protected void colourTextMenuItem_actionPerformed()
2021 viewport.setColourText(colourTextMenuItem.getState());
2022 alignPanel.paintAlignment(true);
2025 protected void displayNonconservedMenuItem_actionPerformed()
2027 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2028 alignPanel.paintAlignment(true);
2031 protected void wrapMenuItem_actionPerformed()
2033 viewport.setWrapAlignment(wrapMenuItem.getState());
2034 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2035 scaleAbove.setEnabled(wrapMenuItem.getState());
2036 scaleLeft.setEnabled(wrapMenuItem.getState());
2037 scaleRight.setEnabled(wrapMenuItem.getState());
2038 alignPanel.paintAlignment(true);
2041 public void overviewMenuItem_actionPerformed()
2043 if (alignPanel.overviewPanel != null)
2048 Frame frame = new Frame();
2049 OverviewPanel overview = new OverviewPanel(alignPanel);
2050 frame.add(overview);
2051 // +50 must allow for applet frame window
2052 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2053 overview.getPreferredSize().width,
2054 overview.getPreferredSize().height + 50);
2057 frame.addWindowListener(new WindowAdapter()
2059 public void windowClosing(WindowEvent e)
2061 alignPanel.setOverviewPanel(null);
2065 alignPanel.setOverviewPanel(overview);
2069 void changeColour(ColourSchemeI cs)
2075 if (viewport.getAbovePIDThreshold())
2077 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2080 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2082 viewport.setGlobalColourScheme(cs);
2086 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2089 if (viewport.getConservationSelected())
2092 Alignment al = (Alignment) viewport.alignment;
2093 Conservation c = new Conservation("All",
2094 ResidueProperties.propHash, 3, al.getSequences(), 0,
2098 c.verdict(false, viewport.ConsPercGaps);
2100 cs.setConservation(c);
2102 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2108 cs.setConservation(null);
2111 cs.setConsensus(viewport.hconsensus);
2114 viewport.setGlobalColourScheme(cs);
2116 if (viewport.getColourAppliesToAllGroups())
2118 Vector groups = viewport.alignment.getGroups();
2119 for (int i = 0; i < groups.size(); i++)
2121 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2128 if (cs instanceof ClustalxColourScheme)
2130 sg.cs = new ClustalxColourScheme(
2131 sg.getSequences(viewport.hiddenRepSequences),
2138 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2139 } catch (Exception ex)
2141 ex.printStackTrace();
2146 if (viewport.getAbovePIDThreshold()
2147 || cs instanceof PIDColourScheme
2148 || cs instanceof Blosum62ColourScheme)
2150 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2151 sg.cs.setConsensus(AAFrequency.calculate(
2152 sg.getSequences(viewport.hiddenRepSequences), 0,
2157 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2160 if (viewport.getConservationSelected())
2162 Conservation c = new Conservation("Group",
2163 ResidueProperties.propHash, 3,
2164 sg.getSequences(viewport.hiddenRepSequences), 0,
2165 viewport.alignment.getWidth() - 1);
2167 c.verdict(false, viewport.ConsPercGaps);
2168 sg.cs.setConservation(c);
2172 sg.cs.setConservation(null);
2173 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2179 if (alignPanel.getOverviewPanel() != null)
2181 alignPanel.getOverviewPanel().updateOverviewImage();
2184 jalview.structure.StructureSelectionManager
2185 .getStructureSelectionManager().sequenceColoursChanged(
2188 alignPanel.paintAlignment(true);
2191 protected void modifyPID_actionPerformed()
2193 if (viewport.getAbovePIDThreshold()
2194 && viewport.globalColourScheme != null)
2196 SliderPanel.setPIDSliderSource(alignPanel,
2197 viewport.getGlobalColourScheme(), "Background");
2198 SliderPanel.showPIDSlider();
2202 protected void modifyConservation_actionPerformed()
2204 if (viewport.getConservationSelected()
2205 && viewport.globalColourScheme != null)
2207 SliderPanel.setConservationSlider(alignPanel,
2208 viewport.globalColourScheme, "Background");
2209 SliderPanel.showConservationSlider();
2213 protected void conservationMenuItem_actionPerformed()
2215 viewport.setConservationSelected(conservationMenuItem.getState());
2217 viewport.setAbovePIDThreshold(false);
2218 abovePIDThreshold.setState(false);
2220 changeColour(viewport.getGlobalColourScheme());
2222 modifyConservation_actionPerformed();
2225 public void abovePIDThreshold_actionPerformed()
2227 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2229 conservationMenuItem.setState(false);
2230 viewport.setConservationSelected(false);
2232 changeColour(viewport.getGlobalColourScheme());
2234 modifyPID_actionPerformed();
2237 public void sortPairwiseMenuItem_actionPerformed()
2239 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2240 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2241 .getAlignment().getSequenceAt(0), null);
2243 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2244 viewport.alignment));
2245 alignPanel.paintAlignment(true);
2248 public void sortIDMenuItem_actionPerformed()
2250 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2251 AlignmentSorter.sortByID(viewport.getAlignment());
2252 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2253 alignPanel.paintAlignment(true);
2256 public void sortLengthMenuItem_actionPerformed()
2258 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2259 AlignmentSorter.sortByLength(viewport.getAlignment());
2260 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2261 viewport.alignment));
2262 alignPanel.paintAlignment(true);
2265 public void sortGroupMenuItem_actionPerformed()
2267 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2268 AlignmentSorter.sortByGroup(viewport.getAlignment());
2269 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2270 viewport.alignment));
2271 alignPanel.paintAlignment(true);
2275 public void removeRedundancyMenuItem_actionPerformed()
2277 new RedundancyPanel(alignPanel);
2280 public void pairwiseAlignmentMenuItem_actionPerformed()
2282 if (viewport.getSelectionGroup() != null
2283 && viewport.getSelectionGroup().getSize() > 1)
2285 Frame frame = new Frame();
2286 frame.add(new PairwiseAlignPanel(alignPanel));
2287 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2292 public void PCAMenuItem_actionPerformed()
2294 // are the sequences aligned?
2295 if (!viewport.alignment.isAligned(false))
2298 int Width = viewport.getAlignment().getWidth();
2300 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2302 current = viewport.getAlignment().getSequenceAt(i);
2304 if (current.getLength() < Width)
2306 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2309 alignPanel.paintAlignment(true);
2312 if ((viewport.getSelectionGroup() != null
2313 && viewport.getSelectionGroup().getSize() < 4 && viewport
2314 .getSelectionGroup().getSize() > 0)
2315 || viewport.getAlignment().getHeight() < 4)
2322 new PCAPanel(viewport);
2323 } catch (java.lang.OutOfMemoryError ex)
2329 public void averageDistanceTreeMenuItem_actionPerformed()
2331 NewTreePanel("AV", "PID", "Average distance tree using PID");
2334 public void neighbourTreeMenuItem_actionPerformed()
2336 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2339 protected void njTreeBlosumMenuItem_actionPerformed()
2341 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2344 protected void avTreeBlosumMenuItem_actionPerformed()
2346 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2349 void NewTreePanel(String type, String pwType, String title)
2351 // are the sequences aligned?
2352 if (!viewport.alignment.isAligned(false))
2355 int Width = viewport.getAlignment().getWidth();
2357 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2359 current = viewport.getAlignment().getSequenceAt(i);
2361 if (current.getLength() < Width)
2363 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2366 alignPanel.paintAlignment(true);
2370 if ((viewport.getSelectionGroup() != null && viewport
2371 .getSelectionGroup().getSize() > 1)
2372 || (viewport.getSelectionGroup() == null && viewport.alignment
2375 final TreePanel tp = new TreePanel(viewport, type, pwType);
2377 addTreeMenuItem(tp, title);
2379 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2383 void loadTree_actionPerformed()
2385 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2386 cap.setText("Paste your Newick tree file here.");
2387 cap.setTreeImport();
2388 Frame frame = new Frame();
2390 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2393 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2395 TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
2396 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2397 addTreeMenuItem(tp, treeFile);
2401 * sort the alignment using the given treePanel
2404 * tree used to sort view
2406 * string used for undo event name
2408 public void sortByTree(TreePanel treePanel, String title)
2410 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2412 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2413 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2414 // HistoryItem.SORT));
2415 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2416 viewport.alignment));
2417 alignPanel.paintAlignment(true);
2421 * Do any automatic reordering of the alignment and add the necessary bits to
2422 * the menu structure for the new tree
2427 protected void addTreeMenuItem(final TreePanel treePanel,
2430 final MenuItem item = new MenuItem(title);
2431 sortByTreeMenu.add(item);
2432 item.addActionListener(new java.awt.event.ActionListener()
2434 public void actionPerformed(ActionEvent evt)
2436 sortByTree(treePanel, title); // treePanel.getTitle());
2440 treePanel.addWindowListener(new WindowAdapter()
2442 public void windowOpened(WindowEvent e)
2444 if (viewport.sortByTree)
2446 sortByTree(treePanel, title);
2448 super.windowOpened(e);
2451 public void windowClosing(WindowEvent e)
2453 sortByTreeMenu.remove(item);
2458 protected void documentation_actionPerformed()
2460 showURL("http://www.jalview.org/help.html", "HELP");
2463 protected void about_actionPerformed()
2466 class AboutPanel extends Canvas
2472 public AboutPanel(String version, String builddate)
2474 this.version = version;
2475 this.builddate = builddate;
2478 public void paint(Graphics g)
2480 g.setColor(Color.white);
2481 g.fillRect(0, 0, getSize().width, getSize().height);
2482 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2483 FontMetrics fm = g.getFontMetrics();
2484 int fh = fm.getHeight();
2486 g.setColor(Color.black);
2487 // TODO: update this text for each release or centrally store it for
2488 // lite and application
2489 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2490 g.drawString("JalviewLite - Release " + version, x, y += fh);
2491 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2492 g.drawString("Build date: " + builddate, x, y += fh);
2493 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2495 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
2497 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2499 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2502 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2504 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2506 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2509 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2511 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2516 Frame frame = new Frame();
2517 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2519 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2523 public void showURL(String url, String target)
2525 if (viewport.applet == null)
2527 System.out.println("Not running as applet - no browser available.");
2533 if (url.indexOf(":") == -1)
2535 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2537 if (url.indexOf("/") == 0)
2539 String codebase = viewport.applet.getCodeBase().toString();
2540 url = codebase.substring(0, codebase.length()
2541 - viewport.applet.getCodeBase().getFile().length())
2546 url = viewport.applet.getCodeBase() + url;
2548 System.out.println("Show url (prepended codebase): " + url);
2552 System.out.println("Show url: " + url);
2554 if (url.indexOf("javascript:") == 0)
2556 // no target for the javascript context
2557 viewport.applet.getAppletContext().showDocument(
2558 new java.net.URL(url));
2562 viewport.applet.getAppletContext().showDocument(
2563 new java.net.URL(url), target);
2565 } catch (Exception ex)
2567 ex.printStackTrace();
2572 // ////////////////////////////////////////////////////////////////////////////////
2573 // JBuilder Graphics here
2575 MenuBar alignFrameMenuBar = new MenuBar();
2577 Menu fileMenu = new Menu("File");
2579 MenuItem loadApplication = new MenuItem("View in Full Application");
2581 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2583 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2585 MenuItem outputFeatures = new MenuItem("Export Features ...");
2587 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2589 MenuItem closeMenuItem = new MenuItem("Close");
2591 Menu editMenu = new Menu("Edit");
2593 Menu viewMenu = new Menu("View");
2595 Menu colourMenu = new Menu("Colour");
2597 Menu calculateMenu = new Menu("Calculate");
2599 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2601 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2603 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2605 MenuItem remove2LeftMenuItem = new MenuItem();
2607 MenuItem remove2RightMenuItem = new MenuItem();
2609 MenuItem removeGappedColumnMenuItem = new MenuItem();
2611 MenuItem removeAllGapsMenuItem = new MenuItem();
2613 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2615 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2617 MenuItem sortPairwiseMenuItem = new MenuItem();
2619 MenuItem sortIDMenuItem = new MenuItem();
2621 MenuItem sortLengthMenuItem = new MenuItem();
2623 MenuItem sortGroupMenuItem = new MenuItem();
2625 MenuItem removeRedundancyMenuItem = new MenuItem();
2627 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2629 MenuItem PCAMenuItem = new MenuItem();
2631 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2633 MenuItem neighbourTreeMenuItem = new MenuItem();
2635 BorderLayout borderLayout1 = new BorderLayout();
2637 public Label statusBar = new Label();
2639 Menu outputTextboxMenu = new Menu();
2641 MenuItem clustalColour = new MenuItem();
2643 MenuItem zappoColour = new MenuItem();
2645 MenuItem taylorColour = new MenuItem();
2647 MenuItem hydrophobicityColour = new MenuItem();
2649 MenuItem helixColour = new MenuItem();
2651 MenuItem strandColour = new MenuItem();
2653 MenuItem turnColour = new MenuItem();
2655 MenuItem buriedColour = new MenuItem();
2657 MenuItem userDefinedColour = new MenuItem();
2659 MenuItem PIDColour = new MenuItem();
2661 MenuItem BLOSUM62Colour = new MenuItem();
2663 MenuItem njTreeBlosumMenuItem = new MenuItem();
2665 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2667 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2669 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2671 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2673 MenuItem alProperties = new MenuItem("Alignment Properties...");
2675 MenuItem overviewMenuItem = new MenuItem();
2677 MenuItem undoMenuItem = new MenuItem();
2679 MenuItem redoMenuItem = new MenuItem();
2681 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2683 MenuItem noColourmenuItem = new MenuItem();
2685 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2687 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2689 MenuItem findMenuItem = new MenuItem();
2691 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2693 MenuItem nucleotideColour = new MenuItem();
2695 MenuItem deleteGroups = new MenuItem();
2697 MenuItem grpsFromSelection = new MenuItem();
2699 MenuItem delete = new MenuItem();
2701 MenuItem copy = new MenuItem();
2703 MenuItem cut = new MenuItem();
2705 Menu pasteMenu = new Menu();
2707 MenuItem pasteNew = new MenuItem();
2709 MenuItem pasteThis = new MenuItem();
2711 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2713 MenuItem font = new MenuItem();
2715 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2717 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2719 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2721 MenuItem modifyPID = new MenuItem();
2723 MenuItem modifyConservation = new MenuItem();
2725 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2726 "Autocalculate Consensus", true);
2728 Menu sortByTreeMenu = new Menu();
2730 Menu sort = new Menu();
2732 Menu calculate = new Menu();
2734 MenuItem inputText = new MenuItem();
2736 Menu helpMenu = new Menu();
2738 MenuItem documentation = new MenuItem();
2740 MenuItem about = new MenuItem();
2742 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2744 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2746 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2748 private void jbInit() throws Exception
2751 setMenuBar(alignFrameMenuBar);
2755 // dynamically fill save as menu with available formats
2756 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2759 item = new MenuItem(
2760 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2762 item.addActionListener(new java.awt.event.ActionListener()
2764 public void actionPerformed(ActionEvent e)
2766 outputText_actionPerformed(e);
2770 outputTextboxMenu.add(item);
2772 closeMenuItem.addActionListener(this);
2773 loadApplication.addActionListener(this);
2775 loadTree.addActionListener(this);
2776 loadAnnotations.addActionListener(this);
2777 outputFeatures.addActionListener(this);
2778 outputAnnotations.addActionListener(this);
2779 selectAllSequenceMenuItem.addActionListener(this);
2780 deselectAllSequenceMenuItem.addActionListener(this);
2781 invertSequenceMenuItem.addActionListener(this);
2782 remove2LeftMenuItem.setLabel("Remove Left");
2783 remove2LeftMenuItem.addActionListener(this);
2784 remove2RightMenuItem.setLabel("Remove Right");
2785 remove2RightMenuItem.addActionListener(this);
2786 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2787 removeGappedColumnMenuItem.addActionListener(this);
2788 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2789 removeAllGapsMenuItem.addActionListener(this);
2790 viewBoxesMenuItem.setLabel("Boxes");
2791 viewBoxesMenuItem.setState(true);
2792 viewBoxesMenuItem.addItemListener(this);
2793 viewTextMenuItem.setLabel("Text");
2794 viewTextMenuItem.setState(true);
2795 viewTextMenuItem.addItemListener(this);
2796 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2797 sortPairwiseMenuItem.addActionListener(this);
2798 sortIDMenuItem.setLabel("by ID");
2799 sortIDMenuItem.addActionListener(this);
2800 sortLengthMenuItem.setLabel("by Length");
2801 sortLengthMenuItem.addActionListener(this);
2802 sortGroupMenuItem.setLabel("by Group");
2803 sortGroupMenuItem.addActionListener(this);
2804 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2805 removeRedundancyMenuItem.addActionListener(this);
2806 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2807 pairwiseAlignmentMenuItem.addActionListener(this);
2808 PCAMenuItem.setLabel("Principal Component Analysis");
2809 PCAMenuItem.addActionListener(this);
2810 averageDistanceTreeMenuItem
2811 .setLabel("Average Distance Using % Identity");
2812 averageDistanceTreeMenuItem.addActionListener(this);
2813 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2814 neighbourTreeMenuItem.addActionListener(this);
2815 statusBar.setBackground(Color.white);
2816 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2817 statusBar.setText("Status bar");
2818 outputTextboxMenu.setLabel("Output to Textbox");
2819 clustalColour.setLabel("Clustalx");
2821 clustalColour.addActionListener(this);
2822 zappoColour.setLabel("Zappo");
2823 zappoColour.addActionListener(this);
2824 taylorColour.setLabel("Taylor");
2825 taylorColour.addActionListener(this);
2826 hydrophobicityColour.setLabel("Hydrophobicity");
2827 hydrophobicityColour.addActionListener(this);
2828 helixColour.setLabel("Helix Propensity");
2829 helixColour.addActionListener(this);
2830 strandColour.setLabel("Strand Propensity");
2831 strandColour.addActionListener(this);
2832 turnColour.setLabel("Turn Propensity");
2833 turnColour.addActionListener(this);
2834 buriedColour.setLabel("Buried Index");
2835 buriedColour.addActionListener(this);
2836 userDefinedColour.setLabel("User Defined...");
2837 userDefinedColour.addActionListener(this);
2838 PIDColour.setLabel("Percentage Identity");
2839 PIDColour.addActionListener(this);
2840 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2841 BLOSUM62Colour.addActionListener(this);
2842 avDistanceTreeBlosumMenuItem
2843 .setLabel("Average Distance Using BLOSUM62");
2844 avDistanceTreeBlosumMenuItem.addActionListener(this);
2845 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2846 njTreeBlosumMenuItem.addActionListener(this);
2847 annotationPanelMenuItem.setLabel("Show Annotations");
2848 annotationPanelMenuItem.addItemListener(this);
2849 colourTextMenuItem.setLabel("Colour Text");
2850 colourTextMenuItem.addItemListener(this);
2851 displayNonconservedMenuItem.setLabel("Show nonconserved");
2852 displayNonconservedMenuItem.addItemListener(this);
2853 alProperties.addActionListener(this);
2854 overviewMenuItem.setLabel("Overview Window");
2855 overviewMenuItem.addActionListener(this);
2856 undoMenuItem.setEnabled(false);
2857 undoMenuItem.setLabel("Undo");
2858 undoMenuItem.addActionListener(this);
2859 redoMenuItem.setEnabled(false);
2860 redoMenuItem.setLabel("Redo");
2861 redoMenuItem.addActionListener(this);
2862 conservationMenuItem.setLabel("by Conservation");
2863 conservationMenuItem.addItemListener(this);
2864 noColourmenuItem.setLabel("None");
2865 noColourmenuItem.addActionListener(this);
2866 wrapMenuItem.setLabel("Wrap");
2867 wrapMenuItem.addItemListener(this);
2868 renderGapsMenuItem.setLabel("Show Gaps");
2869 renderGapsMenuItem.setState(true);
2870 renderGapsMenuItem.addItemListener(this);
2871 findMenuItem.setLabel("Find...");
2872 findMenuItem.addActionListener(this);
2873 abovePIDThreshold.setLabel("Above Identity Threshold");
2874 abovePIDThreshold.addItemListener(this);
2875 nucleotideColour.setLabel("Nucleotide");
2876 nucleotideColour.addActionListener(this);
2877 deleteGroups.setLabel("Undefine Groups");
2878 deleteGroups.addActionListener(this);
2879 grpsFromSelection.setLabel("Make Groups for selection");
2880 grpsFromSelection.addActionListener(this);
2881 copy.setLabel("Copy");
2882 copy.addActionListener(this);
2883 cut.setLabel("Cut");
2884 cut.addActionListener(this);
2885 delete.setLabel("Delete");
2886 delete.addActionListener(this);
2887 pasteMenu.setLabel("Paste");
2888 pasteNew.setLabel("To New Alignment");
2889 pasteNew.addActionListener(this);
2890 pasteThis.setLabel("Add To This Alignment");
2891 pasteThis.addActionListener(this);
2892 applyToAllGroups.setLabel("Apply Colour To All Groups");
2893 applyToAllGroups.setState(true);
2894 applyToAllGroups.addItemListener(this);
2895 font.setLabel("Font...");
2896 font.addActionListener(this);
2897 scaleAbove.setLabel("Scale Above");
2898 scaleAbove.setState(true);
2899 scaleAbove.setEnabled(false);
2900 scaleAbove.addItemListener(this);
2901 scaleLeft.setEnabled(false);
2902 scaleLeft.setState(true);
2903 scaleLeft.setLabel("Scale Left");
2904 scaleLeft.addItemListener(this);
2905 scaleRight.setEnabled(false);
2906 scaleRight.setState(true);
2907 scaleRight.setLabel("Scale Right");
2908 scaleRight.addItemListener(this);
2909 modifyPID.setLabel("Modify Identity Threshold...");
2910 modifyPID.addActionListener(this);
2911 modifyConservation.setLabel("Modify Conservation Threshold...");
2912 modifyConservation.addActionListener(this);
2913 sortByTreeMenu.setLabel("By Tree Order");
2914 sort.setLabel("Sort");
2915 calculate.setLabel("Calculate Tree");
2916 autoCalculate.addItemListener(this);
2917 inputText.setLabel("Input from textbox");
2918 inputText.addActionListener(this);
2919 centreColumnLabelFlag.setLabel("Centre column labels");
2920 centreColumnLabelFlag.addItemListener(this);
2921 followMouseOverFlag.setLabel("Automatic Scrolling");
2922 followMouseOverFlag.addItemListener(this);
2923 helpMenu.setLabel("Help");
2924 documentation.setLabel("Documentation");
2925 documentation.addActionListener(this);
2927 about.setLabel("About...");
2928 about.addActionListener(this);
2929 seqLimits.setState(true);
2930 seqLimits.setLabel("Show Sequence Limits");
2931 seqLimits.addItemListener(this);
2932 featureSettings.setLabel("Feature Settings...");
2933 featureSettings.addActionListener(this);
2934 sequenceFeatures.setLabel("Sequence Features");
2935 sequenceFeatures.addItemListener(this);
2936 sequenceFeatures.setState(false);
2937 annotationColour.setLabel("by Annotation...");
2938 annotationColour.addActionListener(this);
2939 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2940 invertColSel.setLabel("Invert Column Selection");
2941 menu1.setLabel("Show");
2942 showColumns.setLabel("All Columns ");
2943 showSeqs.setLabel("All Sequences");
2944 menu2.setLabel("Hide");
2945 hideColumns.setLabel("Selected Columns");
2946 hideSequences.setLabel("Selected Sequences");
2947 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
2948 hideAllSelection.setLabel("Selected Region");
2949 showAllHidden.setLabel("All Sequences and Columns");
2950 invertColSel.addActionListener(this);
2951 showColumns.addActionListener(this);
2952 showSeqs.addActionListener(this);
2953 hideColumns.addActionListener(this);
2954 hideSequences.addActionListener(this);
2955 hideAllButSelection.addActionListener(this);
2956 hideAllSelection.addActionListener(this);
2957 showAllHidden.addActionListener(this);
2958 formatMenu.setLabel("Format");
2959 selectMenu.setLabel("Select");
2960 newView.setLabel("New View");
2961 newView.addActionListener(this);
2962 alignFrameMenuBar.add(fileMenu);
2963 alignFrameMenuBar.add(editMenu);
2964 alignFrameMenuBar.add(selectMenu);
2965 alignFrameMenuBar.add(viewMenu);
2966 alignFrameMenuBar.add(formatMenu);
2967 alignFrameMenuBar.add(colourMenu);
2968 alignFrameMenuBar.add(calculateMenu);
2969 alignFrameMenuBar.add(helpMenu);
2971 fileMenu.add(inputText);
2972 fileMenu.add(loadTree);
2973 fileMenu.add(loadAnnotations);
2975 fileMenu.addSeparator();
2976 fileMenu.add(outputTextboxMenu);
2977 fileMenu.add(outputFeatures);
2978 fileMenu.add(outputAnnotations);
2980 if (jalviewServletURL != null)
2982 fileMenu.add(loadApplication);
2985 fileMenu.addSeparator();
2986 fileMenu.add(closeMenuItem);
2988 editMenu.add(undoMenuItem);
2989 editMenu.add(redoMenuItem);
2992 editMenu.add(pasteMenu);
2993 editMenu.add(delete);
2994 editMenu.addSeparator();
2995 editMenu.add(remove2LeftMenuItem);
2996 editMenu.add(remove2RightMenuItem);
2997 editMenu.add(removeGappedColumnMenuItem);
2998 editMenu.add(removeAllGapsMenuItem);
2999 editMenu.add(removeRedundancyMenuItem);
3000 viewMenu.add(newView);
3001 viewMenu.addSeparator();
3002 viewMenu.add(menu1);
3003 viewMenu.add(menu2);
3004 viewMenu.addSeparator();
3005 viewMenu.add(followMouseOverFlag);
3006 viewMenu.add(annotationPanelMenuItem);
3007 viewMenu.addSeparator();
3008 viewMenu.add(sequenceFeatures);
3009 viewMenu.add(featureSettings);
3010 viewMenu.addSeparator();
3011 viewMenu.add(alProperties);
3012 viewMenu.addSeparator();
3013 viewMenu.add(overviewMenuItem);
3014 colourMenu.add(applyToAllGroups);
3015 colourMenu.addSeparator();
3016 colourMenu.add(noColourmenuItem);
3017 colourMenu.add(clustalColour);
3018 colourMenu.add(BLOSUM62Colour);
3019 colourMenu.add(PIDColour);
3020 colourMenu.add(zappoColour);
3021 colourMenu.add(taylorColour);
3022 colourMenu.add(hydrophobicityColour);
3023 colourMenu.add(helixColour);
3024 colourMenu.add(strandColour);
3025 colourMenu.add(turnColour);
3026 colourMenu.add(buriedColour);
3027 colourMenu.add(nucleotideColour);
3028 colourMenu.add(userDefinedColour);
3029 colourMenu.addSeparator();
3030 colourMenu.add(conservationMenuItem);
3031 colourMenu.add(modifyConservation);
3032 colourMenu.add(abovePIDThreshold);
3033 colourMenu.add(modifyPID);
3034 colourMenu.add(annotationColour);
3035 calculateMenu.add(sort);
3036 calculateMenu.add(calculate);
3037 calculateMenu.addSeparator();
3038 calculateMenu.add(pairwiseAlignmentMenuItem);
3039 calculateMenu.add(PCAMenuItem);
3040 calculateMenu.add(autoCalculate);
3041 this.add(statusBar, BorderLayout.SOUTH);
3042 pasteMenu.add(pasteNew);
3043 pasteMenu.add(pasteThis);
3044 sort.add(sortIDMenuItem);
3045 sort.add(sortLengthMenuItem);
3046 sort.add(sortByTreeMenu);
3047 sort.add(sortGroupMenuItem);
3048 sort.add(sortPairwiseMenuItem);
3049 calculate.add(averageDistanceTreeMenuItem);
3050 calculate.add(neighbourTreeMenuItem);
3051 calculate.add(avDistanceTreeBlosumMenuItem);
3052 calculate.add(njTreeBlosumMenuItem);
3053 helpMenu.add(documentation);
3054 helpMenu.add(about);
3055 menu1.add(showColumns);
3056 menu1.add(showSeqs);
3057 menu1.add(showAllHidden);
3058 menu2.add(hideColumns);
3059 menu2.add(hideSequences);
3060 menu2.add(hideAllSelection);
3061 menu2.add(hideAllButSelection);
3062 formatMenu.add(font);
3063 formatMenu.add(seqLimits);
3064 formatMenu.add(wrapMenuItem);
3065 formatMenu.add(scaleAbove);
3066 formatMenu.add(scaleLeft);
3067 formatMenu.add(scaleRight);
3068 formatMenu.add(viewBoxesMenuItem);
3069 formatMenu.add(viewTextMenuItem);
3070 formatMenu.add(colourTextMenuItem);
3071 formatMenu.add(displayNonconservedMenuItem);
3072 formatMenu.add(renderGapsMenuItem);
3073 formatMenu.add(centreColumnLabelFlag);
3074 selectMenu.add(findMenuItem);
3075 selectMenu.addSeparator();
3076 selectMenu.add(selectAllSequenceMenuItem);
3077 selectMenu.add(deselectAllSequenceMenuItem);
3078 selectMenu.add(invertSequenceMenuItem);
3079 selectMenu.add(invertColSel);
3080 selectMenu.add(grpsFromSelection);
3081 selectMenu.add(deleteGroups);
3085 MenuItem featureSettings = new MenuItem();
3087 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3089 MenuItem annotationColour = new MenuItem();
3091 MenuItem invertColSel = new MenuItem();
3093 Menu menu1 = new Menu();
3095 MenuItem showColumns = new MenuItem();
3097 MenuItem showSeqs = new MenuItem();
3099 Menu menu2 = new Menu();
3101 MenuItem hideColumns = new MenuItem();
3103 MenuItem hideSequences = new MenuItem();
3105 MenuItem hideAllButSelection = new MenuItem();
3107 MenuItem hideAllSelection = new MenuItem();
3109 MenuItem showAllHidden = new MenuItem();
3111 Menu formatMenu = new Menu();
3113 Menu selectMenu = new Menu();
3115 MenuItem newView = new MenuItem();
3118 * Attach the alignFrame panels after embedding menus, if necessary. This used
3119 * to be called setEmbedded, but is now creates the dropdown menus in a
3120 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3122 * @param reallyEmbedded
3123 * true to attach the view to the applet area on the page rather than
3126 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3131 // Explicly build the embedded menu panel for the on-page applet
3133 // view cannot be closed if its actually on the page
3134 fileMenu.remove(closeMenuItem);
3135 fileMenu.remove(3); // Remove Seperator
3136 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3137 Font.PLAIN, 10, false); // use our own fonts.
3138 // and actually add the components to the applet area
3139 viewport.applet.setLayout(new BorderLayout());
3140 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3141 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3142 alignPanel.setSize(viewport.applet.getSize().width,
3143 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3144 - statusBar.HEIGHT);
3145 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3146 final AlignFrame me = this;
3147 viewport.applet.addFocusListener(new FocusListener()
3151 public void focusLost(FocusEvent e)
3153 if (me.viewport.applet.currentAlignFrame==me) {
3154 me.viewport.applet.currentAlignFrame = null;
3158 public void focusGained(FocusEvent e)
3160 me.viewport.applet.currentAlignFrame = me;
3163 viewport.applet.validate();
3168 // test and embed menu bar if necessary.
3170 if (embedMenuIfNeeded(alignPanel))
3172 // adjust for status bar height too
3173 alignPanel.setSize(getSize().width, getSize().height
3174 - statusBar.HEIGHT);
3176 add(statusBar, BorderLayout.SOUTH);
3177 add(alignPanel, BorderLayout.CENTER);
3178 // and register with the applet so it can pass external API calls to us
3179 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3185 * create a new binding between structures in an existing jmol viewer instance
3186 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3187 * this does not open a new Jmol window, or modify the display of the
3188 * structures in the original jmol window. Note This method doesn't work
3189 * without an additional javascript library to exchange messages between the
3190 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3193 * JmolViewer instance
3194 * @param sequenceIds
3195 * - sequence Ids to search for associations
3197 public SequenceStructureBinding addStructureViewInstance(
3198 Object jmolviewer, String[] sequenceIds)
3200 org.jmol.api.JmolViewer viewer = null;
3203 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3204 } catch (ClassCastException ex)
3206 System.err.println("Unsupported viewer object :"
3207 + jmolviewer.getClass());
3211 System.err.println("Can't use this object as a structure viewer:"
3212 + jmolviewer.getClass());
3215 SequenceI[] seqs = null;
3216 if (sequenceIds == null || sequenceIds.length == 0)
3218 seqs = viewport.getAlignment().getSequencesArray();
3222 Vector sqi = new Vector();
3223 AlignmentI al = viewport.getAlignment();
3224 for (int sid = 0; sid < sequenceIds.length; sid++)
3226 SequenceI sq = al.findName(sequenceIds[sid]);
3234 seqs = new SequenceI[sqi.size()];
3235 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3237 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3246 // TODO: search for a jmv that involves viewer
3248 { // create a new viewer/jalview binding.
3249 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
3255 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3258 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3259 boolean needtoadd = false;
3260 if (toaddpdb != null)
3262 Vector pdbe = toaddpdb.getPDBId();
3263 PDBEntry pdbentry = null;
3264 if (pdbe != null && pdbe.size() > 0)
3266 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3268 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3269 if (!pdbentry.getId().equals(pdbEntryString)
3270 && !pdbentry.getFile().equals(pdbFile))
3280 if (pdbentry == null)
3282 pdbentry = new PDBEntry();
3283 pdbentry.setId(pdbEntryString);
3284 pdbentry.setFile(pdbFile);
3285 needtoadd = true; // add this new entry to sequence.
3287 // resolve data source
3288 // TODO: this code should be a refactored to an io package
3289 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3290 if (protocol == null)
3296 // make a note of the access mode and add
3297 if (pdbentry.getProperty() == null)
3299 pdbentry.setProperty(new Hashtable());
3301 pdbentry.getProperty().put("protocol", protocol);
3302 toaddpdb.addPDBId(pdbentry);
3308 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3312 Vector sequences = new Vector();
3313 for (int i = 0; i < seqs.length; i++)
3315 if (seqs[i] != null)
3317 sequences.addElement(new Object[]
3318 { seqs[i], (chains != null) ? chains[i] : null });
3321 seqs = new SequenceI[sequences.size()];
3322 chains = new String[sequences.size()];
3323 for (int i = 0, isize = sequences.size(); i < isize; i++)
3325 Object[] oj = (Object[]) sequences.elementAt(i);
3327 seqs[i] = (SequenceI) oj[0];
3328 chains[i] = (String) oj[1];
3336 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3337 SequenceI[] seqs, String[] chains, String protocol)
3339 // Scrub any null sequences from the array
3340 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3341 seqs = (SequenceI[]) sqch[0];
3342 chains = (String[]) sqch[1];
3343 if (seqs == null || seqs.length == 0)
3346 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3348 if (protocol == null || protocol.trim().length() == 0
3349 || protocol.equals("null"))
3351 protocol = (String) pdb.getProperty().get("protocol");
3352 if (protocol == null)
3354 System.err.println("Couldn't work out protocol to open structure: "
3359 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3361 // can only do alignments with Jmol
3362 // find the last jmol window assigned to this alignment
3363 jalview.appletgui.AppletJmol ajm = null, tajm;
3364 Vector jmols = applet
3365 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3366 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3368 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3369 if (tajm.ap.alignFrame == this)
3378 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3379 // try and add the pdb structure
3384 // otherwise, create a new window
3385 if (applet.jmolAvailable)
3387 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3389 applet.lastFrameX += 40;
3390 applet.lastFrameY += 40;
3394 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3399 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3400 SequenceI[][] seqs, String[][] chains, String[] protocols)
3402 // TODO Auto-generated method stub
3403 System.err.println("Aligned Structure View: Not yet implemented.");
3407 * modify the current selection, providing the user has not made a selection already.
3408 * @param sel - sequences from this alignment
3409 * @param csel - columns to be selected on the alignment
3411 public void select(SequenceGroup sel, ColumnSelection csel)
3413 alignPanel.seqPanel.selection(sel, csel, null);