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;
24 import java.awt.event.*;
26 import jalview.analysis.*;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.bin.JalviewLite;
29 import jalview.commands.*;
30 import jalview.datamodel.*;
32 import jalview.schemes.*;
33 import jalview.structure.StructureSelectionManager;
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());
74 showGroupConsensus.setState(viewport.showGroupConsensus);
75 showGroupConservation.setState(viewport.showGroupConservation);
76 showConsensusHistogram.setState(viewport.showConsensusHistogram);
77 showSequenceLogo.setState(viewport.showSequenceLogo);
79 seqLimits.setState(viewport.showJVSuffix);
83 String param = applet.getParameter("sortBy");
86 if (param.equalsIgnoreCase("Id"))
88 sortIDMenuItem_actionPerformed();
90 else if (param.equalsIgnoreCase("Pairwise Identity"))
92 sortPairwiseMenuItem_actionPerformed();
94 else if (param.equalsIgnoreCase("Length"))
96 sortLengthMenuItem_actionPerformed();
100 param = applet.getParameter("wrap");
103 if (param.equalsIgnoreCase("true"))
105 wrapMenuItem.setState(true);
106 wrapMenuItem_actionPerformed();
109 param = applet.getParameter("centrecolumnlabels");
112 centreColumnLabelFlag.setState(true);
113 centreColumnLabelFlag_stateChanged();
117 param = applet.getParameter("windowWidth");
120 int width = Integer.parseInt(param);
121 DEFAULT_WIDTH = width;
123 param = applet.getParameter("windowHeight");
126 int height = Integer.parseInt(param);
127 DEFAULT_HEIGHT = height;
129 } catch (Exception ex)
135 // Some JVMS send keyevents to Top frame or lowest panel,
136 // Havent worked out why yet. So add to both this frame and seqCanvas for
138 this.addKeyListener(this);
139 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
140 alignPanel.idPanel.idCanvas.addKeyListener(this);
141 alignPanel.scalePanel.addKeyListener(this);
142 alignPanel.annotationPanel.addKeyListener(this);
143 alignPanel.annotationPanelHolder.addKeyListener(this);
144 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
145 alignPanel.alabels.addKeyListener(this);
146 createAlignFrameWindow(embedded, title);
147 alignPanel.validate();
148 alignPanel.paintAlignment(true);
151 public AlignViewport getAlignViewport()
156 public SeqCanvas getSeqcanvas()
158 return alignPanel.seqPanel.seqCanvas;
168 public void parseFeaturesFile(String file, String type)
170 Hashtable featureLinks = new Hashtable();
171 boolean featuresFile = false;
174 featuresFile = new jalview.io.FeaturesFile(file, type)
175 .parse(viewport.alignment,
176 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
177 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
178 } catch (Exception ex)
180 ex.printStackTrace();
185 if (featureLinks.size() > 0)
187 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
189 viewport.showSequenceFeatures = true;
190 sequenceFeatures.setState(true);
191 if (viewport.featureSettings != null)
193 viewport.featureSettings.refreshTable();
195 alignPanel.paintAlignment(true);
200 public void keyPressed(KeyEvent evt)
202 if (viewport.cursorMode
203 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
204 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
205 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
206 && Character.isDigit(evt.getKeyChar()))
207 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
209 switch (evt.getKeyCode())
211 case 27: // escape key
212 deselectAllSequenceMenuItem_actionPerformed();
214 alignPanel.alabels.cancelDrag();
217 if (evt.isControlDown() || evt.isMetaDown())
219 cut_actionPerformed();
223 if (viewport.cursorMode && !evt.isControlDown())
225 alignPanel.seqPanel.setCursorColumn();
227 if (evt.isControlDown() || evt.isMetaDown())
229 copy_actionPerformed();
233 if (evt.isControlDown())
235 paste(evt.isShiftDown());
239 if (evt.isControlDown() || evt.isMetaDown())
241 selectAllSequenceMenuItem_actionPerformed();
244 case KeyEvent.VK_DOWN:
245 if (viewport.cursorMode)
247 alignPanel.seqPanel.moveCursor(0, 1);
251 moveSelectedSequences(false);
256 if (viewport.cursorMode)
258 alignPanel.seqPanel.moveCursor(0, -1);
262 moveSelectedSequences(true);
266 case KeyEvent.VK_LEFT:
267 if (evt.isAltDown() || !viewport.cursorMode)
268 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
270 alignPanel.seqPanel.moveCursor(-1, 0);
273 case KeyEvent.VK_RIGHT:
274 if (evt.isAltDown() || !viewport.cursorMode)
275 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
277 alignPanel.seqPanel.moveCursor(1, 0);
280 case KeyEvent.VK_SPACE:
281 if (viewport.cursorMode)
283 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
284 || evt.isShiftDown() || evt.isAltDown());
288 case KeyEvent.VK_DELETE:
289 case KeyEvent.VK_BACK_SPACE:
290 if (viewport.cursorMode)
292 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
293 || evt.isShiftDown() || evt.isAltDown());
297 cut_actionPerformed();
298 alignPanel.seqPanel.seqCanvas.repaint();
303 if (viewport.cursorMode)
305 alignPanel.seqPanel.setCursorRow();
309 if (viewport.cursorMode)
311 alignPanel.seqPanel.setCursorPosition();
315 case KeyEvent.VK_ENTER:
316 case KeyEvent.VK_COMMA:
317 if (viewport.cursorMode)
319 alignPanel.seqPanel.setCursorRowAndColumn();
324 if (viewport.cursorMode)
326 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
330 if (viewport.cursorMode)
332 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
337 viewport.cursorMode = !viewport.cursorMode;
338 statusBar.setText("Keyboard editing mode is "
339 + (viewport.cursorMode ? "on" : "off"));
340 if (viewport.cursorMode)
342 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
343 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
348 if (evt.isControlDown())
350 findMenuItem_actionPerformed();
356 boolean toggleSeqs = !evt.isControlDown();
357 boolean toggleCols = !evt.isShiftDown();
358 toggleHiddenRegions(toggleSeqs, toggleCols);
362 case KeyEvent.VK_PAGE_UP:
363 if (viewport.wrapAlignment)
365 alignPanel.scrollUp(true);
369 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
370 - viewport.endSeq + viewport.startSeq);
374 case KeyEvent.VK_PAGE_DOWN:
375 if (viewport.wrapAlignment)
377 alignPanel.scrollUp(false);
381 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
382 + viewport.endSeq - viewport.startSeq);
387 if (evt.isControlDown())
389 undoMenuItem_actionPerformed();
394 if (evt.isControlDown())
396 redoMenuItem_actionPerformed();
401 if (evt.isControlDown())
408 if (evt.isControlDown())
410 trimAlignment(false);
415 if (evt.isControlDown())
417 if (evt.isShiftDown())
419 this.removeAllGapsMenuItem_actionPerformed();
423 removeGappedColumnMenuItem_actionPerformed();
428 if (evt.isControlDown())
432 invertColSel_actionPerformed();
436 invertSequenceMenuItem_actionPerformed();
442 if (evt.isControlDown())
444 this.deleteGroups_actionPerformed();
449 if (evt.isControlDown())
456 alignPanel.paintAlignment(true);
460 * called by key handler and the hide all/show all menu items
465 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
467 boolean hide = false;
468 SequenceGroup sg = viewport.getSelectionGroup();
469 if (!toggleSeqs && !toggleCols)
471 // Hide everything by the current selection - this is a hack - we do the
472 // invert and then hide
473 // first check that there will be visible columns after the invert.
474 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
475 .getSelected().size() > 0)
476 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
479 // now invert the sequence set, if required - empty selection implies
480 // that no hiding is required.
483 invertSequenceMenuItem_actionPerformed();
484 sg = viewport.getSelectionGroup();
488 viewport.expandColSelection(sg, true);
489 // finally invert the column selection and get the new sequence
490 // selection and indicate it should be hidden.
491 invertColSel_actionPerformed();
498 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
501 viewport.hideAllSelectedSeqs();
503 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
505 viewport.showAllHiddenSeqs();
511 if (viewport.colSel.getSelected().size() > 0)
513 viewport.hideSelectedColumns();
516 viewport.selectionGroup = sg;
521 viewport.showAllHiddenColumns();
526 public void keyReleased(KeyEvent evt)
530 public void keyTyped(KeyEvent evt)
534 public void itemStateChanged(ItemEvent evt)
536 if (evt.getSource() == displayNonconservedMenuItem)
538 displayNonconservedMenuItem_actionPerformed();
540 else if (evt.getSource() == colourTextMenuItem)
542 colourTextMenuItem_actionPerformed();
544 else if (evt.getSource() == wrapMenuItem)
546 wrapMenuItem_actionPerformed();
548 else if (evt.getSource() == scaleAbove)
550 viewport.setScaleAboveWrapped(scaleAbove.getState());
552 else if (evt.getSource() == scaleLeft)
554 viewport.setScaleLeftWrapped(scaleLeft.getState());
556 else if (evt.getSource() == scaleRight)
558 viewport.setScaleRightWrapped(scaleRight.getState());
560 else if (evt.getSource() == seqLimits)
562 seqLimits_itemStateChanged();
564 else if (evt.getSource() == viewBoxesMenuItem)
566 viewport.setShowBoxes(viewBoxesMenuItem.getState());
568 else if (evt.getSource() == viewTextMenuItem)
570 viewport.setShowText(viewTextMenuItem.getState());
572 else if (evt.getSource() == renderGapsMenuItem)
574 viewport.setRenderGaps(renderGapsMenuItem.getState());
576 else if (evt.getSource() == annotationPanelMenuItem)
578 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
579 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
581 else if (evt.getSource() == sequenceFeatures)
583 viewport.showSequenceFeatures(sequenceFeatures.getState());
584 alignPanel.seqPanel.seqCanvas.repaint();
586 else if (evt.getSource() == conservationMenuItem)
588 conservationMenuItem_actionPerformed();
590 else if (evt.getSource() == abovePIDThreshold)
592 abovePIDThreshold_actionPerformed();
594 else if (evt.getSource() == applyToAllGroups)
596 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
598 else if (evt.getSource() == autoCalculate)
600 viewport.autocalculateConsensus = autoCalculate.getState();
602 else if (evt.getSource() == this.centreColumnLabelFlag)
604 centreColumnLabelFlag_stateChanged();
606 else if (evt.getSource() == this.followMouseOverFlag)
608 mouseOverFlag_stateChanged();
610 else if (evt.getSource() == showGroupConsensus)
612 showGroupConsensus_actionPerformed();
614 else if (evt.getSource() == showGroupConservation)
616 showGroupConservation_actionPerformed();
618 else if (evt.getSource() == showSequenceLogo)
620 showSequenceLogo_actionPerformed();
622 else if (evt.getSource() == showConsensusHistogram)
624 showConsensusHistogram_actionPerformed();
626 else if (evt.getSource() == applyAutoAnnotationSettings)
628 applyAutoAnnotationSettings_actionPerformed();
630 alignPanel.paintAlignment(true);
633 private void mouseOverFlag_stateChanged()
635 viewport.followHighlight = followMouseOverFlag.getState();
636 // TODO: could kick the scrollTo mechanism to reset view for current
640 private void centreColumnLabelFlag_stateChanged()
642 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
643 this.alignPanel.annotationPanel.repaint();
646 public void actionPerformed(ActionEvent evt)
648 Object source = evt.getSource();
650 if (source == inputText)
652 inputText_actionPerformed();
654 else if (source == loadTree)
656 loadTree_actionPerformed();
658 else if (source == loadApplication)
660 launchFullApplication();
662 else if (source == loadAnnotations)
666 else if (source == outputAnnotations)
668 outputAnnotations(true);
670 else if (source == outputFeatures)
672 outputFeatures(true, "Jalview");
674 else if (source == closeMenuItem)
676 closeMenuItem_actionPerformed();
678 else if (source == copy)
680 copy_actionPerformed();
682 else if (source == undoMenuItem)
684 undoMenuItem_actionPerformed();
686 else if (source == redoMenuItem)
688 redoMenuItem_actionPerformed();
690 else if (source == inputText)
692 inputText_actionPerformed();
694 else if (source == closeMenuItem)
696 closeMenuItem_actionPerformed();
698 else if (source == undoMenuItem)
700 undoMenuItem_actionPerformed();
702 else if (source == redoMenuItem)
704 redoMenuItem_actionPerformed();
706 else if (source == copy)
708 copy_actionPerformed();
710 else if (source == pasteNew)
712 pasteNew_actionPerformed();
714 else if (source == pasteThis)
716 pasteThis_actionPerformed();
718 else if (source == cut)
720 cut_actionPerformed();
722 else if (source == delete)
724 delete_actionPerformed();
726 else if (source == grpsFromSelection)
728 makeGrpsFromSelection_actionPerformed();
730 else if (source == deleteGroups)
732 deleteGroups_actionPerformed();
734 else if (source == selectAllSequenceMenuItem)
736 selectAllSequenceMenuItem_actionPerformed();
738 else if (source == deselectAllSequenceMenuItem)
740 deselectAllSequenceMenuItem_actionPerformed();
742 else if (source == invertSequenceMenuItem)
744 invertSequenceMenuItem_actionPerformed();
746 else if (source == invertColSel)
748 viewport.invertColumnSelection();
749 alignPanel.paintAlignment(true);
751 else if (source == remove2LeftMenuItem)
755 else if (source == remove2RightMenuItem)
757 trimAlignment(false);
759 else if (source == removeGappedColumnMenuItem)
761 removeGappedColumnMenuItem_actionPerformed();
763 else if (source == removeAllGapsMenuItem)
765 removeAllGapsMenuItem_actionPerformed();
767 else if (source == findMenuItem)
769 findMenuItem_actionPerformed();
771 else if (source == font)
773 new FontChooser(alignPanel);
775 else if (source == newView)
779 else if (source == showColumns)
781 viewport.showAllHiddenColumns();
782 alignPanel.paintAlignment(true);
784 else if (source == showSeqs)
786 viewport.showAllHiddenSeqs();
787 alignPanel.paintAlignment(true);
789 else if (source == hideColumns)
791 viewport.hideSelectedColumns();
792 alignPanel.paintAlignment(true);
794 else if (source == hideSequences
795 && viewport.getSelectionGroup() != null)
797 viewport.hideAllSelectedSeqs();
798 alignPanel.paintAlignment(true);
800 else if (source == hideAllButSelection)
802 toggleHiddenRegions(false, false);
803 alignPanel.paintAlignment(true);
805 else if (source == hideAllSelection)
807 SequenceGroup sg = viewport.getSelectionGroup();
808 viewport.expandColSelection(sg, false);
809 viewport.hideAllSelectedSeqs();
810 viewport.hideSelectedColumns();
811 alignPanel.paintAlignment(true);
813 else if (source == showAllHidden)
815 viewport.showAllHiddenColumns();
816 viewport.showAllHiddenSeqs();
817 alignPanel.paintAlignment(true);
819 else if (source == showGroupConsensus)
821 showGroupConsensus_actionPerformed();
823 else if (source == showGroupConservation)
825 showGroupConservation_actionPerformed();
827 else if (source == showSequenceLogo)
829 showSequenceLogo_actionPerformed();
831 else if (source == showConsensusHistogram)
833 showConsensusHistogram_actionPerformed();
835 else if (source == applyAutoAnnotationSettings)
837 applyAutoAnnotationSettings_actionPerformed();
839 else if (source == featureSettings)
841 new FeatureSettings(alignPanel);
843 else if (source == alProperties)
845 StringBuffer contents = new jalview.io.AlignmentProperties(
846 viewport.alignment).formatAsString();
847 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
848 cap.setText(contents.toString());
849 Frame frame = new Frame();
851 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
852 + getTitle(), 400, 250);
854 else if (source == overviewMenuItem)
856 overviewMenuItem_actionPerformed();
858 else if (source == noColourmenuItem)
862 else if (source == clustalColour)
864 abovePIDThreshold.setState(false);
865 changeColour(new ClustalxColourScheme(
866 viewport.alignment.getSequences(),
867 viewport.alignment.getWidth()));
869 else if (source == zappoColour)
871 changeColour(new ZappoColourScheme());
873 else if (source == taylorColour)
875 changeColour(new TaylorColourScheme());
877 else if (source == hydrophobicityColour)
879 changeColour(new HydrophobicColourScheme());
881 else if (source == helixColour)
883 changeColour(new HelixColourScheme());
885 else if (source == strandColour)
887 changeColour(new StrandColourScheme());
889 else if (source == turnColour)
891 changeColour(new TurnColourScheme());
893 else if (source == buriedColour)
895 changeColour(new BuriedColourScheme());
897 else if (source == nucleotideColour)
899 changeColour(new NucleotideColourScheme());
901 else if (source == modifyPID)
903 modifyPID_actionPerformed();
905 else if (source == modifyConservation)
907 modifyConservation_actionPerformed();
909 else if (source == userDefinedColour)
911 new UserDefinedColours(alignPanel, null);
913 else if (source == PIDColour)
915 changeColour(new PIDColourScheme());
917 else if (source == BLOSUM62Colour)
919 changeColour(new Blosum62ColourScheme());
921 else if (source == annotationColour)
923 new AnnotationColourChooser(viewport, alignPanel);
925 else if (source == sortPairwiseMenuItem)
927 sortPairwiseMenuItem_actionPerformed();
929 else if (source == sortIDMenuItem)
931 sortIDMenuItem_actionPerformed();
933 else if (source == sortLengthMenuItem)
935 sortLengthMenuItem_actionPerformed();
937 else if (source == sortGroupMenuItem)
939 sortGroupMenuItem_actionPerformed();
941 else if (source == removeRedundancyMenuItem)
943 removeRedundancyMenuItem_actionPerformed();
945 else if (source == pairwiseAlignmentMenuItem)
947 pairwiseAlignmentMenuItem_actionPerformed();
949 else if (source == PCAMenuItem)
951 PCAMenuItem_actionPerformed();
953 else if (source == averageDistanceTreeMenuItem)
955 averageDistanceTreeMenuItem_actionPerformed();
957 else if (source == neighbourTreeMenuItem)
959 neighbourTreeMenuItem_actionPerformed();
961 else if (source == njTreeBlosumMenuItem)
963 njTreeBlosumMenuItem_actionPerformed();
965 else if (source == avDistanceTreeBlosumMenuItem)
967 avTreeBlosumMenuItem_actionPerformed();
969 else if (source == documentation)
971 documentation_actionPerformed();
973 else if (source == about)
975 about_actionPerformed();
980 public void inputText_actionPerformed()
982 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
983 Frame frame = new Frame();
985 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
988 protected void outputText_actionPerformed(ActionEvent e)
990 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
991 Frame frame = new Frame();
993 jalview.bin.JalviewLite.addFrame(frame,
994 "Alignment output - " + e.getActionCommand(), 600, 500);
995 cap.setText(new AppletFormatAdapter().formatSequences(
996 e.getActionCommand(), viewport.getAlignment(),
997 viewport.showJVSuffix));
1000 public void loadAnnotations()
1002 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1003 cap.setText("Paste your features / annotations file here.");
1004 cap.setAnnotationImport();
1005 Frame frame = new Frame();
1007 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
1011 public String outputAnnotations(boolean displayTextbox)
1013 String annotation = new AnnotationFile().printAnnotations(
1014 viewport.showAnnotation ? viewport.alignment
1015 .getAlignmentAnnotation() : null, viewport.alignment
1017 ((Alignment) viewport.alignment).alignmentProperties);
1021 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1022 Frame frame = new Frame();
1024 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1025 cap.setText(annotation);
1031 private Hashtable getDisplayedFeatureCols()
1033 if (alignPanel.getFeatureRenderer() != null)
1035 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1036 Hashtable fcols = new Hashtable();
1037 Enumeration en = viewport.featuresDisplayed.keys();
1038 while (en.hasMoreElements())
1040 Object col = en.nextElement();
1041 fcols.put(col, fr.featureColours.get(col));
1048 public String outputFeatures(boolean displayTextbox, String format)
1051 if (format.equalsIgnoreCase("Jalview"))
1053 features = new FeaturesFile().printJalviewFormat(
1054 viewport.alignment.getSequencesArray(),
1055 getDisplayedFeatureCols());
1059 features = new FeaturesFile().printGFFFormat(
1060 viewport.alignment.getSequencesArray(),
1061 getDisplayedFeatureCols());
1066 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1067 Frame frame = new Frame();
1069 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1071 cap.setText(features);
1077 void launchFullApplication()
1079 StringBuffer url = new StringBuffer(jalviewServletURL);
1082 + appendProtocol(viewport.applet.getParameter("file")));
1084 if (viewport.applet.getParameter("features") != null)
1086 url.append("&features=");
1087 url.append(appendProtocol(viewport.applet.getParameter("features")));
1090 if (viewport.applet.getParameter("annotations") != null)
1092 url.append("&annotations=");
1093 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1096 if (viewport.applet.getParameter("jnetfile") != null)
1098 url.append("&annotations=");
1099 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1102 if (viewport.applet.getParameter("defaultColour") != null)
1104 url.append("&colour="
1105 + removeWhiteSpace(viewport.applet
1106 .getParameter("defaultColour")));
1109 if (viewport.applet.getParameter("userDefinedColour") != null)
1111 url.append("&colour="
1112 + removeWhiteSpace(viewport.applet
1113 .getParameter("userDefinedColour")));
1115 if (viewport.applet.getParameter("tree") != null)
1118 + appendProtocol(viewport.applet.getParameter("tree")));
1120 if (viewport.applet.getParameter("treeFile") != null)
1123 + appendProtocol(viewport.applet.getParameter("treeFile")));
1126 showURL(url.toString(), "FULL_APP");
1129 String removeWhiteSpace(String colour)
1131 StringBuffer sb = new StringBuffer();
1132 for (int i = 0; i < colour.length(); i++)
1134 if (Character.isWhitespace(colour.charAt(i)))
1140 sb.append(colour.charAt(i));
1144 return sb.toString();
1147 String appendProtocol(String url)
1152 url = URLEncoder.encode(url);
1155 * When we finally deprecate 1.1 compatibility, we can start to use
1156 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1157 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1158 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1159 * ex.printStackTrace(); }
1161 catch (java.net.MalformedURLException ex)
1163 url = viewport.applet.getCodeBase() + url;
1168 public void closeMenuItem_actionPerformed()
1170 PaintRefresher.RemoveComponent(alignPanel);
1171 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1172 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1174 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1185 void updateEditMenuBar()
1188 if (viewport.historyList.size() > 0)
1190 undoMenuItem.setEnabled(true);
1191 CommandI command = (CommandI) viewport.historyList.peek();
1192 undoMenuItem.setLabel("Undo " + command.getDescription());
1196 undoMenuItem.setEnabled(false);
1197 undoMenuItem.setLabel("Undo");
1200 if (viewport.redoList.size() > 0)
1202 redoMenuItem.setEnabled(true);
1204 CommandI command = (CommandI) viewport.redoList.peek();
1205 redoMenuItem.setLabel("Redo " + command.getDescription());
1209 redoMenuItem.setEnabled(false);
1210 redoMenuItem.setLabel("Redo");
1214 public void addHistoryItem(CommandI command)
1216 if (command.getSize() > 0)
1218 viewport.historyList.push(command);
1219 viewport.redoList.removeAllElements();
1220 updateEditMenuBar();
1221 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1231 protected void undoMenuItem_actionPerformed()
1233 if (viewport.historyList.size() < 1)
1238 CommandI command = (CommandI) viewport.historyList.pop();
1239 viewport.redoList.push(command);
1240 command.undoCommand(null);
1242 AlignViewport originalSource = getOriginatingSource(command);
1244 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1245 updateEditMenuBar();
1246 originalSource.firePropertyChange("alignment", null,
1247 originalSource.alignment.getSequences());
1256 protected void redoMenuItem_actionPerformed()
1258 if (viewport.redoList.size() < 1)
1263 CommandI command = (CommandI) viewport.redoList.pop();
1264 viewport.historyList.push(command);
1265 command.doCommand(null);
1267 AlignViewport originalSource = getOriginatingSource(command);
1268 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1270 updateEditMenuBar();
1271 originalSource.firePropertyChange("alignment", null,
1272 originalSource.alignment.getSequences());
1275 AlignViewport getOriginatingSource(CommandI command)
1277 AlignViewport originalSource = null;
1278 // For sequence removal and addition, we need to fire
1279 // the property change event FROM the viewport where the
1280 // original alignment was altered
1281 AlignmentI al = null;
1282 if (command instanceof EditCommand)
1284 EditCommand editCommand = (EditCommand) command;
1285 al = editCommand.getAlignment();
1286 Vector comps = (Vector) PaintRefresher.components.get(viewport
1287 .getSequenceSetId());
1288 for (int i = 0; i < comps.size(); i++)
1290 if (comps.elementAt(i) instanceof AlignmentPanel)
1292 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1294 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1301 if (originalSource == null)
1303 // The original view is closed, we must validate
1304 // the current view against the closed view first
1307 PaintRefresher.validateSequences(al, viewport.alignment);
1310 originalSource = viewport;
1313 return originalSource;
1316 public void moveSelectedSequences(boolean up)
1318 SequenceGroup sg = viewport.getSelectionGroup();
1326 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1328 SequenceI seq = viewport.alignment.getSequenceAt(i);
1329 if (!sg.getSequences(null).contains(seq))
1334 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1335 if (sg.getSequences(null).contains(temp))
1340 viewport.alignment.getSequences().setElementAt(temp, i);
1341 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1346 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1348 SequenceI seq = viewport.alignment.getSequenceAt(i);
1349 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1354 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1355 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1360 viewport.alignment.getSequences().setElementAt(temp, i);
1361 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1365 alignPanel.paintAlignment(true);
1368 synchronized void slideSequences(boolean right, int size)
1370 Vector sg = new Vector();
1371 if (viewport.cursorMode)
1373 sg.addElement(viewport.alignment
1374 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1376 else if (viewport.getSelectionGroup() != null
1377 && viewport.getSelectionGroup().getSize() != viewport.alignment
1380 sg = viewport.getSelectionGroup().getSequences(
1381 viewport.hiddenRepSequences);
1389 Vector invertGroup = new Vector();
1391 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1393 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1394 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1397 SequenceI[] seqs1 = new SequenceI[sg.size()];
1398 for (int i = 0; i < sg.size(); i++)
1399 seqs1[i] = (SequenceI) sg.elementAt(i);
1401 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1402 for (int i = 0; i < invertGroup.size(); i++)
1403 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1405 SlideSequencesCommand ssc;
1407 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1408 size, viewport.getGapCharacter());
1410 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1411 size, viewport.getGapCharacter());
1413 int groupAdjustment = 0;
1414 if (ssc.getGapsInsertedBegin() && right)
1416 if (viewport.cursorMode)
1417 alignPanel.seqPanel.moveCursor(size, 0);
1419 groupAdjustment = size;
1421 else if (!ssc.getGapsInsertedBegin() && !right)
1423 if (viewport.cursorMode)
1424 alignPanel.seqPanel.moveCursor(-size, 0);
1426 groupAdjustment = -size;
1429 if (groupAdjustment != 0)
1431 viewport.getSelectionGroup().setStartRes(
1432 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1433 viewport.getSelectionGroup().setEndRes(
1434 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1437 boolean appendHistoryItem = false;
1438 if (viewport.historyList != null && viewport.historyList.size() > 0
1439 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1441 appendHistoryItem = ssc
1442 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1446 if (!appendHistoryItem)
1447 addHistoryItem(ssc);
1452 static StringBuffer copiedSequences;
1454 static Vector copiedHiddenColumns;
1456 protected void copy_actionPerformed()
1458 if (viewport.getSelectionGroup() == null)
1463 SequenceGroup sg = viewport.getSelectionGroup();
1464 copiedSequences = new StringBuffer();
1465 Hashtable orderedSeqs = new Hashtable();
1466 for (int i = 0; i < sg.getSize(); i++)
1468 SequenceI seq = sg.getSequenceAt(i);
1469 int index = viewport.alignment.findIndex(seq);
1470 orderedSeqs.put(index + "", seq);
1473 int index = 0, startRes, endRes;
1476 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1478 copiedHiddenColumns = new Vector();
1479 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1480 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1483 int[] region = (int[]) viewport.getColumnSelection()
1484 .getHiddenColumns().elementAt(i);
1486 copiedHiddenColumns.addElement(new int[]
1487 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1492 copiedHiddenColumns = null;
1495 for (int i = 0; i < sg.getSize(); i++)
1497 SequenceI seq = null;
1501 if (orderedSeqs.containsKey(index + ""))
1503 seq = (SequenceI) orderedSeqs.get(index + "");
1515 // Returns residue following index if gap
1516 startRes = seq.findPosition(sg.getStartRes());
1519 // Need to find the residue preceeding index if gap
1522 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1524 ch = seq.getCharAt(j);
1525 if (!jalview.util.Comparison.isGap((ch)))
1533 endRes += seq.getStart() - 1;
1536 copiedSequences.append(seq.getName()
1542 + seq.getSequenceAsString(sg.getStartRes(),
1543 sg.getEndRes() + 1) + "\n");
1548 protected void pasteNew_actionPerformed()
1553 protected void pasteThis_actionPerformed()
1558 void paste(boolean newAlignment)
1563 if (copiedSequences == null)
1568 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1569 Vector seqs = new Vector();
1570 while (st.hasMoreElements())
1572 String name = st.nextToken();
1573 int start = Integer.parseInt(st.nextToken());
1574 int end = Integer.parseInt(st.nextToken());
1575 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1577 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1578 for (int i = 0; i < seqs.size(); i++)
1580 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1585 String newtitle = new String("Copied sequences");
1586 if (getTitle().startsWith("Copied sequences"))
1588 newtitle = getTitle();
1592 newtitle = newtitle.concat("- from " + getTitle());
1594 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1595 viewport.applet, newtitle, false);
1596 if (copiedHiddenColumns != null)
1598 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1600 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1601 af.viewport.hideColumns(region[0], region[1]);
1605 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1610 addSequences(newSeqs);
1613 } catch (Exception ex)
1615 } // could be anything being pasted in here
1619 void addSequences(SequenceI[] seqs)
1621 for (int i = 0; i < seqs.length; i++)
1623 viewport.alignment.addSequence(seqs[i]);
1627 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1628 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1630 viewport.setEndSeq(viewport.alignment.getHeight());
1631 viewport.alignment.getWidth();
1632 viewport.firePropertyChange("alignment", null,
1633 viewport.alignment.getSequences());
1637 protected void cut_actionPerformed()
1639 copy_actionPerformed();
1640 delete_actionPerformed();
1643 protected void delete_actionPerformed()
1646 SequenceGroup sg = viewport.getSelectionGroup();
1652 Vector seqs = new Vector();
1654 for (int i = 0; i < sg.getSize(); i++)
1656 seq = sg.getSequenceAt(i);
1657 seqs.addElement(seq);
1660 // If the cut affects all sequences, remove highlighted columns
1661 if (sg.getSize() == viewport.alignment.getHeight())
1663 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1664 sg.getEndRes() + 1);
1667 SequenceI[] cut = new SequenceI[seqs.size()];
1668 for (int i = 0; i < seqs.size(); i++)
1670 cut[i] = (SequenceI) seqs.elementAt(i);
1674 * //ADD HISTORY ITEM
1676 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1677 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1678 viewport.alignment));
1680 viewport.setSelectionGroup(null);
1681 viewport.alignment.deleteGroup(sg);
1683 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1686 if (viewport.getAlignment().getHeight() < 1)
1688 this.setVisible(false);
1690 viewport.sendSelection();
1694 * group consensus toggled
1697 protected void showGroupConsensus_actionPerformed()
1699 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1700 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1705 * group conservation toggled.
1707 protected void showGroupConservation_actionPerformed()
1709 viewport.setShowGroupConservation(showGroupConservation.getState());
1710 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1717 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1718 * .event.ActionEvent)
1720 protected void showConsensusHistogram_actionPerformed()
1722 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1723 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1729 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1730 * .event.ActionEvent)
1732 protected void showSequenceLogo_actionPerformed()
1734 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1735 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1738 protected void applyAutoAnnotationSettings_actionPerformed()
1740 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1743 protected void makeGrpsFromSelection_actionPerformed()
1745 if (viewport.getSelectionGroup() != null)
1747 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
1748 viewport.getSequenceSelection(),
1749 viewport.getAlignmentView(true).getSequenceStrings(
1750 viewport.getGapCharacter()),
1751 viewport.alignment.getGroups());
1752 viewport.alignment.deleteAllGroups();
1753 viewport.sequenceColours = null;
1754 viewport.setSelectionGroup(null);
1755 // set view properties for each group
1756 for (int g = 0; g < gps.length; g++)
1758 // gps[g].setShowunconserved(viewport.getShowUnconserved());
1759 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
1760 viewport.alignment.addGroup(gps[g]);
1761 Color col = new Color((int) (Math.random() * 255),
1762 (int) (Math.random() * 255), (int) (Math.random() * 255));
1763 col = col.brighter();
1764 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
1765 .hasMoreElements(); viewport.setSequenceColour(
1766 (SequenceI) sq.nextElement(), col))
1769 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1770 alignPanel.updateAnnotation();
1771 alignPanel.paintAlignment(true);
1775 protected void deleteGroups_actionPerformed()
1777 viewport.alignment.deleteAllGroups();
1778 viewport.sequenceColours = null;
1779 viewport.setSelectionGroup(null);
1781 alignPanel.paintAlignment(true);
1784 public void selectAllSequenceMenuItem_actionPerformed()
1786 SequenceGroup sg = new SequenceGroup();
1787 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1789 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1791 sg.setEndRes(viewport.alignment.getWidth() - 1);
1792 viewport.setSelectionGroup(sg);
1793 alignPanel.paintAlignment(true);
1794 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1795 viewport.sendSelection();
1798 public void deselectAllSequenceMenuItem_actionPerformed()
1800 if (viewport.cursorMode)
1802 alignPanel.seqPanel.keyboardNo1 = null;
1803 alignPanel.seqPanel.keyboardNo2 = null;
1805 viewport.setSelectionGroup(null);
1806 viewport.getColumnSelection().clear();
1807 viewport.setSelectionGroup(null);
1808 alignPanel.idPanel.idCanvas.searchResults = null;
1809 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1810 alignPanel.paintAlignment(true);
1811 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1812 viewport.sendSelection();
1815 public void invertSequenceMenuItem_actionPerformed()
1817 SequenceGroup sg = viewport.getSelectionGroup();
1818 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1820 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1823 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1824 viewport.sendSelection();
1827 public void invertColSel_actionPerformed()
1829 viewport.invertColumnSelection();
1830 alignPanel.paintAlignment(true);
1831 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1832 viewport.sendSelection();
1835 void trimAlignment(boolean trimLeft)
1837 ColumnSelection colSel = viewport.getColumnSelection();
1840 if (colSel.size() > 0)
1844 column = colSel.getMin();
1848 column = colSel.getMax();
1852 if (viewport.getSelectionGroup() != null)
1854 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1855 viewport.hiddenRepSequences);
1859 seqs = viewport.alignment.getSequencesArray();
1862 TrimRegionCommand trimRegion;
1865 trimRegion = new TrimRegionCommand("Remove Left",
1866 TrimRegionCommand.TRIM_LEFT, seqs, column,
1867 viewport.alignment, viewport.colSel,
1868 viewport.selectionGroup);
1869 viewport.setStartRes(0);
1873 trimRegion = new TrimRegionCommand("Remove Right",
1874 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1875 viewport.alignment, viewport.colSel,
1876 viewport.selectionGroup);
1879 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1881 addHistoryItem(trimRegion);
1883 Vector groups = viewport.alignment.getGroups();
1885 for (int i = 0; i < groups.size(); i++)
1887 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1889 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1890 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1892 viewport.alignment.deleteGroup(sg);
1896 viewport.firePropertyChange("alignment", null, viewport
1897 .getAlignment().getSequences());
1901 public void removeGappedColumnMenuItem_actionPerformed()
1903 int start = 0, end = viewport.alignment.getWidth() - 1;
1906 if (viewport.getSelectionGroup() != null)
1908 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1909 viewport.hiddenRepSequences);
1910 start = viewport.getSelectionGroup().getStartRes();
1911 end = viewport.getSelectionGroup().getEndRes();
1915 seqs = viewport.alignment.getSequencesArray();
1918 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1919 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1921 addHistoryItem(removeGapCols);
1923 statusBar.setText("Removed " + removeGapCols.getSize()
1924 + " empty columns.");
1926 // This is to maintain viewport position on first residue
1927 // of first sequence
1928 SequenceI seq = viewport.alignment.getSequenceAt(0);
1929 int startRes = seq.findPosition(viewport.startRes);
1930 // ShiftList shifts;
1931 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1932 // edit.alColumnChanges=shifts.getInverse();
1933 // if (viewport.hasHiddenColumns)
1934 // viewport.getColumnSelection().compensateForEdits(shifts);
1935 viewport.setStartRes(seq.findIndex(startRes) - 1);
1936 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1941 public void removeAllGapsMenuItem_actionPerformed()
1943 int start = 0, end = viewport.alignment.getWidth() - 1;
1946 if (viewport.getSelectionGroup() != null)
1948 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1949 viewport.hiddenRepSequences);
1950 start = viewport.getSelectionGroup().getStartRes();
1951 end = viewport.getSelectionGroup().getEndRes();
1955 seqs = viewport.alignment.getSequencesArray();
1958 // This is to maintain viewport position on first residue
1959 // of first sequence
1960 SequenceI seq = viewport.alignment.getSequenceAt(0);
1961 int startRes = seq.findPosition(viewport.startRes);
1963 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1964 viewport.alignment));
1966 viewport.setStartRes(seq.findIndex(startRes) - 1);
1968 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1973 public void findMenuItem_actionPerformed()
1975 new Finder(alignPanel);
1979 * create a new view derived from the current view
1982 * @return frame for the new view
1984 public AlignFrame newView(String viewtitle)
1987 if (viewport.hasHiddenRows)
1989 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1990 .getFullAlignment().getSequencesArray());
1994 newal = new Alignment(viewport.alignment.getSequencesArray());
1997 if (viewport.alignment.getAlignmentAnnotation() != null)
1999 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
2001 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
2003 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
2008 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2010 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
2011 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2012 PaintRefresher.Register(newaf.alignPanel,
2013 newaf.alignPanel.av.getSequenceSetId());
2015 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2016 newaf.alignPanel.av.getSequenceSetId());
2017 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2018 newaf.alignPanel.av.getSequenceSetId());
2020 Vector comps = (Vector) PaintRefresher.components.get(viewport
2021 .getSequenceSetId());
2023 for (int i = 0; i < comps.size(); i++)
2025 if (comps.elementAt(i) instanceof AlignmentPanel)
2031 String title = new String(this.getTitle());
2032 if (viewtitle != null)
2034 title = viewtitle + " ( " + title + ")";
2038 if (title.indexOf("(View") > -1)
2040 title = title.substring(0, title.indexOf("(View"));
2042 title += "(View " + viewSize + ")";
2045 newaf.setTitle(title.toString());
2047 newaf.viewport.historyList = viewport.historyList;
2048 newaf.viewport.redoList = viewport.redoList;
2054 * @return list of feature groups on the view
2056 public String[] getFeatureGroups()
2058 FeatureRenderer fr = null;
2059 if (alignPanel != null
2060 && (fr = alignPanel.getFeatureRenderer()) != null)
2062 return fr.getGroups();
2068 * get sequence feature groups that are hidden or shown
2074 public String[] getFeatureGroupsOfState(boolean visible)
2076 FeatureRenderer fr = null;
2077 if (alignPanel != null
2078 && (fr = alignPanel.getFeatureRenderer()) != null)
2080 return fr.getGroups(visible);
2086 * Change the display state for the given feature groups
2089 * list of group strings
2091 * visible or invisible
2093 public void setFeatureGroupState(String[] groups, boolean state)
2095 FeatureRenderer fr = null;
2096 this.sequenceFeatures.setState(true);
2097 viewport.showSequenceFeatures(true);
2098 if (alignPanel != null
2099 && (fr = alignPanel.getFeatureRenderer()) != null)
2101 fr.setGroupState(groups, state);
2102 alignPanel.seqPanel.seqCanvas.repaint();
2103 if (alignPanel.overviewPanel != null)
2105 alignPanel.overviewPanel.updateOverviewImage();
2110 public void seqLimits_itemStateChanged()
2112 viewport.setShowJVSuffix(seqLimits.getState());
2113 alignPanel.fontChanged();
2114 alignPanel.paintAlignment(true);
2117 protected void colourTextMenuItem_actionPerformed()
2119 viewport.setColourText(colourTextMenuItem.getState());
2120 alignPanel.paintAlignment(true);
2123 protected void displayNonconservedMenuItem_actionPerformed()
2125 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2126 alignPanel.paintAlignment(true);
2129 protected void wrapMenuItem_actionPerformed()
2131 viewport.setWrapAlignment(wrapMenuItem.getState());
2132 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2133 scaleAbove.setEnabled(wrapMenuItem.getState());
2134 scaleLeft.setEnabled(wrapMenuItem.getState());
2135 scaleRight.setEnabled(wrapMenuItem.getState());
2136 alignPanel.paintAlignment(true);
2139 public void overviewMenuItem_actionPerformed()
2141 if (alignPanel.overviewPanel != null)
2146 Frame frame = new Frame();
2147 OverviewPanel overview = new OverviewPanel(alignPanel);
2148 frame.add(overview);
2149 // +50 must allow for applet frame window
2150 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2151 overview.getPreferredSize().width,
2152 overview.getPreferredSize().height + 50);
2155 frame.addWindowListener(new WindowAdapter()
2157 public void windowClosing(WindowEvent e)
2159 alignPanel.setOverviewPanel(null);
2163 alignPanel.setOverviewPanel(overview);
2167 void changeColour(ColourSchemeI cs)
2173 if (viewport.getAbovePIDThreshold())
2175 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2178 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2180 viewport.setGlobalColourScheme(cs);
2184 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2187 if (viewport.getConservationSelected())
2190 Alignment al = (Alignment) viewport.alignment;
2191 Conservation c = new Conservation("All",
2192 ResidueProperties.propHash, 3, al.getSequences(), 0,
2196 c.verdict(false, viewport.ConsPercGaps);
2198 cs.setConservation(c);
2200 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2206 cs.setConservation(null);
2209 cs.setConsensus(viewport.hconsensus);
2212 viewport.setGlobalColourScheme(cs);
2214 if (viewport.getColourAppliesToAllGroups())
2216 Vector groups = viewport.alignment.getGroups();
2217 for (int i = 0; i < groups.size(); i++)
2219 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2226 if (cs instanceof ClustalxColourScheme)
2228 sg.cs = new ClustalxColourScheme(
2229 sg.getSequences(viewport.hiddenRepSequences),
2236 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2237 } catch (Exception ex)
2239 ex.printStackTrace();
2244 if (viewport.getAbovePIDThreshold()
2245 || cs instanceof PIDColourScheme
2246 || cs instanceof Blosum62ColourScheme)
2248 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2249 sg.cs.setConsensus(AAFrequency.calculate(
2250 sg.getSequences(viewport.hiddenRepSequences), 0,
2255 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2258 if (viewport.getConservationSelected())
2260 Conservation c = new Conservation("Group",
2261 ResidueProperties.propHash, 3,
2262 sg.getSequences(viewport.hiddenRepSequences), 0,
2263 viewport.alignment.getWidth() - 1);
2265 c.verdict(false, viewport.ConsPercGaps);
2266 sg.cs.setConservation(c);
2270 sg.cs.setConservation(null);
2271 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2277 if (alignPanel.getOverviewPanel() != null)
2279 alignPanel.getOverviewPanel().updateOverviewImage();
2282 jalview.structure.StructureSelectionManager
2283 .getStructureSelectionManager().sequenceColoursChanged(
2286 alignPanel.paintAlignment(true);
2289 protected void modifyPID_actionPerformed()
2291 if (viewport.getAbovePIDThreshold()
2292 && viewport.globalColourScheme != null)
2294 SliderPanel.setPIDSliderSource(alignPanel,
2295 viewport.getGlobalColourScheme(), "Background");
2296 SliderPanel.showPIDSlider();
2300 protected void modifyConservation_actionPerformed()
2302 if (viewport.getConservationSelected()
2303 && viewport.globalColourScheme != null)
2305 SliderPanel.setConservationSlider(alignPanel,
2306 viewport.globalColourScheme, "Background");
2307 SliderPanel.showConservationSlider();
2311 protected void conservationMenuItem_actionPerformed()
2313 viewport.setConservationSelected(conservationMenuItem.getState());
2315 viewport.setAbovePIDThreshold(false);
2316 abovePIDThreshold.setState(false);
2318 changeColour(viewport.getGlobalColourScheme());
2320 modifyConservation_actionPerformed();
2323 public void abovePIDThreshold_actionPerformed()
2325 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2327 conservationMenuItem.setState(false);
2328 viewport.setConservationSelected(false);
2330 changeColour(viewport.getGlobalColourScheme());
2332 modifyPID_actionPerformed();
2335 public void sortPairwiseMenuItem_actionPerformed()
2337 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2338 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2339 .getAlignment().getSequenceAt(0), null);
2341 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2342 viewport.alignment));
2343 alignPanel.paintAlignment(true);
2346 public void sortIDMenuItem_actionPerformed()
2348 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2349 AlignmentSorter.sortByID(viewport.getAlignment());
2350 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2351 alignPanel.paintAlignment(true);
2354 public void sortLengthMenuItem_actionPerformed()
2356 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2357 AlignmentSorter.sortByLength(viewport.getAlignment());
2358 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2359 viewport.alignment));
2360 alignPanel.paintAlignment(true);
2363 public void sortGroupMenuItem_actionPerformed()
2365 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2366 AlignmentSorter.sortByGroup(viewport.getAlignment());
2367 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2368 viewport.alignment));
2369 alignPanel.paintAlignment(true);
2373 public void removeRedundancyMenuItem_actionPerformed()
2375 new RedundancyPanel(alignPanel);
2378 public void pairwiseAlignmentMenuItem_actionPerformed()
2380 if (viewport.getSelectionGroup() != null
2381 && viewport.getSelectionGroup().getSize() > 1)
2383 Frame frame = new Frame();
2384 frame.add(new PairwiseAlignPanel(alignPanel));
2385 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2390 public void PCAMenuItem_actionPerformed()
2392 // are the sequences aligned?
2393 if (!viewport.alignment.isAligned(false))
2396 int Width = viewport.getAlignment().getWidth();
2398 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2400 current = viewport.getAlignment().getSequenceAt(i);
2402 if (current.getLength() < Width)
2404 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2407 alignPanel.paintAlignment(true);
2410 if ((viewport.getSelectionGroup() != null
2411 && viewport.getSelectionGroup().getSize() < 4 && viewport
2412 .getSelectionGroup().getSize() > 0)
2413 || viewport.getAlignment().getHeight() < 4)
2420 new PCAPanel(viewport);
2421 } catch (java.lang.OutOfMemoryError ex)
2427 public void averageDistanceTreeMenuItem_actionPerformed()
2429 NewTreePanel("AV", "PID", "Average distance tree using PID");
2432 public void neighbourTreeMenuItem_actionPerformed()
2434 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2437 protected void njTreeBlosumMenuItem_actionPerformed()
2439 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2442 protected void avTreeBlosumMenuItem_actionPerformed()
2444 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2447 void NewTreePanel(String type, String pwType, String title)
2449 // are the sequences aligned?
2450 if (!viewport.alignment.isAligned(false))
2453 int Width = viewport.getAlignment().getWidth();
2455 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2457 current = viewport.getAlignment().getSequenceAt(i);
2459 if (current.getLength() < Width)
2461 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2464 alignPanel.paintAlignment(true);
2468 if ((viewport.getSelectionGroup() != null && viewport
2469 .getSelectionGroup().getSize() > 1)
2470 || (viewport.getSelectionGroup() == null && viewport.alignment
2473 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2475 addTreeMenuItem(tp, title);
2477 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2481 void loadTree_actionPerformed()
2483 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2484 cap.setText("Paste your Newick tree file here.");
2485 cap.setTreeImport();
2486 Frame frame = new Frame();
2488 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2491 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2493 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
2494 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2495 addTreeMenuItem(tp, treeFile);
2499 * sort the alignment using the given treePanel
2502 * tree used to sort view
2504 * string used for undo event name
2506 public void sortByTree(TreePanel treePanel, String title)
2508 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2510 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2511 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2512 // HistoryItem.SORT));
2513 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2514 viewport.alignment));
2515 alignPanel.paintAlignment(true);
2519 * Do any automatic reordering of the alignment and add the necessary bits to
2520 * the menu structure for the new tree
2525 protected void addTreeMenuItem(final TreePanel treePanel,
2528 final MenuItem item = new MenuItem(title);
2529 sortByTreeMenu.add(item);
2530 item.addActionListener(new java.awt.event.ActionListener()
2532 public void actionPerformed(ActionEvent evt)
2534 sortByTree(treePanel, title); // treePanel.getTitle());
2538 treePanel.addWindowListener(new WindowAdapter()
2540 public void windowOpened(WindowEvent e)
2542 if (viewport.sortByTree)
2544 sortByTree(treePanel, title);
2546 super.windowOpened(e);
2549 public void windowClosing(WindowEvent e)
2551 sortByTreeMenu.remove(item);
2555 public boolean sortBy(AlignmentOrder alorder, String undoname)
2557 SequenceI[] oldOrder = viewport.getAlignment()
2558 .getSequencesArray();
2559 if (viewport.applet.debug)
2561 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
2563 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2566 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
2568 alignPanel.paintAlignment(true);
2571 protected void documentation_actionPerformed()
2573 showURL("http://www.jalview.org/help.html", "HELP");
2576 protected void about_actionPerformed()
2579 class AboutPanel extends Canvas
2585 public AboutPanel(String version, String builddate)
2587 this.version = version;
2588 this.builddate = builddate;
2591 public void paint(Graphics g)
2593 g.setColor(Color.white);
2594 g.fillRect(0, 0, getSize().width, getSize().height);
2595 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2596 FontMetrics fm = g.getFontMetrics();
2597 int fh = fm.getHeight();
2599 g.setColor(Color.black);
2600 // TODO: update this text for each release or centrally store it for
2601 // lite and application
2602 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2603 g.drawString("JalviewLite - Release " + version, x, y += fh);
2604 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2605 g.drawString("Build date: " + builddate, x, y += fh);
2606 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2608 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
2610 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2612 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2615 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2617 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2619 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2622 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2624 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2629 Frame frame = new Frame();
2630 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2632 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2636 public void showURL(String url, String target)
2638 if (viewport.applet == null)
2640 System.out.println("Not running as applet - no browser available.");
2646 if (url.indexOf(":") == -1)
2648 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2650 if (url.indexOf("/") == 0)
2652 String codebase = viewport.applet.getCodeBase().toString();
2653 url = codebase.substring(0, codebase.length()
2654 - viewport.applet.getCodeBase().getFile().length())
2659 url = viewport.applet.getCodeBase() + url;
2661 System.out.println("Show url (prepended codebase): " + url);
2665 System.out.println("Show url: " + url);
2667 if (url.indexOf("javascript:") == 0)
2669 // no target for the javascript context
2670 viewport.applet.getAppletContext().showDocument(
2671 new java.net.URL(url));
2675 viewport.applet.getAppletContext().showDocument(
2676 new java.net.URL(url), target);
2678 } catch (Exception ex)
2680 ex.printStackTrace();
2685 // ////////////////////////////////////////////////////////////////////////////////
2686 // JBuilder Graphics here
2688 MenuBar alignFrameMenuBar = new MenuBar();
2690 Menu fileMenu = new Menu("File");
2692 MenuItem loadApplication = new MenuItem("View in Full Application");
2694 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2696 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2698 MenuItem outputFeatures = new MenuItem("Export Features ...");
2700 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2702 MenuItem closeMenuItem = new MenuItem("Close");
2704 Menu editMenu = new Menu("Edit");
2706 Menu viewMenu = new Menu("View");
2708 Menu colourMenu = new Menu("Colour");
2710 Menu calculateMenu = new Menu("Calculate");
2712 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2714 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2716 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2718 MenuItem remove2LeftMenuItem = new MenuItem();
2720 MenuItem remove2RightMenuItem = new MenuItem();
2722 MenuItem removeGappedColumnMenuItem = new MenuItem();
2724 MenuItem removeAllGapsMenuItem = new MenuItem();
2726 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2728 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2730 MenuItem sortPairwiseMenuItem = new MenuItem();
2732 MenuItem sortIDMenuItem = new MenuItem();
2734 MenuItem sortLengthMenuItem = new MenuItem();
2736 MenuItem sortGroupMenuItem = new MenuItem();
2738 MenuItem removeRedundancyMenuItem = new MenuItem();
2740 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2742 MenuItem PCAMenuItem = new MenuItem();
2744 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2746 MenuItem neighbourTreeMenuItem = new MenuItem();
2748 BorderLayout borderLayout1 = new BorderLayout();
2750 public Label statusBar = new Label();
2752 Menu outputTextboxMenu = new Menu();
2754 MenuItem clustalColour = new MenuItem();
2756 MenuItem zappoColour = new MenuItem();
2758 MenuItem taylorColour = new MenuItem();
2760 MenuItem hydrophobicityColour = new MenuItem();
2762 MenuItem helixColour = new MenuItem();
2764 MenuItem strandColour = new MenuItem();
2766 MenuItem turnColour = new MenuItem();
2768 MenuItem buriedColour = new MenuItem();
2770 MenuItem userDefinedColour = new MenuItem();
2772 MenuItem PIDColour = new MenuItem();
2774 MenuItem BLOSUM62Colour = new MenuItem();
2776 MenuItem njTreeBlosumMenuItem = new MenuItem();
2778 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2780 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2782 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2784 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2786 MenuItem alProperties = new MenuItem("Alignment Properties...");
2788 MenuItem overviewMenuItem = new MenuItem();
2790 MenuItem undoMenuItem = new MenuItem();
2792 MenuItem redoMenuItem = new MenuItem();
2794 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2796 MenuItem noColourmenuItem = new MenuItem();
2798 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2800 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2802 MenuItem findMenuItem = new MenuItem();
2804 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2806 MenuItem nucleotideColour = new MenuItem();
2808 MenuItem deleteGroups = new MenuItem();
2810 MenuItem grpsFromSelection = new MenuItem();
2812 MenuItem delete = new MenuItem();
2814 MenuItem copy = new MenuItem();
2816 MenuItem cut = new MenuItem();
2818 Menu pasteMenu = new Menu();
2820 MenuItem pasteNew = new MenuItem();
2822 MenuItem pasteThis = new MenuItem();
2824 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2826 MenuItem font = new MenuItem();
2828 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2830 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2832 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2834 MenuItem modifyPID = new MenuItem();
2836 MenuItem modifyConservation = new MenuItem();
2838 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2839 "Autocalculate Consensus", true);
2841 Menu sortByTreeMenu = new Menu();
2843 Menu sort = new Menu();
2845 Menu calculate = new Menu();
2847 MenuItem inputText = new MenuItem();
2849 Menu helpMenu = new Menu();
2851 MenuItem documentation = new MenuItem();
2853 MenuItem about = new MenuItem();
2855 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2857 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2859 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2860 Menu autoAnnMenu=new Menu();
2861 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
2862 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2863 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2864 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2865 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2867 private void jbInit() throws Exception
2870 setMenuBar(alignFrameMenuBar);
2874 // dynamically fill save as menu with available formats
2875 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2878 item = new MenuItem(
2879 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2881 item.addActionListener(new java.awt.event.ActionListener()
2883 public void actionPerformed(ActionEvent e)
2885 outputText_actionPerformed(e);
2889 outputTextboxMenu.add(item);
2891 closeMenuItem.addActionListener(this);
2892 loadApplication.addActionListener(this);
2894 loadTree.addActionListener(this);
2895 loadAnnotations.addActionListener(this);
2896 outputFeatures.addActionListener(this);
2897 outputAnnotations.addActionListener(this);
2898 selectAllSequenceMenuItem.addActionListener(this);
2899 deselectAllSequenceMenuItem.addActionListener(this);
2900 invertSequenceMenuItem.addActionListener(this);
2901 remove2LeftMenuItem.setLabel("Remove Left");
2902 remove2LeftMenuItem.addActionListener(this);
2903 remove2RightMenuItem.setLabel("Remove Right");
2904 remove2RightMenuItem.addActionListener(this);
2905 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2906 removeGappedColumnMenuItem.addActionListener(this);
2907 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2908 removeAllGapsMenuItem.addActionListener(this);
2909 viewBoxesMenuItem.setLabel("Boxes");
2910 viewBoxesMenuItem.setState(true);
2911 viewBoxesMenuItem.addItemListener(this);
2912 viewTextMenuItem.setLabel("Text");
2913 viewTextMenuItem.setState(true);
2914 viewTextMenuItem.addItemListener(this);
2915 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2916 sortPairwiseMenuItem.addActionListener(this);
2917 sortIDMenuItem.setLabel("by ID");
2918 sortIDMenuItem.addActionListener(this);
2919 sortLengthMenuItem.setLabel("by Length");
2920 sortLengthMenuItem.addActionListener(this);
2921 sortGroupMenuItem.setLabel("by Group");
2922 sortGroupMenuItem.addActionListener(this);
2923 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2924 removeRedundancyMenuItem.addActionListener(this);
2925 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2926 pairwiseAlignmentMenuItem.addActionListener(this);
2927 PCAMenuItem.setLabel("Principal Component Analysis");
2928 PCAMenuItem.addActionListener(this);
2929 averageDistanceTreeMenuItem
2930 .setLabel("Average Distance Using % Identity");
2931 averageDistanceTreeMenuItem.addActionListener(this);
2932 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2933 neighbourTreeMenuItem.addActionListener(this);
2934 statusBar.setBackground(Color.white);
2935 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2936 statusBar.setText("Status bar");
2937 outputTextboxMenu.setLabel("Output to Textbox");
2938 clustalColour.setLabel("Clustalx");
2940 clustalColour.addActionListener(this);
2941 zappoColour.setLabel("Zappo");
2942 zappoColour.addActionListener(this);
2943 taylorColour.setLabel("Taylor");
2944 taylorColour.addActionListener(this);
2945 hydrophobicityColour.setLabel("Hydrophobicity");
2946 hydrophobicityColour.addActionListener(this);
2947 helixColour.setLabel("Helix Propensity");
2948 helixColour.addActionListener(this);
2949 strandColour.setLabel("Strand Propensity");
2950 strandColour.addActionListener(this);
2951 turnColour.setLabel("Turn Propensity");
2952 turnColour.addActionListener(this);
2953 buriedColour.setLabel("Buried Index");
2954 buriedColour.addActionListener(this);
2955 userDefinedColour.setLabel("User Defined...");
2956 userDefinedColour.addActionListener(this);
2957 PIDColour.setLabel("Percentage Identity");
2958 PIDColour.addActionListener(this);
2959 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2960 BLOSUM62Colour.addActionListener(this);
2961 avDistanceTreeBlosumMenuItem
2962 .setLabel("Average Distance Using BLOSUM62");
2963 avDistanceTreeBlosumMenuItem.addActionListener(this);
2964 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2965 njTreeBlosumMenuItem.addActionListener(this);
2966 annotationPanelMenuItem.setLabel("Show Annotations");
2967 annotationPanelMenuItem.addItemListener(this);
2968 colourTextMenuItem.setLabel("Colour Text");
2969 colourTextMenuItem.addItemListener(this);
2970 displayNonconservedMenuItem.setLabel("Show nonconserved");
2971 displayNonconservedMenuItem.addItemListener(this);
2972 alProperties.addActionListener(this);
2973 overviewMenuItem.setLabel("Overview Window");
2974 overviewMenuItem.addActionListener(this);
2975 undoMenuItem.setEnabled(false);
2976 undoMenuItem.setLabel("Undo");
2977 undoMenuItem.addActionListener(this);
2978 redoMenuItem.setEnabled(false);
2979 redoMenuItem.setLabel("Redo");
2980 redoMenuItem.addActionListener(this);
2981 conservationMenuItem.setLabel("by Conservation");
2982 conservationMenuItem.addItemListener(this);
2983 noColourmenuItem.setLabel("None");
2984 noColourmenuItem.addActionListener(this);
2985 wrapMenuItem.setLabel("Wrap");
2986 wrapMenuItem.addItemListener(this);
2987 renderGapsMenuItem.setLabel("Show Gaps");
2988 renderGapsMenuItem.setState(true);
2989 renderGapsMenuItem.addItemListener(this);
2990 findMenuItem.setLabel("Find...");
2991 findMenuItem.addActionListener(this);
2992 abovePIDThreshold.setLabel("Above Identity Threshold");
2993 abovePIDThreshold.addItemListener(this);
2994 nucleotideColour.setLabel("Nucleotide");
2995 nucleotideColour.addActionListener(this);
2996 deleteGroups.setLabel("Undefine Groups");
2997 deleteGroups.addActionListener(this);
2998 grpsFromSelection.setLabel("Make Groups for selection");
2999 grpsFromSelection.addActionListener(this);
3000 copy.setLabel("Copy");
3001 copy.addActionListener(this);
3002 cut.setLabel("Cut");
3003 cut.addActionListener(this);
3004 delete.setLabel("Delete");
3005 delete.addActionListener(this);
3006 pasteMenu.setLabel("Paste");
3007 pasteNew.setLabel("To New Alignment");
3008 pasteNew.addActionListener(this);
3009 pasteThis.setLabel("Add To This Alignment");
3010 pasteThis.addActionListener(this);
3011 applyToAllGroups.setLabel("Apply Colour To All Groups");
3012 applyToAllGroups.setState(true);
3013 applyToAllGroups.addItemListener(this);
3014 font.setLabel("Font...");
3015 font.addActionListener(this);
3016 scaleAbove.setLabel("Scale Above");
3017 scaleAbove.setState(true);
3018 scaleAbove.setEnabled(false);
3019 scaleAbove.addItemListener(this);
3020 scaleLeft.setEnabled(false);
3021 scaleLeft.setState(true);
3022 scaleLeft.setLabel("Scale Left");
3023 scaleLeft.addItemListener(this);
3024 scaleRight.setEnabled(false);
3025 scaleRight.setState(true);
3026 scaleRight.setLabel("Scale Right");
3027 scaleRight.addItemListener(this);
3028 modifyPID.setLabel("Modify Identity Threshold...");
3029 modifyPID.addActionListener(this);
3030 modifyConservation.setLabel("Modify Conservation Threshold...");
3031 modifyConservation.addActionListener(this);
3032 sortByTreeMenu.setLabel("By Tree Order");
3033 sort.setLabel("Sort");
3034 calculate.setLabel("Calculate Tree");
3035 autoCalculate.addItemListener(this);
3036 inputText.setLabel("Input from textbox");
3037 inputText.addActionListener(this);
3038 centreColumnLabelFlag.setLabel("Centre column labels");
3039 centreColumnLabelFlag.addItemListener(this);
3040 followMouseOverFlag.setLabel("Automatic Scrolling");
3041 followMouseOverFlag.addItemListener(this);
3042 helpMenu.setLabel("Help");
3043 documentation.setLabel("Documentation");
3044 documentation.addActionListener(this);
3046 about.setLabel("About...");
3047 about.addActionListener(this);
3048 seqLimits.setState(true);
3049 seqLimits.setLabel("Show Sequence Limits");
3050 seqLimits.addItemListener(this);
3051 featureSettings.setLabel("Feature Settings...");
3052 featureSettings.addActionListener(this);
3053 sequenceFeatures.setLabel("Sequence Features");
3054 sequenceFeatures.addItemListener(this);
3055 sequenceFeatures.setState(false);
3056 annotationColour.setLabel("by Annotation...");
3057 annotationColour.addActionListener(this);
3058 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
3059 invertColSel.setLabel("Invert Column Selection");
3060 menu1.setLabel("Show");
3061 showColumns.setLabel("All Columns ");
3062 showSeqs.setLabel("All Sequences");
3063 menu2.setLabel("Hide");
3064 hideColumns.setLabel("Selected Columns");
3065 hideSequences.setLabel("Selected Sequences");
3066 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
3067 hideAllSelection.setLabel("Selected Region");
3068 showAllHidden.setLabel("All Sequences and Columns");
3069 showGroupConsensus.setLabel("Group Consensus");
3070 showGroupConservation.setLabel("Group Conservation");
3071 showConsensusHistogram.setLabel("Show Consensus Histogram");
3072 showSequenceLogo.setLabel("Show Consensus Logo");
3073 applyAutoAnnotationSettings.setLabel("Apply to all groups");
3074 applyAutoAnnotationSettings.setState(true);
3075 autoAnnMenu.setLabel("Autocalculated Annotation");
3077 invertColSel.addActionListener(this);
3078 showColumns.addActionListener(this);
3079 showSeqs.addActionListener(this);
3080 hideColumns.addActionListener(this);
3081 hideSequences.addActionListener(this);
3082 hideAllButSelection.addActionListener(this);
3083 hideAllSelection.addActionListener(this);
3084 showAllHidden.addActionListener(this);
3085 showGroupConsensus.addItemListener(this);
3086 showGroupConservation.addItemListener(this);
3087 showConsensusHistogram.addItemListener(this);
3088 showSequenceLogo.addItemListener(this);
3089 applyAutoAnnotationSettings.addItemListener(this);
3090 formatMenu.setLabel("Format");
3091 selectMenu.setLabel("Select");
3092 newView.setLabel("New View");
3093 newView.addActionListener(this);
3094 alignFrameMenuBar.add(fileMenu);
3095 alignFrameMenuBar.add(editMenu);
3096 alignFrameMenuBar.add(selectMenu);
3097 alignFrameMenuBar.add(viewMenu);
3098 alignFrameMenuBar.add(formatMenu);
3099 alignFrameMenuBar.add(colourMenu);
3100 alignFrameMenuBar.add(calculateMenu);
3101 alignFrameMenuBar.add(helpMenu);
3103 fileMenu.add(inputText);
3104 fileMenu.add(loadTree);
3105 fileMenu.add(loadAnnotations);
3107 fileMenu.addSeparator();
3108 fileMenu.add(outputTextboxMenu);
3109 fileMenu.add(outputFeatures);
3110 fileMenu.add(outputAnnotations);
3112 if (jalviewServletURL != null)
3114 fileMenu.add(loadApplication);
3117 fileMenu.addSeparator();
3118 fileMenu.add(closeMenuItem);
3120 editMenu.add(undoMenuItem);
3121 editMenu.add(redoMenuItem);
3124 editMenu.add(pasteMenu);
3125 editMenu.add(delete);
3126 editMenu.addSeparator();
3127 editMenu.add(remove2LeftMenuItem);
3128 editMenu.add(remove2RightMenuItem);
3129 editMenu.add(removeGappedColumnMenuItem);
3130 editMenu.add(removeAllGapsMenuItem);
3131 editMenu.add(removeRedundancyMenuItem);
3132 viewMenu.add(newView);
3133 viewMenu.addSeparator();
3134 viewMenu.add(menu1);
3135 viewMenu.add(menu2);
3136 viewMenu.addSeparator();
3137 viewMenu.add(followMouseOverFlag);
3138 viewMenu.add(annotationPanelMenuItem);
3139 autoAnnMenu.add(applyAutoAnnotationSettings);
3140 autoAnnMenu.add(showConsensusHistogram);
3141 autoAnnMenu.add(showSequenceLogo);
3142 autoAnnMenu.addSeparator();
3143 autoAnnMenu.add(showGroupConservation);
3144 autoAnnMenu.add(showGroupConsensus);
3145 viewMenu.add(autoAnnMenu);
3146 viewMenu.addSeparator();
3147 viewMenu.add(sequenceFeatures);
3148 viewMenu.add(featureSettings);
3149 viewMenu.addSeparator();
3150 viewMenu.add(alProperties);
3151 viewMenu.addSeparator();
3152 viewMenu.add(overviewMenuItem);
3153 colourMenu.add(applyToAllGroups);
3154 colourMenu.addSeparator();
3155 colourMenu.add(noColourmenuItem);
3156 colourMenu.add(clustalColour);
3157 colourMenu.add(BLOSUM62Colour);
3158 colourMenu.add(PIDColour);
3159 colourMenu.add(zappoColour);
3160 colourMenu.add(taylorColour);
3161 colourMenu.add(hydrophobicityColour);
3162 colourMenu.add(helixColour);
3163 colourMenu.add(strandColour);
3164 colourMenu.add(turnColour);
3165 colourMenu.add(buriedColour);
3166 colourMenu.add(nucleotideColour);
3167 colourMenu.add(userDefinedColour);
3168 colourMenu.addSeparator();
3169 colourMenu.add(conservationMenuItem);
3170 colourMenu.add(modifyConservation);
3171 colourMenu.add(abovePIDThreshold);
3172 colourMenu.add(modifyPID);
3173 colourMenu.add(annotationColour);
3174 calculateMenu.add(sort);
3175 calculateMenu.add(calculate);
3176 calculateMenu.addSeparator();
3177 calculateMenu.add(pairwiseAlignmentMenuItem);
3178 calculateMenu.add(PCAMenuItem);
3179 calculateMenu.add(autoCalculate);
3180 this.add(statusBar, BorderLayout.SOUTH);
3181 pasteMenu.add(pasteNew);
3182 pasteMenu.add(pasteThis);
3183 sort.add(sortIDMenuItem);
3184 sort.add(sortLengthMenuItem);
3185 sort.add(sortByTreeMenu);
3186 sort.add(sortGroupMenuItem);
3187 sort.add(sortPairwiseMenuItem);
3188 calculate.add(averageDistanceTreeMenuItem);
3189 calculate.add(neighbourTreeMenuItem);
3190 calculate.add(avDistanceTreeBlosumMenuItem);
3191 calculate.add(njTreeBlosumMenuItem);
3192 helpMenu.add(documentation);
3193 helpMenu.add(about);
3194 menu1.add(showColumns);
3195 menu1.add(showSeqs);
3196 menu1.add(showAllHidden);
3197 menu2.add(hideColumns);
3198 menu2.add(hideSequences);
3199 menu2.add(hideAllSelection);
3200 menu2.add(hideAllButSelection);
3201 formatMenu.add(font);
3202 formatMenu.add(seqLimits);
3203 formatMenu.add(wrapMenuItem);
3204 formatMenu.add(scaleAbove);
3205 formatMenu.add(scaleLeft);
3206 formatMenu.add(scaleRight);
3207 formatMenu.add(viewBoxesMenuItem);
3208 formatMenu.add(viewTextMenuItem);
3209 formatMenu.add(colourTextMenuItem);
3210 formatMenu.add(displayNonconservedMenuItem);
3211 formatMenu.add(renderGapsMenuItem);
3212 formatMenu.add(centreColumnLabelFlag);
3213 selectMenu.add(findMenuItem);
3214 selectMenu.addSeparator();
3215 selectMenu.add(selectAllSequenceMenuItem);
3216 selectMenu.add(deselectAllSequenceMenuItem);
3217 selectMenu.add(invertSequenceMenuItem);
3218 selectMenu.add(invertColSel);
3219 selectMenu.add(grpsFromSelection);
3220 selectMenu.add(deleteGroups);
3224 MenuItem featureSettings = new MenuItem();
3226 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3228 MenuItem annotationColour = new MenuItem();
3230 MenuItem invertColSel = new MenuItem();
3232 Menu menu1 = new Menu();
3234 MenuItem showColumns = new MenuItem();
3236 MenuItem showSeqs = new MenuItem();
3238 Menu menu2 = new Menu();
3240 MenuItem hideColumns = new MenuItem();
3242 MenuItem hideSequences = new MenuItem();
3244 MenuItem hideAllButSelection = new MenuItem();
3246 MenuItem hideAllSelection = new MenuItem();
3248 MenuItem showAllHidden = new MenuItem();
3250 Menu formatMenu = new Menu();
3252 Menu selectMenu = new Menu();
3254 MenuItem newView = new MenuItem();
3257 * Attach the alignFrame panels after embedding menus, if necessary. This used
3258 * to be called setEmbedded, but is now creates the dropdown menus in a
3259 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3261 * @param reallyEmbedded
3262 * true to attach the view to the applet area on the page rather than
3265 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3270 // Explicly build the embedded menu panel for the on-page applet
3272 // view cannot be closed if its actually on the page
3273 fileMenu.remove(closeMenuItem);
3274 fileMenu.remove(3); // Remove Seperator
3275 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3276 Font.PLAIN, 10, false); // use our own fonts.
3277 // and actually add the components to the applet area
3278 viewport.applet.setLayout(new BorderLayout());
3279 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3280 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3281 alignPanel.setSize(viewport.applet.getSize().width,
3282 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3283 - statusBar.HEIGHT);
3284 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3285 final AlignFrame me = this;
3286 viewport.applet.addFocusListener(new FocusListener()
3290 public void focusLost(FocusEvent e)
3292 if (me.viewport.applet.currentAlignFrame==me) {
3293 me.viewport.applet.currentAlignFrame = null;
3297 public void focusGained(FocusEvent e)
3299 me.viewport.applet.currentAlignFrame = me;
3302 viewport.applet.validate();
3307 // test and embed menu bar if necessary.
3309 if (embedMenuIfNeeded(alignPanel))
3311 // adjust for status bar height too
3312 alignPanel.setSize(getSize().width, getSize().height
3313 - statusBar.HEIGHT);
3315 add(statusBar, BorderLayout.SOUTH);
3316 add(alignPanel, BorderLayout.CENTER);
3317 // and register with the applet so it can pass external API calls to us
3318 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3324 * create a new binding between structures in an existing jmol viewer instance
3325 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3326 * this does not open a new Jmol window, or modify the display of the
3327 * structures in the original jmol window. Note This method doesn't work
3328 * without an additional javascript library to exchange messages between the
3329 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3332 * JmolViewer instance
3333 * @param sequenceIds
3334 * - sequence Ids to search for associations
3336 public SequenceStructureBinding addStructureViewInstance(
3337 Object jmolviewer, String[] sequenceIds)
3339 org.jmol.api.JmolViewer viewer = null;
3342 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3343 } catch (ClassCastException ex)
3345 System.err.println("Unsupported viewer object :"
3346 + jmolviewer.getClass());
3350 System.err.println("Can't use this object as a structure viewer:"
3351 + jmolviewer.getClass());
3354 SequenceI[] seqs = null;
3355 if (sequenceIds == null || sequenceIds.length == 0)
3357 seqs = viewport.getAlignment().getSequencesArray();
3361 Vector sqi = new Vector();
3362 AlignmentI al = viewport.getAlignment();
3363 for (int sid = 0; sid < sequenceIds.length; sid++)
3365 SequenceI sq = al.findName(sequenceIds[sid]);
3373 seqs = new SequenceI[sqi.size()];
3374 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3376 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3385 // TODO: search for a jmv that involves viewer
3387 { // create a new viewer/jalview binding.
3388 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
3394 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3397 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3398 boolean needtoadd = false;
3399 if (toaddpdb != null)
3401 Vector pdbe = toaddpdb.getPDBId();
3402 PDBEntry pdbentry = null;
3403 if (pdbe != null && pdbe.size() > 0)
3405 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3407 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3408 if (!pdbentry.getId().equals(pdbEntryString)
3409 && !pdbentry.getFile().equals(pdbFile))
3419 if (pdbentry == null)
3421 pdbentry = new PDBEntry();
3422 pdbentry.setId(pdbEntryString);
3423 pdbentry.setFile(pdbFile);
3424 needtoadd = true; // add this new entry to sequence.
3426 // resolve data source
3427 // TODO: this code should be a refactored to an io package
3428 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3429 if (protocol == null)
3435 // make a note of the access mode and add
3436 if (pdbentry.getProperty() == null)
3438 pdbentry.setProperty(new Hashtable());
3440 pdbentry.getProperty().put("protocol", protocol);
3441 toaddpdb.addPDBId(pdbentry);
3447 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3451 Vector sequences = new Vector();
3452 for (int i = 0; i < seqs.length; i++)
3454 if (seqs[i] != null)
3456 sequences.addElement(new Object[]
3457 { seqs[i], (chains != null) ? chains[i] : null });
3460 seqs = new SequenceI[sequences.size()];
3461 chains = new String[sequences.size()];
3462 for (int i = 0, isize = sequences.size(); i < isize; i++)
3464 Object[] oj = (Object[]) sequences.elementAt(i);
3466 seqs[i] = (SequenceI) oj[0];
3467 chains[i] = (String) oj[1];
3475 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3476 SequenceI[] seqs, String[] chains, String protocol)
3478 // Scrub any null sequences from the array
3479 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3480 seqs = (SequenceI[]) sqch[0];
3481 chains = (String[]) sqch[1];
3482 if (seqs == null || seqs.length == 0)
3485 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3487 if (protocol == null || protocol.trim().length() == 0
3488 || protocol.equals("null"))
3490 protocol = (String) pdb.getProperty().get("protocol");
3491 if (protocol == null)
3493 System.err.println("Couldn't work out protocol to open structure: "
3498 if (applet.useXtrnalSviewer)
3500 // register the association(s) and quit, don't create any windows.
3501 StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
3504 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3506 // can only do alignments with Jmol
3507 // find the last jmol window assigned to this alignment
3508 jalview.appletgui.AppletJmol ajm = null, tajm;
3509 Vector jmols = applet
3510 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3511 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3513 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3514 if (tajm.ap.alignFrame == this)
3523 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3524 // try and add the pdb structure
3529 // otherwise, create a new window
3530 if (applet.jmolAvailable)
3532 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3534 applet.lastFrameX += 40;
3535 applet.lastFrameY += 40;
3539 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3544 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3545 SequenceI[][] seqs, String[][] chains, String[] protocols)
3547 // TODO Auto-generated method stub
3548 System.err.println("Aligned Structure View: Not yet implemented.");
3552 * modify the current selection, providing the user has not made a selection already.
3553 * @param sel - sequences from this alignment
3554 * @param csel - columns to be selected on the alignment
3556 public void select(SequenceGroup sel, ColumnSelection csel)
3558 alignPanel.seqPanel.selection(sel, csel, null);