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.applet.Applet;
26 import java.awt.event.*;
28 import org.jmol.api.JmolViewer;
30 import jalview.analysis.*;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.*;
34 import jalview.datamodel.*;
36 import jalview.schemes.*;
38 public class AlignFrame extends EmbmenuFrame implements ActionListener,
39 ItemListener, KeyListener
41 public AlignmentPanel alignPanel;
43 public AlignViewport viewport;
45 int DEFAULT_WIDTH = 700;
47 int DEFAULT_HEIGHT = 500;
49 String jalviewServletURL;
51 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
52 String title, boolean embedded)
57 jalviewServletURL = applet.getParameter("APPLICATION_URL");
63 } catch (Exception ex)
68 viewport = new AlignViewport(al, applet);
69 alignPanel = new AlignmentPanel(this, viewport);
71 viewport.updateConservation(alignPanel);
72 viewport.updateConsensus(alignPanel);
74 annotationPanelMenuItem.setState(viewport.showAnnotation);
75 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
77 seqLimits.setState(viewport.showJVSuffix);
81 String param = applet.getParameter("sortBy");
84 if (param.equalsIgnoreCase("Id"))
86 sortIDMenuItem_actionPerformed();
88 else if (param.equalsIgnoreCase("Pairwise Identity"))
90 sortPairwiseMenuItem_actionPerformed();
92 else if (param.equalsIgnoreCase("Length"))
94 sortLengthMenuItem_actionPerformed();
98 param = applet.getParameter("wrap");
101 if (param.equalsIgnoreCase("true"))
103 wrapMenuItem.setState(true);
104 wrapMenuItem_actionPerformed();
107 param = applet.getParameter("centrecolumnlabels");
110 centreColumnLabelFlag.setState(true);
111 centreColumnLabelFlag_stateChanged();
115 param = applet.getParameter("windowWidth");
118 int width = Integer.parseInt(param);
119 DEFAULT_WIDTH = width;
121 param = applet.getParameter("windowHeight");
124 int height = Integer.parseInt(param);
125 DEFAULT_HEIGHT = height;
127 } catch (Exception ex)
133 // Some JVMS send keyevents to Top frame or lowest panel,
134 // Havent worked out why yet. So add to both this frame and seqCanvas for
136 this.addKeyListener(this);
137 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
138 alignPanel.idPanel.idCanvas.addKeyListener(this);
139 alignPanel.scalePanel.addKeyListener(this);
140 alignPanel.annotationPanel.addKeyListener(this);
141 createAlignFrameWindow(embedded, title);
142 alignPanel.validate();
143 alignPanel.paintAlignment(true);
146 public AlignViewport getAlignViewport()
151 public SeqCanvas getSeqcanvas()
153 return alignPanel.seqPanel.seqCanvas;
163 public void parseFeaturesFile(String file, String type)
165 Hashtable featureLinks = new Hashtable();
166 boolean featuresFile = false;
169 featuresFile = new jalview.io.FeaturesFile(file, type)
170 .parse(viewport.alignment,
171 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
173 } catch (Exception ex)
175 ex.printStackTrace();
180 if (featureLinks.size() > 0)
182 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
184 viewport.showSequenceFeatures = true;
185 sequenceFeatures.setState(true);
186 if (viewport.featureSettings != null)
188 viewport.featureSettings.refreshTable();
190 alignPanel.paintAlignment(true);
195 public void keyPressed(KeyEvent evt)
197 if (viewport.cursorMode
198 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
199 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
200 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
201 && Character.isDigit(evt.getKeyChar()))
202 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
204 switch (evt.getKeyCode())
206 case 27: // escape key
207 deselectAllSequenceMenuItem_actionPerformed();
210 if (evt.isControlDown() || evt.isMetaDown())
212 cut_actionPerformed();
216 if (viewport.cursorMode && !evt.isControlDown())
218 alignPanel.seqPanel.setCursorColumn();
220 if (evt.isControlDown() || evt.isMetaDown())
222 copy_actionPerformed();
226 if (evt.isControlDown())
228 paste(evt.isShiftDown());
232 if (evt.isControlDown() || evt.isMetaDown())
234 selectAllSequenceMenuItem_actionPerformed();
237 case KeyEvent.VK_DOWN:
238 if (viewport.cursorMode)
240 alignPanel.seqPanel.moveCursor(0, 1);
244 moveSelectedSequences(false);
249 if (viewport.cursorMode)
251 alignPanel.seqPanel.moveCursor(0, -1);
255 moveSelectedSequences(true);
259 case KeyEvent.VK_LEFT:
260 if (evt.isAltDown() || !viewport.cursorMode)
261 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
263 alignPanel.seqPanel.moveCursor(-1, 0);
266 case KeyEvent.VK_RIGHT:
267 if (evt.isAltDown() || !viewport.cursorMode)
268 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
270 alignPanel.seqPanel.moveCursor(1, 0);
273 case KeyEvent.VK_SPACE:
274 if (viewport.cursorMode)
276 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
277 || evt.isShiftDown() || evt.isAltDown());
281 case KeyEvent.VK_DELETE:
282 case KeyEvent.VK_BACK_SPACE:
283 if (viewport.cursorMode)
285 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
286 || evt.isShiftDown() || evt.isAltDown());
290 cut_actionPerformed();
291 alignPanel.seqPanel.seqCanvas.repaint();
296 if (viewport.cursorMode)
298 alignPanel.seqPanel.setCursorRow();
302 if (viewport.cursorMode)
304 alignPanel.seqPanel.setCursorPosition();
308 case KeyEvent.VK_ENTER:
309 case KeyEvent.VK_COMMA:
310 if (viewport.cursorMode)
312 alignPanel.seqPanel.setCursorRowAndColumn();
317 if (viewport.cursorMode)
319 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
323 if (viewport.cursorMode)
325 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
330 viewport.cursorMode = !viewport.cursorMode;
331 statusBar.setText("Keyboard editing mode is "
332 + (viewport.cursorMode ? "on" : "off"));
333 if (viewport.cursorMode)
335 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
336 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
341 if (evt.isControlDown())
343 findMenuItem_actionPerformed();
349 boolean toggleSeqs = !evt.isControlDown();
350 boolean toggleCols = !evt.isShiftDown();
351 toggleHiddenRegions(toggleSeqs, toggleCols);
355 case KeyEvent.VK_PAGE_UP:
356 if (viewport.wrapAlignment)
358 alignPanel.scrollUp(true);
362 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
363 - viewport.endSeq + viewport.startSeq);
367 case KeyEvent.VK_PAGE_DOWN:
368 if (viewport.wrapAlignment)
370 alignPanel.scrollUp(false);
374 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
375 + viewport.endSeq - viewport.startSeq);
380 if (evt.isControlDown())
382 undoMenuItem_actionPerformed();
387 if (evt.isControlDown())
389 redoMenuItem_actionPerformed();
394 if (evt.isControlDown())
401 if (evt.isControlDown())
403 trimAlignment(false);
408 if (evt.isControlDown())
410 if (evt.isShiftDown())
412 this.removeAllGapsMenuItem_actionPerformed();
416 removeGappedColumnMenuItem_actionPerformed();
421 if (evt.isControlDown())
425 invertColSel_actionPerformed();
429 invertSequenceMenuItem_actionPerformed();
435 if (evt.isControlDown())
437 this.deleteGroups_actionPerformed();
442 if (evt.isControlDown())
449 alignPanel.paintAlignment(true);
453 * called by key handler and the hide all/show all menu items
458 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
460 boolean hide = false;
461 SequenceGroup sg = viewport.getSelectionGroup();
462 if (!toggleSeqs && !toggleCols)
464 // Hide everything by the current selection - this is a hack - we do the
465 // invert and then hide
466 // first check that there will be visible columns after the invert.
467 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
468 .getSelected().size() > 0)
469 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
472 // now invert the sequence set, if required - empty selection implies
473 // that no hiding is required.
476 invertSequenceMenuItem_actionPerformed();
477 sg = viewport.getSelectionGroup();
481 viewport.expandColSelection(sg, true);
482 // finally invert the column selection and get the new sequence
483 // selection and indicate it should be hidden.
484 invertColSel_actionPerformed();
491 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
494 viewport.hideAllSelectedSeqs();
496 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
498 viewport.showAllHiddenSeqs();
504 if (viewport.colSel.getSelected().size() > 0)
506 viewport.hideSelectedColumns();
509 viewport.selectionGroup = sg;
514 viewport.showAllHiddenColumns();
519 public void keyReleased(KeyEvent evt)
523 public void keyTyped(KeyEvent evt)
527 public void itemStateChanged(ItemEvent evt)
529 if (evt.getSource() == displayNonconservedMenuItem)
531 displayNonconservedMenuItem_actionPerformed();
533 else if (evt.getSource() == colourTextMenuItem)
535 colourTextMenuItem_actionPerformed();
537 else if (evt.getSource() == wrapMenuItem)
539 wrapMenuItem_actionPerformed();
541 else if (evt.getSource() == scaleAbove)
543 viewport.setScaleAboveWrapped(scaleAbove.getState());
545 else if (evt.getSource() == scaleLeft)
547 viewport.setScaleLeftWrapped(scaleLeft.getState());
549 else if (evt.getSource() == scaleRight)
551 viewport.setScaleRightWrapped(scaleRight.getState());
553 else if (evt.getSource() == seqLimits)
555 seqLimits_itemStateChanged();
557 else if (evt.getSource() == viewBoxesMenuItem)
559 viewport.setShowBoxes(viewBoxesMenuItem.getState());
561 else if (evt.getSource() == viewTextMenuItem)
563 viewport.setShowText(viewTextMenuItem.getState());
565 else if (evt.getSource() == renderGapsMenuItem)
567 viewport.setRenderGaps(renderGapsMenuItem.getState());
569 else if (evt.getSource() == annotationPanelMenuItem)
571 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
572 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
574 else if (evt.getSource() == sequenceFeatures)
576 viewport.showSequenceFeatures(sequenceFeatures.getState());
577 alignPanel.seqPanel.seqCanvas.repaint();
579 else if (evt.getSource() == conservationMenuItem)
581 conservationMenuItem_actionPerformed();
583 else if (evt.getSource() == abovePIDThreshold)
585 abovePIDThreshold_actionPerformed();
587 else if (evt.getSource() == applyToAllGroups)
589 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
591 else if (evt.getSource() == autoCalculate)
593 viewport.autocalculateConsensus = autoCalculate.getState();
595 else if (evt.getSource() == this.centreColumnLabelFlag)
597 centreColumnLabelFlag_stateChanged();
599 else if (evt.getSource() == this.followMouseOverFlag)
601 mouseOverFlag_stateChanged();
604 alignPanel.paintAlignment(true);
607 private void mouseOverFlag_stateChanged()
609 viewport.followHighlight = followMouseOverFlag.getState();
610 // TODO: could kick the scrollTo mechanism to reset view for current
614 private void centreColumnLabelFlag_stateChanged()
616 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
617 this.alignPanel.annotationPanel.repaint();
620 public void actionPerformed(ActionEvent evt)
622 Object source = evt.getSource();
624 if (source == inputText)
626 inputText_actionPerformed();
628 else if (source == loadTree)
630 loadTree_actionPerformed();
632 else if (source == loadApplication)
634 launchFullApplication();
636 else if (source == loadAnnotations)
640 else if (source == outputAnnotations)
642 outputAnnotations(true);
644 else if (source == outputFeatures)
646 outputFeatures(true, "Jalview");
648 else if (source == closeMenuItem)
650 closeMenuItem_actionPerformed();
652 else if (source == copy)
654 copy_actionPerformed();
656 else if (source == undoMenuItem)
658 undoMenuItem_actionPerformed();
660 else if (source == redoMenuItem)
662 redoMenuItem_actionPerformed();
664 else if (source == inputText)
666 inputText_actionPerformed();
668 else if (source == closeMenuItem)
670 closeMenuItem_actionPerformed();
672 else if (source == undoMenuItem)
674 undoMenuItem_actionPerformed();
676 else if (source == redoMenuItem)
678 redoMenuItem_actionPerformed();
680 else if (source == copy)
682 copy_actionPerformed();
684 else if (source == pasteNew)
686 pasteNew_actionPerformed();
688 else if (source == pasteThis)
690 pasteThis_actionPerformed();
692 else if (source == cut)
694 cut_actionPerformed();
696 else if (source == delete)
698 delete_actionPerformed();
700 else if (source == grpsFromSelection)
702 makeGrpsFromSelection_actionPerformed();
704 else if (source == deleteGroups)
706 deleteGroups_actionPerformed();
708 else if (source == selectAllSequenceMenuItem)
710 selectAllSequenceMenuItem_actionPerformed();
712 else if (source == deselectAllSequenceMenuItem)
714 deselectAllSequenceMenuItem_actionPerformed();
716 else if (source == invertSequenceMenuItem)
718 invertSequenceMenuItem_actionPerformed();
720 else if (source == invertColSel)
722 viewport.invertColumnSelection();
723 alignPanel.paintAlignment(true);
725 else if (source == remove2LeftMenuItem)
729 else if (source == remove2RightMenuItem)
731 trimAlignment(false);
733 else if (source == removeGappedColumnMenuItem)
735 removeGappedColumnMenuItem_actionPerformed();
737 else if (source == removeAllGapsMenuItem)
739 removeAllGapsMenuItem_actionPerformed();
741 else if (source == findMenuItem)
743 findMenuItem_actionPerformed();
745 else if (source == font)
747 new FontChooser(alignPanel);
749 else if (source == newView)
753 else if (source == showColumns)
755 viewport.showAllHiddenColumns();
756 alignPanel.paintAlignment(true);
758 else if (source == showSeqs)
760 viewport.showAllHiddenSeqs();
761 alignPanel.paintAlignment(true);
763 else if (source == hideColumns)
765 viewport.hideSelectedColumns();
766 alignPanel.paintAlignment(true);
768 else if (source == hideSequences
769 && viewport.getSelectionGroup() != null)
771 viewport.hideAllSelectedSeqs();
772 alignPanel.paintAlignment(true);
774 else if (source == hideAllButSelection)
776 toggleHiddenRegions(false, false);
777 alignPanel.paintAlignment(true);
779 else if (source == hideAllSelection)
781 SequenceGroup sg = viewport.getSelectionGroup();
782 viewport.expandColSelection(sg, false);
783 viewport.hideAllSelectedSeqs();
784 viewport.hideSelectedColumns();
785 alignPanel.paintAlignment(true);
787 else if (source == showAllHidden)
789 viewport.showAllHiddenColumns();
790 viewport.showAllHiddenSeqs();
791 alignPanel.paintAlignment(true);
793 else if (source == featureSettings)
795 new FeatureSettings(alignPanel);
797 else if (source == alProperties)
799 StringBuffer contents = new StringBuffer();
802 int min = Integer.MAX_VALUE, max = 0;
803 for (int i = 0; i < viewport.alignment.getHeight(); i++)
805 int size = viewport.alignment.getSequenceAt(i).getEnd()
806 - viewport.alignment.getSequenceAt(i).getStart();
813 avg = avg / (float) viewport.alignment.getHeight();
815 contents.append("\nSequences: " + viewport.alignment.getHeight());
816 contents.append("\nMinimum Sequence Length: " + min);
817 contents.append("\nMaximum Sequence Length: " + max);
818 contents.append("\nAverage Length: " + (int) avg);
820 if (((Alignment) viewport.alignment).alignmentProperties != null)
822 Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
823 Enumeration en = props.keys();
824 while (en.hasMoreElements())
826 String key = en.nextElement().toString();
827 contents.append("\n" + key + "\t" + props.get(key));
831 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
832 cap.setText(contents.toString());
833 Frame frame = new Frame();
835 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
836 + getTitle(), 400, 250);
838 else if (source == overviewMenuItem)
840 overviewMenuItem_actionPerformed();
842 else if (source == noColourmenuItem)
846 else if (source == clustalColour)
848 abovePIDThreshold.setState(false);
849 changeColour(new ClustalxColourScheme(
850 viewport.alignment.getSequences(),
851 viewport.alignment.getWidth()));
853 else if (source == zappoColour)
855 changeColour(new ZappoColourScheme());
857 else if (source == taylorColour)
859 changeColour(new TaylorColourScheme());
861 else if (source == hydrophobicityColour)
863 changeColour(new HydrophobicColourScheme());
865 else if (source == helixColour)
867 changeColour(new HelixColourScheme());
869 else if (source == strandColour)
871 changeColour(new StrandColourScheme());
873 else if (source == turnColour)
875 changeColour(new TurnColourScheme());
877 else if (source == buriedColour)
879 changeColour(new BuriedColourScheme());
881 else if (source == nucleotideColour)
883 changeColour(new NucleotideColourScheme());
885 else if (source == modifyPID)
887 modifyPID_actionPerformed();
889 else if (source == modifyConservation)
891 modifyConservation_actionPerformed();
893 else if (source == userDefinedColour)
895 new UserDefinedColours(alignPanel, null);
897 else if (source == PIDColour)
899 changeColour(new PIDColourScheme());
901 else if (source == BLOSUM62Colour)
903 changeColour(new Blosum62ColourScheme());
905 else if (source == annotationColour)
907 new AnnotationColourChooser(viewport, alignPanel);
909 else if (source == sortPairwiseMenuItem)
911 sortPairwiseMenuItem_actionPerformed();
913 else if (source == sortIDMenuItem)
915 sortIDMenuItem_actionPerformed();
917 else if (source == sortLengthMenuItem)
919 sortLengthMenuItem_actionPerformed();
921 else if (source == sortGroupMenuItem)
923 sortGroupMenuItem_actionPerformed();
925 else if (source == removeRedundancyMenuItem)
927 removeRedundancyMenuItem_actionPerformed();
929 else if (source == pairwiseAlignmentMenuItem)
931 pairwiseAlignmentMenuItem_actionPerformed();
933 else if (source == PCAMenuItem)
935 PCAMenuItem_actionPerformed();
937 else if (source == averageDistanceTreeMenuItem)
939 averageDistanceTreeMenuItem_actionPerformed();
941 else if (source == neighbourTreeMenuItem)
943 neighbourTreeMenuItem_actionPerformed();
945 else if (source == njTreeBlosumMenuItem)
947 njTreeBlosumMenuItem_actionPerformed();
949 else if (source == avDistanceTreeBlosumMenuItem)
951 avTreeBlosumMenuItem_actionPerformed();
953 else if (source == documentation)
955 documentation_actionPerformed();
957 else if (source == about)
959 about_actionPerformed();
964 public void inputText_actionPerformed()
966 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
967 Frame frame = new Frame();
969 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
972 protected void outputText_actionPerformed(ActionEvent e)
974 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
975 Frame frame = new Frame();
977 jalview.bin.JalviewLite.addFrame(frame,
978 "Alignment output - " + e.getActionCommand(), 600, 500);
979 cap.setText(new AppletFormatAdapter().formatSequences(
980 e.getActionCommand(), viewport.getAlignment(),
981 viewport.showJVSuffix));
984 public void loadAnnotations()
986 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
987 cap.setText("Paste your features / annotations file here.");
988 cap.setAnnotationImport();
989 Frame frame = new Frame();
991 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
995 public String outputAnnotations(boolean displayTextbox)
997 String annotation = new AnnotationFile().printAnnotations(
998 viewport.showAnnotation ? viewport.alignment
999 .getAlignmentAnnotation() : null, viewport.alignment
1001 ((Alignment) viewport.alignment).alignmentProperties);
1005 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1006 Frame frame = new Frame();
1008 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1009 cap.setText(annotation);
1015 private Hashtable getDisplayedFeatureCols()
1017 if (alignPanel.getFeatureRenderer() != null)
1019 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1020 Hashtable fcols = new Hashtable();
1021 Enumeration en = viewport.featuresDisplayed.keys();
1022 while (en.hasMoreElements())
1024 Object col = en.nextElement();
1025 fcols.put(col, fr.featureColours.get(col));
1032 public String outputFeatures(boolean displayTextbox, String format)
1035 if (format.equalsIgnoreCase("Jalview"))
1037 features = new FeaturesFile().printJalviewFormat(
1038 viewport.alignment.getSequencesArray(),
1039 getDisplayedFeatureCols());
1043 features = new FeaturesFile().printGFFFormat(
1044 viewport.alignment.getSequencesArray(),
1045 getDisplayedFeatureCols());
1050 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1051 Frame frame = new Frame();
1053 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1055 cap.setText(features);
1061 void launchFullApplication()
1063 StringBuffer url = new StringBuffer(jalviewServletURL);
1066 + appendProtocol(viewport.applet.getParameter("file")));
1068 if (viewport.applet.getParameter("features") != null)
1070 url.append("&features=");
1071 url.append(appendProtocol(viewport.applet.getParameter("features")));
1074 if (viewport.applet.getParameter("annotations") != null)
1076 url.append("&annotations=");
1077 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1080 if (viewport.applet.getParameter("jnetfile") != null)
1082 url.append("&annotations=");
1083 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1086 if (viewport.applet.getParameter("defaultColour") != null)
1088 url.append("&colour="
1089 + removeWhiteSpace(viewport.applet
1090 .getParameter("defaultColour")));
1093 if (viewport.applet.getParameter("userDefinedColour") != null)
1095 url.append("&colour="
1096 + removeWhiteSpace(viewport.applet
1097 .getParameter("userDefinedColour")));
1099 if (viewport.applet.getParameter("tree") != null)
1102 + appendProtocol(viewport.applet.getParameter("tree")));
1104 if (viewport.applet.getParameter("treeFile") != null)
1107 + appendProtocol(viewport.applet.getParameter("treeFile")));
1110 showURL(url.toString(), "FULL_APP");
1113 String removeWhiteSpace(String colour)
1115 StringBuffer sb = new StringBuffer();
1116 for (int i = 0; i < colour.length(); i++)
1118 if (Character.isWhitespace(colour.charAt(i)))
1124 sb.append(colour.charAt(i));
1128 return sb.toString();
1131 String appendProtocol(String url)
1136 url = URLEncoder.encode(url);
1139 * When we finally deprecate 1.1 compatibility, we can start to use
1140 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1141 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1142 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1143 * ex.printStackTrace(); }
1145 catch (java.net.MalformedURLException ex)
1147 url = viewport.applet.getCodeBase() + url;
1152 public void closeMenuItem_actionPerformed()
1154 PaintRefresher.RemoveComponent(alignPanel);
1155 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1156 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1158 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1169 void updateEditMenuBar()
1172 if (viewport.historyList.size() > 0)
1174 undoMenuItem.setEnabled(true);
1175 CommandI command = (CommandI) viewport.historyList.peek();
1176 undoMenuItem.setLabel("Undo " + command.getDescription());
1180 undoMenuItem.setEnabled(false);
1181 undoMenuItem.setLabel("Undo");
1184 if (viewport.redoList.size() > 0)
1186 redoMenuItem.setEnabled(true);
1188 CommandI command = (CommandI) viewport.redoList.peek();
1189 redoMenuItem.setLabel("Redo " + command.getDescription());
1193 redoMenuItem.setEnabled(false);
1194 redoMenuItem.setLabel("Redo");
1198 public void addHistoryItem(CommandI command)
1200 if (command.getSize() > 0)
1202 viewport.historyList.push(command);
1203 viewport.redoList.removeAllElements();
1204 updateEditMenuBar();
1205 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1215 protected void undoMenuItem_actionPerformed()
1217 if (viewport.historyList.size() < 1)
1222 CommandI command = (CommandI) viewport.historyList.pop();
1223 viewport.redoList.push(command);
1224 command.undoCommand(null);
1226 AlignViewport originalSource = getOriginatingSource(command);
1228 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1229 updateEditMenuBar();
1230 originalSource.firePropertyChange("alignment", null,
1231 originalSource.alignment.getSequences());
1240 protected void redoMenuItem_actionPerformed()
1242 if (viewport.redoList.size() < 1)
1247 CommandI command = (CommandI) viewport.redoList.pop();
1248 viewport.historyList.push(command);
1249 command.doCommand(null);
1251 AlignViewport originalSource = getOriginatingSource(command);
1252 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1254 updateEditMenuBar();
1255 originalSource.firePropertyChange("alignment", null,
1256 originalSource.alignment.getSequences());
1259 AlignViewport getOriginatingSource(CommandI command)
1261 AlignViewport originalSource = null;
1262 // For sequence removal and addition, we need to fire
1263 // the property change event FROM the viewport where the
1264 // original alignment was altered
1265 AlignmentI al = null;
1266 if (command instanceof EditCommand)
1268 EditCommand editCommand = (EditCommand) command;
1269 al = editCommand.getAlignment();
1270 Vector comps = (Vector) PaintRefresher.components.get(viewport
1271 .getSequenceSetId());
1272 for (int i = 0; i < comps.size(); i++)
1274 if (comps.elementAt(i) instanceof AlignmentPanel)
1276 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1278 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1285 if (originalSource == null)
1287 // The original view is closed, we must validate
1288 // the current view against the closed view first
1291 PaintRefresher.validateSequences(al, viewport.alignment);
1294 originalSource = viewport;
1297 return originalSource;
1300 public void moveSelectedSequences(boolean up)
1302 SequenceGroup sg = viewport.getSelectionGroup();
1310 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1312 SequenceI seq = viewport.alignment.getSequenceAt(i);
1313 if (!sg.getSequences(null).contains(seq))
1318 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1319 if (sg.getSequences(null).contains(temp))
1324 viewport.alignment.getSequences().setElementAt(temp, i);
1325 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1330 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1332 SequenceI seq = viewport.alignment.getSequenceAt(i);
1333 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1338 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1339 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1344 viewport.alignment.getSequences().setElementAt(temp, i);
1345 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1349 alignPanel.paintAlignment(true);
1352 synchronized void slideSequences(boolean right, int size)
1354 Vector sg = new Vector();
1355 if (viewport.cursorMode)
1357 sg.addElement(viewport.alignment
1358 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1360 else if (viewport.getSelectionGroup() != null
1361 && viewport.getSelectionGroup().getSize() != viewport.alignment
1364 sg = viewport.getSelectionGroup().getSequences(
1365 viewport.hiddenRepSequences);
1373 Vector invertGroup = new Vector();
1375 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1377 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1378 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1381 SequenceI[] seqs1 = new SequenceI[sg.size()];
1382 for (int i = 0; i < sg.size(); i++)
1383 seqs1[i] = (SequenceI) sg.elementAt(i);
1385 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1386 for (int i = 0; i < invertGroup.size(); i++)
1387 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1389 SlideSequencesCommand ssc;
1391 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1392 size, viewport.getGapCharacter());
1394 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1395 size, viewport.getGapCharacter());
1397 int groupAdjustment = 0;
1398 if (ssc.getGapsInsertedBegin() && right)
1400 if (viewport.cursorMode)
1401 alignPanel.seqPanel.moveCursor(size, 0);
1403 groupAdjustment = size;
1405 else if (!ssc.getGapsInsertedBegin() && !right)
1407 if (viewport.cursorMode)
1408 alignPanel.seqPanel.moveCursor(-size, 0);
1410 groupAdjustment = -size;
1413 if (groupAdjustment != 0)
1415 viewport.getSelectionGroup().setStartRes(
1416 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1417 viewport.getSelectionGroup().setEndRes(
1418 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1421 boolean appendHistoryItem = false;
1422 if (viewport.historyList != null && viewport.historyList.size() > 0
1423 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1425 appendHistoryItem = ssc
1426 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1430 if (!appendHistoryItem)
1431 addHistoryItem(ssc);
1436 static StringBuffer copiedSequences;
1438 static Vector copiedHiddenColumns;
1440 protected void copy_actionPerformed()
1442 if (viewport.getSelectionGroup() == null)
1447 SequenceGroup sg = viewport.getSelectionGroup();
1448 copiedSequences = new StringBuffer();
1449 Hashtable orderedSeqs = new Hashtable();
1450 for (int i = 0; i < sg.getSize(); i++)
1452 SequenceI seq = sg.getSequenceAt(i);
1453 int index = viewport.alignment.findIndex(seq);
1454 orderedSeqs.put(index + "", seq);
1457 int index = 0, startRes, endRes;
1460 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1462 copiedHiddenColumns = new Vector();
1463 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1464 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1467 int[] region = (int[]) viewport.getColumnSelection()
1468 .getHiddenColumns().elementAt(i);
1470 copiedHiddenColumns.addElement(new int[]
1471 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1476 copiedHiddenColumns = null;
1479 for (int i = 0; i < sg.getSize(); i++)
1481 SequenceI seq = null;
1485 if (orderedSeqs.containsKey(index + ""))
1487 seq = (SequenceI) orderedSeqs.get(index + "");
1499 // Returns residue following index if gap
1500 startRes = seq.findPosition(sg.getStartRes());
1503 // Need to find the residue preceeding index if gap
1506 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1508 ch = seq.getCharAt(j);
1509 if (!jalview.util.Comparison.isGap((ch)))
1517 endRes += seq.getStart() - 1;
1520 copiedSequences.append(seq.getName()
1526 + seq.getSequenceAsString(sg.getStartRes(),
1527 sg.getEndRes() + 1) + "\n");
1532 protected void pasteNew_actionPerformed()
1537 protected void pasteThis_actionPerformed()
1542 void paste(boolean newAlignment)
1547 if (copiedSequences == null)
1552 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1553 Vector seqs = new Vector();
1554 while (st.hasMoreElements())
1556 String name = st.nextToken();
1557 int start = Integer.parseInt(st.nextToken());
1558 int end = Integer.parseInt(st.nextToken());
1559 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1561 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1562 for (int i = 0; i < seqs.size(); i++)
1564 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1569 String newtitle = new String("Copied sequences");
1570 if (getTitle().startsWith("Copied sequences"))
1572 newtitle = getTitle();
1576 newtitle = newtitle.concat("- from " + getTitle());
1578 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1579 viewport.applet, newtitle, false);
1580 if (copiedHiddenColumns != null)
1582 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1584 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1585 af.viewport.hideColumns(region[0], region[1]);
1589 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1594 addSequences(newSeqs);
1597 } catch (Exception ex)
1599 } // could be anything being pasted in here
1603 void addSequences(SequenceI[] seqs)
1605 for (int i = 0; i < seqs.length; i++)
1607 viewport.alignment.addSequence(seqs[i]);
1611 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1612 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1614 viewport.setEndSeq(viewport.alignment.getHeight());
1615 viewport.alignment.getWidth();
1616 viewport.firePropertyChange("alignment", null,
1617 viewport.alignment.getSequences());
1621 protected void cut_actionPerformed()
1623 copy_actionPerformed();
1624 delete_actionPerformed();
1627 protected void delete_actionPerformed()
1630 SequenceGroup sg = viewport.getSelectionGroup();
1636 Vector seqs = new Vector();
1638 for (int i = 0; i < sg.getSize(); i++)
1640 seq = sg.getSequenceAt(i);
1641 seqs.addElement(seq);
1644 // If the cut affects all sequences, remove highlighted columns
1645 if (sg.getSize() == viewport.alignment.getHeight())
1647 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1648 sg.getEndRes() + 1);
1651 SequenceI[] cut = new SequenceI[seqs.size()];
1652 for (int i = 0; i < seqs.size(); i++)
1654 cut[i] = (SequenceI) seqs.elementAt(i);
1658 * //ADD HISTORY ITEM
1660 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1661 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1662 viewport.alignment));
1664 viewport.setSelectionGroup(null);
1665 viewport.alignment.deleteGroup(sg);
1667 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1670 if (viewport.getAlignment().getHeight() < 1)
1672 this.setVisible(false);
1676 protected void makeGrpsFromSelection_actionPerformed()
1678 if (viewport.getSelectionGroup() != null)
1680 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
1681 viewport.getSequenceSelection(),
1682 viewport.getAlignmentView(true).getSequenceStrings(
1683 viewport.getGapCharacter()),
1684 viewport.alignment.getGroups());
1685 viewport.alignment.deleteAllGroups();
1686 viewport.sequenceColours = null;
1687 viewport.setSelectionGroup(null);
1688 // set view properties for each group
1689 for (int g = 0; g < gps.length; g++)
1691 // gps[g].setShowunconserved(viewport.getShowUnconserved());
1692 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
1693 viewport.alignment.addGroup(gps[g]);
1694 Color col = new Color((int) (Math.random() * 255),
1695 (int) (Math.random() * 255), (int) (Math.random() * 255));
1696 col = col.brighter();
1697 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
1698 .hasMoreElements(); viewport.setSequenceColour(
1699 (SequenceI) sq.nextElement(), col))
1702 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1703 // alignPanel.updateAnnotation();
1704 alignPanel.paintAlignment(true);
1708 protected void deleteGroups_actionPerformed()
1710 viewport.alignment.deleteAllGroups();
1711 viewport.sequenceColours = null;
1712 viewport.setSelectionGroup(null);
1714 alignPanel.paintAlignment(true);
1717 public void selectAllSequenceMenuItem_actionPerformed()
1719 SequenceGroup sg = new SequenceGroup();
1720 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1722 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1724 sg.setEndRes(viewport.alignment.getWidth() - 1);
1725 viewport.setSelectionGroup(sg);
1726 alignPanel.paintAlignment(true);
1727 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1730 public void deselectAllSequenceMenuItem_actionPerformed()
1732 if (viewport.cursorMode)
1734 alignPanel.seqPanel.keyboardNo1 = null;
1735 alignPanel.seqPanel.keyboardNo2 = null;
1737 viewport.setSelectionGroup(null);
1738 viewport.getColumnSelection().clear();
1739 viewport.setSelectionGroup(null);
1740 alignPanel.idPanel.idCanvas.searchResults = null;
1741 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1742 alignPanel.paintAlignment(true);
1743 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1746 public void invertSequenceMenuItem_actionPerformed()
1748 SequenceGroup sg = viewport.getSelectionGroup();
1749 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1751 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1754 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1757 public void invertColSel_actionPerformed()
1759 viewport.invertColumnSelection();
1760 alignPanel.paintAlignment(true);
1761 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1764 void trimAlignment(boolean trimLeft)
1766 ColumnSelection colSel = viewport.getColumnSelection();
1769 if (colSel.size() > 0)
1773 column = colSel.getMin();
1777 column = colSel.getMax();
1781 if (viewport.getSelectionGroup() != null)
1783 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1784 viewport.hiddenRepSequences);
1788 seqs = viewport.alignment.getSequencesArray();
1791 TrimRegionCommand trimRegion;
1794 trimRegion = new TrimRegionCommand("Remove Left",
1795 TrimRegionCommand.TRIM_LEFT, seqs, column,
1796 viewport.alignment, viewport.colSel,
1797 viewport.selectionGroup);
1798 viewport.setStartRes(0);
1802 trimRegion = new TrimRegionCommand("Remove Right",
1803 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1804 viewport.alignment, viewport.colSel,
1805 viewport.selectionGroup);
1808 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1810 addHistoryItem(trimRegion);
1812 Vector groups = viewport.alignment.getGroups();
1814 for (int i = 0; i < groups.size(); i++)
1816 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1818 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1819 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1821 viewport.alignment.deleteGroup(sg);
1825 viewport.firePropertyChange("alignment", null, viewport
1826 .getAlignment().getSequences());
1830 public void removeGappedColumnMenuItem_actionPerformed()
1832 int start = 0, end = viewport.alignment.getWidth() - 1;
1835 if (viewport.getSelectionGroup() != null)
1837 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1838 viewport.hiddenRepSequences);
1839 start = viewport.getSelectionGroup().getStartRes();
1840 end = viewport.getSelectionGroup().getEndRes();
1844 seqs = viewport.alignment.getSequencesArray();
1847 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1848 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1850 addHistoryItem(removeGapCols);
1852 statusBar.setText("Removed " + removeGapCols.getSize()
1853 + " empty columns.");
1855 // This is to maintain viewport position on first residue
1856 // of first sequence
1857 SequenceI seq = viewport.alignment.getSequenceAt(0);
1858 int startRes = seq.findPosition(viewport.startRes);
1859 // ShiftList shifts;
1860 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1861 // edit.alColumnChanges=shifts.getInverse();
1862 // if (viewport.hasHiddenColumns)
1863 // viewport.getColumnSelection().compensateForEdits(shifts);
1864 viewport.setStartRes(seq.findIndex(startRes) - 1);
1865 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1870 public void removeAllGapsMenuItem_actionPerformed()
1872 int start = 0, end = viewport.alignment.getWidth() - 1;
1875 if (viewport.getSelectionGroup() != null)
1877 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1878 viewport.hiddenRepSequences);
1879 start = viewport.getSelectionGroup().getStartRes();
1880 end = viewport.getSelectionGroup().getEndRes();
1884 seqs = viewport.alignment.getSequencesArray();
1887 // This is to maintain viewport position on first residue
1888 // of first sequence
1889 SequenceI seq = viewport.alignment.getSequenceAt(0);
1890 int startRes = seq.findPosition(viewport.startRes);
1892 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1893 viewport.alignment));
1895 viewport.setStartRes(seq.findIndex(startRes) - 1);
1897 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1902 public void findMenuItem_actionPerformed()
1904 new Finder(alignPanel);
1908 * create a new view derived from the current view
1911 * @return frame for the new view
1913 public AlignFrame newView(String viewtitle)
1916 if (viewport.hasHiddenRows)
1918 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1919 .getFullAlignment().getSequencesArray());
1923 newal = new Alignment(viewport.alignment.getSequencesArray());
1926 if (viewport.alignment.getAlignmentAnnotation() != null)
1928 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
1930 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
1932 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
1937 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
1939 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
1940 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
1941 PaintRefresher.Register(newaf.alignPanel,
1942 newaf.alignPanel.av.getSequenceSetId());
1944 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
1945 newaf.alignPanel.av.getSequenceSetId());
1946 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
1947 newaf.alignPanel.av.getSequenceSetId());
1949 Vector comps = (Vector) PaintRefresher.components.get(viewport
1950 .getSequenceSetId());
1952 for (int i = 0; i < comps.size(); i++)
1954 if (comps.elementAt(i) instanceof AlignmentPanel)
1960 String title = new String(this.getTitle());
1961 if (viewtitle != null)
1963 title = viewtitle + " ( " + title + ")";
1967 if (title.indexOf("(View") > -1)
1969 title = title.substring(0, title.indexOf("(View"));
1971 title += "(View " + viewSize + ")";
1974 newaf.setTitle(title.toString());
1976 newaf.viewport.historyList = viewport.historyList;
1977 newaf.viewport.redoList = viewport.redoList;
1983 * @return list of feature groups on the view
1985 public String[] getFeatureGroups()
1987 FeatureRenderer fr = null;
1988 if (alignPanel != null
1989 && (fr = alignPanel.getFeatureRenderer()) != null)
1991 return fr.getGroups();
1997 * get sequence feature groups that are hidden or shown
2003 public String[] getFeatureGroupsOfState(boolean visible)
2005 FeatureRenderer fr = null;
2006 if (alignPanel != null
2007 && (fr = alignPanel.getFeatureRenderer()) != null)
2009 return fr.getGroups(visible);
2015 * Change the display state for the given feature groups
2018 * list of group strings
2020 * visible or invisible
2022 public void setFeatureGroupState(String[] groups, boolean state)
2024 FeatureRenderer fr = null;
2025 this.sequenceFeatures.setState(true);
2026 viewport.showSequenceFeatures(true);
2027 if (alignPanel != null
2028 && (fr = alignPanel.getFeatureRenderer()) != null)
2030 fr.setGroupState(groups, state);
2031 alignPanel.seqPanel.seqCanvas.repaint();
2032 if (alignPanel.overviewPanel != null)
2034 alignPanel.overviewPanel.updateOverviewImage();
2039 public void seqLimits_itemStateChanged()
2041 viewport.setShowJVSuffix(seqLimits.getState());
2042 alignPanel.fontChanged();
2043 alignPanel.paintAlignment(true);
2046 protected void colourTextMenuItem_actionPerformed()
2048 viewport.setColourText(colourTextMenuItem.getState());
2049 alignPanel.paintAlignment(true);
2052 protected void displayNonconservedMenuItem_actionPerformed()
2054 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2055 alignPanel.paintAlignment(true);
2058 protected void wrapMenuItem_actionPerformed()
2060 viewport.setWrapAlignment(wrapMenuItem.getState());
2061 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2062 scaleAbove.setEnabled(wrapMenuItem.getState());
2063 scaleLeft.setEnabled(wrapMenuItem.getState());
2064 scaleRight.setEnabled(wrapMenuItem.getState());
2065 alignPanel.paintAlignment(true);
2068 public void overviewMenuItem_actionPerformed()
2070 if (alignPanel.overviewPanel != null)
2075 Frame frame = new Frame();
2076 OverviewPanel overview = new OverviewPanel(alignPanel);
2077 frame.add(overview);
2078 // +50 must allow for applet frame window
2079 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2080 overview.getPreferredSize().width,
2081 overview.getPreferredSize().height + 50);
2084 frame.addWindowListener(new WindowAdapter()
2086 public void windowClosing(WindowEvent e)
2088 alignPanel.setOverviewPanel(null);
2092 alignPanel.setOverviewPanel(overview);
2096 void changeColour(ColourSchemeI cs)
2102 if (viewport.getAbovePIDThreshold())
2104 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2107 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2109 viewport.setGlobalColourScheme(cs);
2113 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2116 if (viewport.getConservationSelected())
2119 Alignment al = (Alignment) viewport.alignment;
2120 Conservation c = new Conservation("All",
2121 ResidueProperties.propHash, 3, al.getSequences(), 0,
2125 c.verdict(false, viewport.ConsPercGaps);
2127 cs.setConservation(c);
2129 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2135 cs.setConservation(null);
2138 cs.setConsensus(viewport.hconsensus);
2141 viewport.setGlobalColourScheme(cs);
2143 if (viewport.getColourAppliesToAllGroups())
2145 Vector groups = viewport.alignment.getGroups();
2146 for (int i = 0; i < groups.size(); i++)
2148 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2155 if (cs instanceof ClustalxColourScheme)
2157 sg.cs = new ClustalxColourScheme(
2158 sg.getSequences(viewport.hiddenRepSequences),
2165 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2166 } catch (Exception ex)
2168 ex.printStackTrace();
2173 if (viewport.getAbovePIDThreshold()
2174 || cs instanceof PIDColourScheme
2175 || cs instanceof Blosum62ColourScheme)
2177 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2178 sg.cs.setConsensus(AAFrequency.calculate(
2179 sg.getSequences(viewport.hiddenRepSequences), 0,
2184 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2187 if (viewport.getConservationSelected())
2189 Conservation c = new Conservation("Group",
2190 ResidueProperties.propHash, 3,
2191 sg.getSequences(viewport.hiddenRepSequences), 0,
2192 viewport.alignment.getWidth() - 1);
2194 c.verdict(false, viewport.ConsPercGaps);
2195 sg.cs.setConservation(c);
2199 sg.cs.setConservation(null);
2200 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2206 if (alignPanel.getOverviewPanel() != null)
2208 alignPanel.getOverviewPanel().updateOverviewImage();
2211 jalview.structure.StructureSelectionManager
2212 .getStructureSelectionManager().sequenceColoursChanged(
2215 alignPanel.paintAlignment(true);
2218 protected void modifyPID_actionPerformed()
2220 if (viewport.getAbovePIDThreshold()
2221 && viewport.globalColourScheme != null)
2223 SliderPanel.setPIDSliderSource(alignPanel,
2224 viewport.getGlobalColourScheme(), "Background");
2225 SliderPanel.showPIDSlider();
2229 protected void modifyConservation_actionPerformed()
2231 if (viewport.getConservationSelected()
2232 && viewport.globalColourScheme != null)
2234 SliderPanel.setConservationSlider(alignPanel,
2235 viewport.globalColourScheme, "Background");
2236 SliderPanel.showConservationSlider();
2240 protected void conservationMenuItem_actionPerformed()
2242 viewport.setConservationSelected(conservationMenuItem.getState());
2244 viewport.setAbovePIDThreshold(false);
2245 abovePIDThreshold.setState(false);
2247 changeColour(viewport.getGlobalColourScheme());
2249 modifyConservation_actionPerformed();
2252 public void abovePIDThreshold_actionPerformed()
2254 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2256 conservationMenuItem.setState(false);
2257 viewport.setConservationSelected(false);
2259 changeColour(viewport.getGlobalColourScheme());
2261 modifyPID_actionPerformed();
2264 public void sortPairwiseMenuItem_actionPerformed()
2266 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2267 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2268 .getAlignment().getSequenceAt(0), null);
2270 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2271 viewport.alignment));
2272 alignPanel.paintAlignment(true);
2275 public void sortIDMenuItem_actionPerformed()
2277 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2278 AlignmentSorter.sortByID(viewport.getAlignment());
2279 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2280 alignPanel.paintAlignment(true);
2283 public void sortLengthMenuItem_actionPerformed()
2285 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2286 AlignmentSorter.sortByLength(viewport.getAlignment());
2287 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2288 viewport.alignment));
2289 alignPanel.paintAlignment(true);
2292 public void sortGroupMenuItem_actionPerformed()
2294 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2295 AlignmentSorter.sortByGroup(viewport.getAlignment());
2296 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2297 viewport.alignment));
2298 alignPanel.paintAlignment(true);
2302 public void removeRedundancyMenuItem_actionPerformed()
2304 new RedundancyPanel(alignPanel);
2307 public void pairwiseAlignmentMenuItem_actionPerformed()
2309 if (viewport.getSelectionGroup() != null
2310 && viewport.getSelectionGroup().getSize() > 1)
2312 Frame frame = new Frame();
2313 frame.add(new PairwiseAlignPanel(alignPanel));
2314 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2319 public void PCAMenuItem_actionPerformed()
2321 // are the sequences aligned?
2322 if (!viewport.alignment.isAligned(false))
2325 int Width = viewport.getAlignment().getWidth();
2327 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2329 current = viewport.getAlignment().getSequenceAt(i);
2331 if (current.getLength() < Width)
2333 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2336 alignPanel.paintAlignment(true);
2339 if ((viewport.getSelectionGroup() != null
2340 && viewport.getSelectionGroup().getSize() < 4 && viewport
2341 .getSelectionGroup().getSize() > 0)
2342 || viewport.getAlignment().getHeight() < 4)
2349 new PCAPanel(viewport);
2350 } catch (java.lang.OutOfMemoryError ex)
2356 public void averageDistanceTreeMenuItem_actionPerformed()
2358 NewTreePanel("AV", "PID", "Average distance tree using PID");
2361 public void neighbourTreeMenuItem_actionPerformed()
2363 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2366 protected void njTreeBlosumMenuItem_actionPerformed()
2368 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2371 protected void avTreeBlosumMenuItem_actionPerformed()
2373 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2376 void NewTreePanel(String type, String pwType, String title)
2378 // are the sequences aligned?
2379 if (!viewport.alignment.isAligned(false))
2382 int Width = viewport.getAlignment().getWidth();
2384 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2386 current = viewport.getAlignment().getSequenceAt(i);
2388 if (current.getLength() < Width)
2390 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2393 alignPanel.paintAlignment(true);
2397 if ((viewport.getSelectionGroup() != null && viewport
2398 .getSelectionGroup().getSize() > 1)
2399 || (viewport.getSelectionGroup() == null && viewport.alignment
2402 final TreePanel tp = new TreePanel(viewport, type, pwType);
2404 addTreeMenuItem(tp, title);
2406 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2410 void loadTree_actionPerformed()
2412 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2413 cap.setText("Paste your Newick tree file here.");
2414 cap.setTreeImport();
2415 Frame frame = new Frame();
2417 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2420 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2422 TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
2423 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2424 addTreeMenuItem(tp, treeFile);
2428 * sort the alignment using the given treePanel
2431 * tree used to sort view
2433 * string used for undo event name
2435 public void sortByTree(TreePanel treePanel, String title)
2437 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2439 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2440 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2441 // HistoryItem.SORT));
2442 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2443 viewport.alignment));
2444 alignPanel.paintAlignment(true);
2448 * Do any automatic reordering of the alignment and add the necessary bits to
2449 * the menu structure for the new tree
2454 protected void addTreeMenuItem(final TreePanel treePanel,
2457 final MenuItem item = new MenuItem(title);
2458 sortByTreeMenu.add(item);
2459 item.addActionListener(new java.awt.event.ActionListener()
2461 public void actionPerformed(ActionEvent evt)
2463 sortByTree(treePanel, title); // treePanel.getTitle());
2467 treePanel.addWindowListener(new WindowAdapter()
2469 public void windowOpened(WindowEvent e)
2471 if (viewport.sortByTree)
2473 sortByTree(treePanel, title);
2475 super.windowOpened(e);
2478 public void windowClosing(WindowEvent e)
2480 sortByTreeMenu.remove(item);
2485 protected void documentation_actionPerformed()
2487 showURL("http://www.jalview.org/help.html", "HELP");
2490 protected void about_actionPerformed()
2493 class AboutPanel extends Canvas
2499 public AboutPanel(String version, String builddate)
2501 this.version = version;
2502 this.builddate = builddate;
2505 public void paint(Graphics g)
2507 g.setColor(Color.white);
2508 g.fillRect(0, 0, getSize().width, getSize().height);
2509 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2510 FontMetrics fm = g.getFontMetrics();
2511 int fh = fm.getHeight();
2513 g.setColor(Color.black);
2514 // TODO: update this text for each release or centrally store it for
2515 // lite and application
2516 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2517 g.drawString("JalviewLite - Release " + version, x, y += fh);
2518 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2519 g.drawString("Build date: " + builddate, x, y += fh);
2520 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2522 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
2524 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2526 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2529 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2531 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2533 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2536 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2538 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2543 Frame frame = new Frame();
2544 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2546 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2550 public void showURL(String url, String target)
2552 if (viewport.applet == null)
2554 System.out.println("Not running as applet - no browser available.");
2560 if (url.indexOf(":") == -1)
2562 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2564 if (url.indexOf("/") == 0)
2566 String codebase = viewport.applet.getCodeBase().toString();
2567 url = codebase.substring(0, codebase.length()
2568 - viewport.applet.getCodeBase().getFile().length())
2573 url = viewport.applet.getCodeBase() + url;
2575 System.out.println("Show url (prepended codebase): " + url);
2579 System.out.println("Show url: " + url);
2581 if (url.indexOf("javascript:") == 0)
2583 // no target for the javascript context
2584 viewport.applet.getAppletContext().showDocument(
2585 new java.net.URL(url));
2589 viewport.applet.getAppletContext().showDocument(
2590 new java.net.URL(url), target);
2592 } catch (Exception ex)
2594 ex.printStackTrace();
2599 // ////////////////////////////////////////////////////////////////////////////////
2600 // JBuilder Graphics here
2602 MenuBar alignFrameMenuBar = new MenuBar();
2604 Menu fileMenu = new Menu("File");
2606 MenuItem loadApplication = new MenuItem("View in Full Application");
2608 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2610 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2612 MenuItem outputFeatures = new MenuItem("Export Features ...");
2614 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2616 MenuItem closeMenuItem = new MenuItem("Close");
2618 Menu editMenu = new Menu("Edit");
2620 Menu viewMenu = new Menu("View");
2622 Menu colourMenu = new Menu("Colour");
2624 Menu calculateMenu = new Menu("Calculate");
2626 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2628 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2630 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2632 MenuItem remove2LeftMenuItem = new MenuItem();
2634 MenuItem remove2RightMenuItem = new MenuItem();
2636 MenuItem removeGappedColumnMenuItem = new MenuItem();
2638 MenuItem removeAllGapsMenuItem = new MenuItem();
2640 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2642 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2644 MenuItem sortPairwiseMenuItem = new MenuItem();
2646 MenuItem sortIDMenuItem = new MenuItem();
2648 MenuItem sortLengthMenuItem = new MenuItem();
2650 MenuItem sortGroupMenuItem = new MenuItem();
2652 MenuItem removeRedundancyMenuItem = new MenuItem();
2654 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2656 MenuItem PCAMenuItem = new MenuItem();
2658 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2660 MenuItem neighbourTreeMenuItem = new MenuItem();
2662 BorderLayout borderLayout1 = new BorderLayout();
2664 public Label statusBar = new Label();
2666 Menu outputTextboxMenu = new Menu();
2668 MenuItem clustalColour = new MenuItem();
2670 MenuItem zappoColour = new MenuItem();
2672 MenuItem taylorColour = new MenuItem();
2674 MenuItem hydrophobicityColour = new MenuItem();
2676 MenuItem helixColour = new MenuItem();
2678 MenuItem strandColour = new MenuItem();
2680 MenuItem turnColour = new MenuItem();
2682 MenuItem buriedColour = new MenuItem();
2684 MenuItem userDefinedColour = new MenuItem();
2686 MenuItem PIDColour = new MenuItem();
2688 MenuItem BLOSUM62Colour = new MenuItem();
2690 MenuItem njTreeBlosumMenuItem = new MenuItem();
2692 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2694 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2696 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2698 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2700 MenuItem alProperties = new MenuItem("Alignment Properties...");
2702 MenuItem overviewMenuItem = new MenuItem();
2704 MenuItem undoMenuItem = new MenuItem();
2706 MenuItem redoMenuItem = new MenuItem();
2708 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2710 MenuItem noColourmenuItem = new MenuItem();
2712 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2714 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2716 MenuItem findMenuItem = new MenuItem();
2718 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2720 MenuItem nucleotideColour = new MenuItem();
2722 MenuItem deleteGroups = new MenuItem();
2724 MenuItem grpsFromSelection = new MenuItem();
2726 MenuItem delete = new MenuItem();
2728 MenuItem copy = new MenuItem();
2730 MenuItem cut = new MenuItem();
2732 Menu pasteMenu = new Menu();
2734 MenuItem pasteNew = new MenuItem();
2736 MenuItem pasteThis = new MenuItem();
2738 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2740 MenuItem font = new MenuItem();
2742 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2744 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2746 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2748 MenuItem modifyPID = new MenuItem();
2750 MenuItem modifyConservation = new MenuItem();
2752 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2753 "Autocalculate Consensus", true);
2755 Menu sortByTreeMenu = new Menu();
2757 Menu sort = new Menu();
2759 Menu calculate = new Menu();
2761 MenuItem inputText = new MenuItem();
2763 Menu helpMenu = new Menu();
2765 MenuItem documentation = new MenuItem();
2767 MenuItem about = new MenuItem();
2769 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2771 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2773 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2775 private void jbInit() throws Exception
2778 setMenuBar(alignFrameMenuBar);
2782 // dynamically fill save as menu with available formats
2783 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2786 item = new MenuItem(
2787 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2789 item.addActionListener(new java.awt.event.ActionListener()
2791 public void actionPerformed(ActionEvent e)
2793 outputText_actionPerformed(e);
2797 outputTextboxMenu.add(item);
2799 closeMenuItem.addActionListener(this);
2800 loadApplication.addActionListener(this);
2802 loadTree.addActionListener(this);
2803 loadAnnotations.addActionListener(this);
2804 outputFeatures.addActionListener(this);
2805 outputAnnotations.addActionListener(this);
2806 selectAllSequenceMenuItem.addActionListener(this);
2807 deselectAllSequenceMenuItem.addActionListener(this);
2808 invertSequenceMenuItem.addActionListener(this);
2809 remove2LeftMenuItem.setLabel("Remove Left");
2810 remove2LeftMenuItem.addActionListener(this);
2811 remove2RightMenuItem.setLabel("Remove Right");
2812 remove2RightMenuItem.addActionListener(this);
2813 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2814 removeGappedColumnMenuItem.addActionListener(this);
2815 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2816 removeAllGapsMenuItem.addActionListener(this);
2817 viewBoxesMenuItem.setLabel("Boxes");
2818 viewBoxesMenuItem.setState(true);
2819 viewBoxesMenuItem.addItemListener(this);
2820 viewTextMenuItem.setLabel("Text");
2821 viewTextMenuItem.setState(true);
2822 viewTextMenuItem.addItemListener(this);
2823 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2824 sortPairwiseMenuItem.addActionListener(this);
2825 sortIDMenuItem.setLabel("by ID");
2826 sortIDMenuItem.addActionListener(this);
2827 sortLengthMenuItem.setLabel("by Length");
2828 sortLengthMenuItem.addActionListener(this);
2829 sortGroupMenuItem.setLabel("by Group");
2830 sortGroupMenuItem.addActionListener(this);
2831 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2832 removeRedundancyMenuItem.addActionListener(this);
2833 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2834 pairwiseAlignmentMenuItem.addActionListener(this);
2835 PCAMenuItem.setLabel("Principal Component Analysis");
2836 PCAMenuItem.addActionListener(this);
2837 averageDistanceTreeMenuItem
2838 .setLabel("Average Distance Using % Identity");
2839 averageDistanceTreeMenuItem.addActionListener(this);
2840 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2841 neighbourTreeMenuItem.addActionListener(this);
2842 statusBar.setBackground(Color.white);
2843 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2844 statusBar.setText("Status bar");
2845 outputTextboxMenu.setLabel("Output to Textbox");
2846 clustalColour.setLabel("Clustalx");
2848 clustalColour.addActionListener(this);
2849 zappoColour.setLabel("Zappo");
2850 zappoColour.addActionListener(this);
2851 taylorColour.setLabel("Taylor");
2852 taylorColour.addActionListener(this);
2853 hydrophobicityColour.setLabel("Hydrophobicity");
2854 hydrophobicityColour.addActionListener(this);
2855 helixColour.setLabel("Helix Propensity");
2856 helixColour.addActionListener(this);
2857 strandColour.setLabel("Strand Propensity");
2858 strandColour.addActionListener(this);
2859 turnColour.setLabel("Turn Propensity");
2860 turnColour.addActionListener(this);
2861 buriedColour.setLabel("Buried Index");
2862 buriedColour.addActionListener(this);
2863 userDefinedColour.setLabel("User Defined...");
2864 userDefinedColour.addActionListener(this);
2865 PIDColour.setLabel("Percentage Identity");
2866 PIDColour.addActionListener(this);
2867 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2868 BLOSUM62Colour.addActionListener(this);
2869 avDistanceTreeBlosumMenuItem
2870 .setLabel("Average Distance Using BLOSUM62");
2871 avDistanceTreeBlosumMenuItem.addActionListener(this);
2872 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2873 njTreeBlosumMenuItem.addActionListener(this);
2874 annotationPanelMenuItem.setLabel("Show Annotations");
2875 annotationPanelMenuItem.addItemListener(this);
2876 colourTextMenuItem.setLabel("Colour Text");
2877 colourTextMenuItem.addItemListener(this);
2878 displayNonconservedMenuItem.setLabel("Show nonconserved");
2879 displayNonconservedMenuItem.addItemListener(this);
2880 alProperties.addActionListener(this);
2881 overviewMenuItem.setLabel("Overview Window");
2882 overviewMenuItem.addActionListener(this);
2883 undoMenuItem.setEnabled(false);
2884 undoMenuItem.setLabel("Undo");
2885 undoMenuItem.addActionListener(this);
2886 redoMenuItem.setEnabled(false);
2887 redoMenuItem.setLabel("Redo");
2888 redoMenuItem.addActionListener(this);
2889 conservationMenuItem.setLabel("by Conservation");
2890 conservationMenuItem.addItemListener(this);
2891 noColourmenuItem.setLabel("None");
2892 noColourmenuItem.addActionListener(this);
2893 wrapMenuItem.setLabel("Wrap");
2894 wrapMenuItem.addItemListener(this);
2895 renderGapsMenuItem.setLabel("Show Gaps");
2896 renderGapsMenuItem.setState(true);
2897 renderGapsMenuItem.addItemListener(this);
2898 findMenuItem.setLabel("Find...");
2899 findMenuItem.addActionListener(this);
2900 abovePIDThreshold.setLabel("Above Identity Threshold");
2901 abovePIDThreshold.addItemListener(this);
2902 nucleotideColour.setLabel("Nucleotide");
2903 nucleotideColour.addActionListener(this);
2904 deleteGroups.setLabel("Undefine Groups");
2905 deleteGroups.addActionListener(this);
2906 grpsFromSelection.setLabel("Make Groups for selection");
2907 grpsFromSelection.addActionListener(this);
2908 copy.setLabel("Copy");
2909 copy.addActionListener(this);
2910 cut.setLabel("Cut");
2911 cut.addActionListener(this);
2912 delete.setLabel("Delete");
2913 delete.addActionListener(this);
2914 pasteMenu.setLabel("Paste");
2915 pasteNew.setLabel("To New Alignment");
2916 pasteNew.addActionListener(this);
2917 pasteThis.setLabel("Add To This Alignment");
2918 pasteThis.addActionListener(this);
2919 applyToAllGroups.setLabel("Apply Colour To All Groups");
2920 applyToAllGroups.setState(true);
2921 applyToAllGroups.addItemListener(this);
2922 font.setLabel("Font...");
2923 font.addActionListener(this);
2924 scaleAbove.setLabel("Scale Above");
2925 scaleAbove.setState(true);
2926 scaleAbove.setEnabled(false);
2927 scaleAbove.addItemListener(this);
2928 scaleLeft.setEnabled(false);
2929 scaleLeft.setState(true);
2930 scaleLeft.setLabel("Scale Left");
2931 scaleLeft.addItemListener(this);
2932 scaleRight.setEnabled(false);
2933 scaleRight.setState(true);
2934 scaleRight.setLabel("Scale Right");
2935 scaleRight.addItemListener(this);
2936 modifyPID.setLabel("Modify Identity Threshold...");
2937 modifyPID.addActionListener(this);
2938 modifyConservation.setLabel("Modify Conservation Threshold...");
2939 modifyConservation.addActionListener(this);
2940 sortByTreeMenu.setLabel("By Tree Order");
2941 sort.setLabel("Sort");
2942 calculate.setLabel("Calculate Tree");
2943 autoCalculate.addItemListener(this);
2944 inputText.setLabel("Input from textbox");
2945 inputText.addActionListener(this);
2946 centreColumnLabelFlag.setLabel("Centre column labels");
2947 centreColumnLabelFlag.addItemListener(this);
2948 followMouseOverFlag.setLabel("Automatic Scrolling");
2949 followMouseOverFlag.addItemListener(this);
2950 helpMenu.setLabel("Help");
2951 documentation.setLabel("Documentation");
2952 documentation.addActionListener(this);
2954 about.setLabel("About...");
2955 about.addActionListener(this);
2956 seqLimits.setState(true);
2957 seqLimits.setLabel("Show Sequence Limits");
2958 seqLimits.addItemListener(this);
2959 featureSettings.setLabel("Feature Settings...");
2960 featureSettings.addActionListener(this);
2961 sequenceFeatures.setLabel("Sequence Features");
2962 sequenceFeatures.addItemListener(this);
2963 sequenceFeatures.setState(false);
2964 annotationColour.setLabel("by Annotation...");
2965 annotationColour.addActionListener(this);
2966 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2967 invertColSel.setLabel("Invert Column Selection");
2968 menu1.setLabel("Show");
2969 showColumns.setLabel("All Columns ");
2970 showSeqs.setLabel("All Sequences");
2971 menu2.setLabel("Hide");
2972 hideColumns.setLabel("Selected Columns");
2973 hideSequences.setLabel("Selected Sequences");
2974 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
2975 hideAllSelection.setLabel("Selected Region");
2976 showAllHidden.setLabel("All Sequences and Columns");
2977 invertColSel.addActionListener(this);
2978 showColumns.addActionListener(this);
2979 showSeqs.addActionListener(this);
2980 hideColumns.addActionListener(this);
2981 hideSequences.addActionListener(this);
2982 hideAllButSelection.addActionListener(this);
2983 hideAllSelection.addActionListener(this);
2984 showAllHidden.addActionListener(this);
2985 formatMenu.setLabel("Format");
2986 selectMenu.setLabel("Select");
2987 newView.setLabel("New View");
2988 newView.addActionListener(this);
2989 alignFrameMenuBar.add(fileMenu);
2990 alignFrameMenuBar.add(editMenu);
2991 alignFrameMenuBar.add(selectMenu);
2992 alignFrameMenuBar.add(viewMenu);
2993 alignFrameMenuBar.add(formatMenu);
2994 alignFrameMenuBar.add(colourMenu);
2995 alignFrameMenuBar.add(calculateMenu);
2996 alignFrameMenuBar.add(helpMenu);
2998 fileMenu.add(inputText);
2999 fileMenu.add(loadTree);
3000 fileMenu.add(loadAnnotations);
3002 fileMenu.addSeparator();
3003 fileMenu.add(outputTextboxMenu);
3004 fileMenu.add(outputFeatures);
3005 fileMenu.add(outputAnnotations);
3007 if (jalviewServletURL != null)
3009 fileMenu.add(loadApplication);
3012 fileMenu.addSeparator();
3013 fileMenu.add(closeMenuItem);
3015 editMenu.add(undoMenuItem);
3016 editMenu.add(redoMenuItem);
3019 editMenu.add(pasteMenu);
3020 editMenu.add(delete);
3021 editMenu.addSeparator();
3022 editMenu.add(remove2LeftMenuItem);
3023 editMenu.add(remove2RightMenuItem);
3024 editMenu.add(removeGappedColumnMenuItem);
3025 editMenu.add(removeAllGapsMenuItem);
3026 editMenu.add(removeRedundancyMenuItem);
3027 viewMenu.add(newView);
3028 viewMenu.addSeparator();
3029 viewMenu.add(menu1);
3030 viewMenu.add(menu2);
3031 viewMenu.addSeparator();
3032 viewMenu.add(followMouseOverFlag);
3033 viewMenu.add(annotationPanelMenuItem);
3034 viewMenu.addSeparator();
3035 viewMenu.add(sequenceFeatures);
3036 viewMenu.add(featureSettings);
3037 viewMenu.addSeparator();
3038 viewMenu.add(alProperties);
3039 viewMenu.addSeparator();
3040 viewMenu.add(overviewMenuItem);
3041 colourMenu.add(applyToAllGroups);
3042 colourMenu.addSeparator();
3043 colourMenu.add(noColourmenuItem);
3044 colourMenu.add(clustalColour);
3045 colourMenu.add(BLOSUM62Colour);
3046 colourMenu.add(PIDColour);
3047 colourMenu.add(zappoColour);
3048 colourMenu.add(taylorColour);
3049 colourMenu.add(hydrophobicityColour);
3050 colourMenu.add(helixColour);
3051 colourMenu.add(strandColour);
3052 colourMenu.add(turnColour);
3053 colourMenu.add(buriedColour);
3054 colourMenu.add(nucleotideColour);
3055 colourMenu.add(userDefinedColour);
3056 colourMenu.addSeparator();
3057 colourMenu.add(conservationMenuItem);
3058 colourMenu.add(modifyConservation);
3059 colourMenu.add(abovePIDThreshold);
3060 colourMenu.add(modifyPID);
3061 colourMenu.add(annotationColour);
3062 calculateMenu.add(sort);
3063 calculateMenu.add(calculate);
3064 calculateMenu.addSeparator();
3065 calculateMenu.add(pairwiseAlignmentMenuItem);
3066 calculateMenu.add(PCAMenuItem);
3067 calculateMenu.add(autoCalculate);
3068 this.add(statusBar, BorderLayout.SOUTH);
3069 pasteMenu.add(pasteNew);
3070 pasteMenu.add(pasteThis);
3071 sort.add(sortIDMenuItem);
3072 sort.add(sortLengthMenuItem);
3073 sort.add(sortByTreeMenu);
3074 sort.add(sortGroupMenuItem);
3075 sort.add(sortPairwiseMenuItem);
3076 calculate.add(averageDistanceTreeMenuItem);
3077 calculate.add(neighbourTreeMenuItem);
3078 calculate.add(avDistanceTreeBlosumMenuItem);
3079 calculate.add(njTreeBlosumMenuItem);
3080 helpMenu.add(documentation);
3081 helpMenu.add(about);
3082 menu1.add(showColumns);
3083 menu1.add(showSeqs);
3084 menu1.add(showAllHidden);
3085 menu2.add(hideColumns);
3086 menu2.add(hideSequences);
3087 menu2.add(hideAllSelection);
3088 menu2.add(hideAllButSelection);
3089 formatMenu.add(font);
3090 formatMenu.add(seqLimits);
3091 formatMenu.add(wrapMenuItem);
3092 formatMenu.add(scaleAbove);
3093 formatMenu.add(scaleLeft);
3094 formatMenu.add(scaleRight);
3095 formatMenu.add(viewBoxesMenuItem);
3096 formatMenu.add(viewTextMenuItem);
3097 formatMenu.add(colourTextMenuItem);
3098 formatMenu.add(displayNonconservedMenuItem);
3099 formatMenu.add(renderGapsMenuItem);
3100 formatMenu.add(centreColumnLabelFlag);
3101 selectMenu.add(findMenuItem);
3102 selectMenu.addSeparator();
3103 selectMenu.add(selectAllSequenceMenuItem);
3104 selectMenu.add(deselectAllSequenceMenuItem);
3105 selectMenu.add(invertSequenceMenuItem);
3106 selectMenu.add(invertColSel);
3107 selectMenu.add(grpsFromSelection);
3108 selectMenu.add(deleteGroups);
3112 MenuItem featureSettings = new MenuItem();
3114 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3116 MenuItem annotationColour = new MenuItem();
3118 MenuItem invertColSel = new MenuItem();
3120 Menu menu1 = new Menu();
3122 MenuItem showColumns = new MenuItem();
3124 MenuItem showSeqs = new MenuItem();
3126 Menu menu2 = new Menu();
3128 MenuItem hideColumns = new MenuItem();
3130 MenuItem hideSequences = new MenuItem();
3132 MenuItem hideAllButSelection = new MenuItem();
3134 MenuItem hideAllSelection = new MenuItem();
3136 MenuItem showAllHidden = new MenuItem();
3138 Menu formatMenu = new Menu();
3140 Menu selectMenu = new Menu();
3142 MenuItem newView = new MenuItem();
3145 * Attach the alignFrame panels after embedding menus, if necessary. This used
3146 * to be called setEmbedded, but is now creates the dropdown menus in a
3147 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3149 * @param reallyEmbedded
3150 * true to attach the view to the applet area on the page rather than
3153 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3158 // Explicly build the embedded menu panel for the on-page applet
3160 // view cannot be closed if its actually on the page
3161 fileMenu.remove(closeMenuItem);
3162 fileMenu.remove(3); // Remove Seperator
3163 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3164 Font.PLAIN, 10, false); // use our own fonts.
3165 // and actually add the components to the applet area
3166 viewport.applet.setLayout(new BorderLayout());
3167 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3168 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3169 alignPanel.setSize(viewport.applet.getSize().width,
3170 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3171 - statusBar.HEIGHT);
3172 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3173 viewport.applet.validate();
3178 // test and embed menu bar if necessary.
3180 if (embedMenuIfNeeded(alignPanel))
3182 // adjust for status bar height too
3183 alignPanel.setSize(getSize().width, getSize().height
3184 - statusBar.HEIGHT);
3186 add(statusBar, BorderLayout.SOUTH);
3187 add(alignPanel, BorderLayout.CENTER);
3188 // and register with the applet so it can pass external API calls to us
3189 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3195 * create a new binding between structures in an existing jmol viewer instance
3196 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3197 * this does not open a new Jmol window, or modify the display of the
3198 * structures in the original jmol window. Note
3201 * JmolViewer instance
3202 * @param sequenceIds
3203 * - sequence Ids to search for associations This method doesn't
3204 * work. See http://issues.jalview.org/browse/JAL-621
3206 * public SequenceStructureBinding addStructureViewInstance(Object
3207 * jmolviewer, String[] sequenceIds) { org.jmol.api.JmolViewer
3208 * viewer=null; try { viewer = (org.jmol.api.JmolViewer) jmolviewer;
3209 * } catch (ClassCastException ex) {
3210 * System.err.println("Unsupported viewer object :"
3211 * +jmolviewer.getClass()); } if (viewer==null) {
3212 * System.err.println("Can't use this object as a structure viewer:"
3213 * +jmolviewer.getClass()); return null; } SequenceI[] seqs=null; if
3214 * (sequenceIds==null || sequenceIds.length==0) { seqs =
3215 * viewport.getAlignment().getSequencesArray(); } else { Vector
3216 * sqi=new Vector(); AlignmentI al = viewport.getAlignment(); for
3217 * (int sid=0;sid<sequenceIds.length;sid++) { SequenceI sq =
3218 * al.findName(sequenceIds[sid]); if (sq!=null) { sqi.addElement(sq);
3219 * } } if (sqi.size()>0) { seqs = new SequenceI[sqi.size()]; for (int
3220 * sid=0,sSize=sqi.size();sid<sSize;sid++) { seqs[sid] = (SequenceI)
3221 * sqi.elementAt(sid); } } else { return null; } } ExtJmol jmv=null;
3222 * // TODO: search for a jmv that involves viewer if (jmv==null){ //
3223 * create a new viewer/jalview binding. jmv = new ExtJmol(viewer,
3224 * alignPanel, seqs); } return jmv;
3228 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3231 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3232 boolean needtoadd = false;
3233 if (toaddpdb != null)
3235 Vector pdbe = toaddpdb.getPDBId();
3236 PDBEntry pdbentry = null;
3237 if (pdbe != null && pdbe.size() > 0)
3239 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3241 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3242 if (!pdbentry.getId().equals(pdbEntryString)
3243 && !pdbentry.getFile().equals(pdbFile))
3253 if (pdbentry == null)
3255 pdbentry = new PDBEntry();
3256 pdbentry.setId(pdbEntryString);
3257 pdbentry.setFile(pdbFile);
3258 needtoadd = true; // add this new entry to sequence.
3260 // resolve data source
3261 // TODO: this code should be a refactored to an io package
3262 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3263 if (protocol == null)
3269 // make a note of the access mode and add
3270 if (pdbentry.getProperty() == null)
3272 pdbentry.setProperty(new Hashtable());
3274 pdbentry.getProperty().put("protocol", protocol);
3275 toaddpdb.addPDBId(pdbentry);
3281 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3285 Vector sequences = new Vector();
3286 for (int i = 0; i < seqs.length; i++)
3288 if (seqs[i] != null)
3290 sequences.addElement(new Object[]
3291 { seqs[i], (chains != null) ? chains[i] : null });
3294 seqs = new SequenceI[sequences.size()];
3295 chains = new String[sequences.size()];
3296 for (int i = 0, isize = sequences.size(); i < isize; i++)
3298 Object[] oj = (Object[]) sequences.elementAt(i);
3300 seqs[i] = (SequenceI) oj[0];
3301 chains[i] = (String) oj[1];
3309 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3310 SequenceI[] seqs, String[] chains, String protocol)
3312 // Scrub any null sequences from the array
3313 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3314 seqs = (SequenceI[]) sqch[0];
3315 chains = (String[]) sqch[1];
3316 if (seqs == null || seqs.length == 0)
3319 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3321 if (protocol == null || protocol.trim().length() == 0
3322 || protocol.equals("null"))
3324 protocol = (String) pdb.getProperty().get("protocol");
3325 if (protocol == null)
3327 System.err.println("Couldn't work out protocol to open structure: "
3332 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3334 // can only do alignments with Jmol
3335 // find the last jmol window assigned to this alignment
3336 jalview.appletgui.AppletJmol ajm = null, tajm;
3337 Vector jmols = applet
3338 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3339 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3341 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3342 if (tajm.ap.alignFrame == this)
3351 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3352 // try and add the pdb structure
3357 // otherwise, create a new window
3358 if (applet.jmolAvailable)
3360 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3362 applet.lastFrameX += 40;
3363 applet.lastFrameY += 40;
3367 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3372 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3373 SequenceI[][] seqs, String[][] chains, String[] protocols)
3375 // TODO Auto-generated method stub
3376 System.err.println("Aligned Structure View: Not yet implemented.");