X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=0f0ba4ed1db61b93853f523ba33606953b3a014b;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=2e9b7ea111949424111aef1907c16204147bda9c;hpb=ccd341fe829d12e0ec54be126ad561a7ce1a2987;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java old mode 100755 new mode 100644 index 2e9b7ea..0f0ba4e --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -17,19 +17,77 @@ */ package jalview.appletgui; -import java.net.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.Conservation; import jalview.api.SequenceStructureBinding; import jalview.bin.JalviewLite; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AnnotationFile; +import jalview.io.AppletFormatAdapter; +import jalview.io.FeaturesFile; +import jalview.io.TCoffeeScoreFile; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.structure.StructureSelectionManager; + +import java.awt.BorderLayout; +import java.awt.Canvas; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.IOException; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.StringTokenizer; +import java.util.Vector; public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener @@ -47,7 +105,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded) { - if (applet != null) { jalviewServletURL = applet.getParameter("APPLICATION_URL"); @@ -68,12 +125,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.updateConsensus(alignPanel); annotationPanelMenuItem.setState(viewport.showAnnotation); - displayNonconservedMenuItem.setState(viewport.getShowunconserved()); + displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); followMouseOverFlag.setState(viewport.getFollowHighlight()); - showGroupConsensus.setState(viewport.showGroupConsensus); - showGroupConservation.setState(viewport.showGroupConservation); - showConsensusHistogram.setState(viewport.showConsensusHistogram); - showSequenceLogo.setState(viewport.showSequenceLogo); + showGroupConsensus.setState(viewport.isShowGroupConsensus()); + showGroupConservation.setState(viewport.isShowGroupConservation()); + showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); + showSequenceLogo.setState(viewport.isShowSequenceLogo()); + normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); seqLimits.setState(viewport.showJVSuffix); @@ -130,7 +188,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } - + if (viewport.getAlignment().isNucleotide()) + { + viewport.updateStrucConsensus(alignPanel); + if (viewport.getAlignment().hasRNAStructure()) + { + RNAHelixColour.setEnabled(true); + } + else + { + RNAHelixColour.setEnabled(false); + } + } + else + { + RNAHelixColour.setEnabled(false); + purinePyrimidineColour.setEnabled(false); + } // Some JVMS send keyevents to Top frame or lowest panel, // Havent worked out why yet. So add to both this frame and seqCanvas for // now @@ -139,8 +213,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.idPanel.idCanvas.addKeyListener(this); alignPanel.scalePanel.addKeyListener(this); alignPanel.annotationPanel.addKeyListener(this); + alignPanel.annotationPanelHolder.addKeyListener(this); + alignPanel.annotationSpaceFillerHolder.addKeyListener(this); + alignPanel.alabels.addKeyListener(this); createAlignFrameWindow(embedded, title); - alignPanel.validate(); + + validate(); + alignPanel.adjustAnnotationHeight(); alignPanel.paintAlignment(true); } @@ -155,22 +234,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } /** - * DOCUMENT ME! + * Load a features file onto the alignment * - * @param String - * DOCUMENT ME! + * @param file + * file URL, content, or other resolvable path + * @param type + * is protocol for accessing data referred to by file */ - public void parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, String type) + { + return parseFeaturesFile(file, type, true); + } + + /** + * Load a features file onto the alignment + * + * @param file + * file URL, content, or other resolvable path + * @param type + * is protocol for accessing data referred to by file + * @param autoenabledisplay + * when true, display features flag will be automatically enabled if + * features are loaded + * @return true if data parsed as a features file + */ + public boolean parseFeaturesFile(String file, String type, + boolean autoenabledisplay) { + // TODO: test if importing a features file onto an alignment which already + // has features with links overwrites the original links. + Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try { featuresFile = new jalview.io.FeaturesFile(file, type) - .parse(viewport.alignment, - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, - featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false)); + .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureColours, featureLinks, + true, viewport.applet.getDefaultParameter( + "relaxedidmatch", false)); } catch (Exception ex) { ex.printStackTrace(); @@ -182,17 +285,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; } - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); + if (autoenabledisplay) + { + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + } if (viewport.featureSettings != null) { viewport.featureSettings.refreshTable(); } alignPanel.paintAlignment(true); + statusBar.setText("Successfully added features to alignment."); } - + return featuresFile; } + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -206,6 +314,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { case 27: // escape key deselectAllSequenceMenuItem_actionPerformed(); + + alignPanel.alabels.cancelDrag(); break; case KeyEvent.VK_X: if (evt.isControlDown() || evt.isMetaDown()) @@ -465,8 +575,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. - if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel - .getSelected().size() > 0) + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -489,12 +600,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleSeqs) { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) { hide = true; viewport.hideAllSelectedSeqs(); } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) { viewport.showAllHiddenSeqs(); } @@ -502,12 +614,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleCols) { - if (viewport.colSel.getSelected().size() > 0) + if (viewport.getColumnSelection().getSelected().size() > 0) { viewport.hideSelectedColumns(); if (!toggleSeqs) { - viewport.selectionGroup = sg; + viewport.setSelectionGroup(sg); } } else if (!hide) @@ -517,14 +629,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } + @Override public void keyReleased(KeyEvent evt) { } + @Override public void keyTyped(KeyEvent evt) { } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == displayNonconservedMenuItem) @@ -591,7 +706,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (evt.getSource() == autoCalculate) { - viewport.autocalculateConsensus = autoCalculate.getState(); + viewport.autoCalculateConsensus = autoCalculate.getState(); + } + else if (evt.getSource() == sortByTree) + { + viewport.sortByTree = sortByTree.getState(); } else if (evt.getSource() == this.centreColumnLabelFlag) { @@ -613,6 +732,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { showSequenceLogo_actionPerformed(); } + else if (evt.getSource() == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } else if (evt.getSource() == showConsensusHistogram) { showConsensusHistogram_actionPerformed(); @@ -637,6 +760,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.alignPanel.annotationPanel.repaint(); } + @Override public void actionPerformed(ActionEvent evt) { Object source = evt.getSource(); @@ -822,6 +946,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { showSequenceLogo_actionPerformed(); } + else if (source == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } else if (source == showConsensusHistogram) { showConsensusHistogram_actionPerformed(); @@ -837,7 +965,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == alProperties) { StringBuffer contents = new jalview.io.AlignmentProperties( - viewport.alignment).formatAsString(); + viewport.getAlignment()).formatAsString(); CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); cap.setText(contents.toString()); Frame frame = new Frame(); @@ -856,9 +984,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == clustalColour) { abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), - viewport.alignment.getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), null)); } else if (source == zappoColour) { @@ -892,6 +1018,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new NucleotideColourScheme()); } + else if (source == purinePyrimidineColour) + { + changeColour(new PurinePyrimidineColourScheme()); + } + else if (source == RNAHelixColour) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } else if (source == modifyPID) { modifyPID_actionPerformed(); @@ -912,6 +1046,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new Blosum62ColourScheme()); } + else if (source == tcoffeeColour) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } else if (source == annotationColour) { new AnnotationColourChooser(viewport, alignPanel); @@ -994,7 +1132,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void loadAnnotations() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your features / annotations file here."); + cap.setText("Paste your features / annotations / T-coffee score file here."); cap.setAnnotationImport(); Frame frame = new Frame(); frame.add(cap); @@ -1005,10 +1143,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public String outputAnnotations(boolean displayTextbox) { String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), ((Alignment) viewport + .getAlignment()).alignmentProperties); if (displayTextbox) { @@ -1024,7 +1162,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, private Hashtable getDisplayedFeatureCols() { - if (alignPanel.getFeatureRenderer() != null) + if (alignPanel.getFeatureRenderer() != null + && viewport.featuresDisplayed != null) { FeatureRenderer fr = alignPanel.getFeatureRenderer(); Hashtable fcols = new Hashtable(); @@ -1044,26 +1183,40 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, String features; if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat( - viewport.alignment.getSequencesArray(), + features = new FeaturesFile().printJalviewFormat(viewport + .getAlignment().getSequencesArray(), getDisplayedFeatureCols()); } else { - features = new FeaturesFile().printGFFFormat( - viewport.alignment.getSequencesArray(), - getDisplayedFeatureCols()); + features = new FeaturesFile().printGFFFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } if (displayTextbox) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + boolean frimport = false; + if (features == null || features.equals("No Features Visible")) + { + features = "# No features visible - paste some and import them here."; + frimport = true; + } + + CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this); + if (frimport) + { + cap.setAnnotationImport(); + } Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500); - cap.setText(features); } + else + { + if (features == null) + features = ""; + } return features; } @@ -1162,19 +1315,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void closeMenuItem_actionPerformed() { PaintRefresher.RemoveComponent(alignPanel); - PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + if (alignPanel.seqPanel != null + && alignPanel.seqPanel.seqCanvas != null) + { + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + } + if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null) + { + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + } if (PaintRefresher.components.size() == 0 && viewport.applet == null) { System.exit(0); } - + else + { + } + viewport = null; + alignPanel = null; this.dispose(); } /** - * DOCUMENT ME! + * TODO: JAL-1104 */ void updateEditMenuBar() { @@ -1205,6 +1369,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } + /** + * TODO: JAL-1104 + */ public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1212,12 +1379,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.historyList.push(command); viewport.redoList.removeAllElements(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + viewport.updateHiddenColumns(); } } /** - * DOCUMENT ME! + * TODO: JAL-1104 DOCUMENT ME! * * @param e * DOCUMENT ME! @@ -1234,15 +1401,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, command.undoCommand(null); AlignViewport originalSource = getOriginatingSource(command); - - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + // JBPNote Test + if (originalSource != viewport) + { + System.err + .println("Warning: Viewport object mismatch whilst undoing"); + } + originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = + // viewport.getColumnSelection().getHiddenColumns() + // != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } /** - * DOCUMENT ME! + * TODO: JAL-1104 DOCUMENT ME! * * @param e * DOCUMENT ME! @@ -1259,11 +1433,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, command.doCommand(null); AlignViewport originalSource = getOriginatingSource(command); - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + // JBPNote Test + if (originalSource != viewport) + { + System.err + .println("Warning: Viewport object mismatch whilst re-doing"); + } + originalSource.updateHiddenColumns(); // sethasHiddenColumns(); = + // viewport.getColumnSelection().getHiddenColumns() + // != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } AlignViewport getOriginatingSource(CommandI command) @@ -1283,7 +1465,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (comps.elementAt(i) instanceof AlignmentPanel) { - if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) { originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; @@ -1298,7 +1480,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1314,65 +1496,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { return; } - - if (up) - { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); - } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - + viewport.getAlignment().moveSelectedSequencesByOne(sg, + up ? null : viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true); } synchronized void slideSequences(boolean right, int size) { - Vector sg = new Vector(); + List sg = new Vector(); if (viewport.cursorMode) { - sg.addElement(viewport.alignment - .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + sg.add(viewport.getAlignment().getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport.alignment - .getHeight()) + && viewport.getSelectionGroup().getSize() != viewport + .getAlignment().getHeight()) { sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1380,21 +1522,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return; } - Vector invertGroup = new Vector(); + Vector invertGroup = new Vector(); - for (int i = 0; i < viewport.alignment.getHeight(); i++) + for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { - if (!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); } - SequenceI[] seqs1 = new SequenceI[sg.size()]; - for (int i = 0; i < sg.size(); i++) - seqs1[i] = (SequenceI) sg.elementAt(i); + SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); - SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup + .size()]); for (int i = 0; i < invertGroup.size(); i++) - seqs2[i] = (SequenceI) invertGroup.elementAt(i); + seqs2[i] = invertGroup.elementAt(i); SlideSequencesCommand ssc; if (right) @@ -1460,14 +1601,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); + int index = viewport.getAlignment().findIndex(seq); orderedSeqs.put(index + "", seq); } int index = 0, startRes, endRes; char ch; - if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); @@ -1614,17 +1755,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { for (int i = 0; i < seqs.length; i++) { - viewport.alignment.addSequence(seqs[i]); + viewport.getAlignment().addSequence(seqs[i]); } // !newAlignment addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, - seqs, 0, viewport.alignment.getWidth(), viewport.alignment)); + seqs, 0, viewport.getAlignment().getWidth(), + viewport.getAlignment())); - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, - viewport.alignment.getSequences()); + viewport.setEndSeq(viewport.getAlignment().getHeight()); + viewport.getAlignment().getWidth(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } @@ -1652,7 +1794,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) + if (sg.getSize() == viewport.getAlignment().getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); @@ -1669,10 +1811,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, */ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + viewport.getAlignment())); viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -1716,6 +1858,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + /* * (non-Javadoc) * @@ -1729,6 +1872,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + protected void normSequenceLogo_actionPerformed() + { + showSequenceLogo.setState(true); + viewport.setShowSequenceLogo(true); + viewport.setNormaliseSequenceLogo(normSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + protected void applyAutoAnnotationSettings_actionPerformed() { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); @@ -1741,9 +1892,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( viewport.getSequenceSelection(), viewport.getAlignmentView(true).getSequenceStrings( - viewport.getGapCharacter()), - viewport.alignment.getGroups()); - viewport.alignment.deleteAllGroups(); + viewport.getGapCharacter()), viewport.getAlignment() + .getGroups()); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); // set view properties for each group @@ -1751,14 +1902,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // gps[g].setShowunconserved(viewport.getShowUnconserved()); gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); - viewport.alignment.addGroup(gps[g]); + viewport.getAlignment().addGroup(gps[g]); Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); col = col.brighter(); - for (Enumeration sq = gps[g].getSequences(null).elements(); sq - .hasMoreElements(); viewport.setSequenceColour( - (SequenceI) sq.nextElement(), col)) - ; + for (SequenceI sq : gps[g].getSequences(null)) + viewport.setSequenceColour(sq, col); } PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); @@ -1768,7 +1917,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void deleteGroups_actionPerformed() { - viewport.alignment.deleteAllGroups(); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); @@ -1782,7 +1931,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth() - 1); + sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); @@ -1846,11 +1995,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } TrimRegionCommand trimRegion; @@ -1858,32 +2007,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { trimRegion = new TrimRegionCommand("Remove Left", TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); } statusBar.setText("Removed " + trimRegion.getSize() + " columns."); addHistoryItem(trimRegion); - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) + for (SequenceGroup sg : viewport.getAlignment().getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } @@ -1894,23 +2039,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void removeGappedColumnMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } RemoveGapColCommand removeGapCols = new RemoveGapColCommand( - "Remove Gapped Columns", seqs, start, end, viewport.alignment); + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); addHistoryItem(removeGapCols); @@ -1919,7 +2065,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); @@ -1934,28 +2080,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void removeAllGapsMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.alignment)); + viewport.getAlignment())); viewport.setStartRes(seq.findIndex(startRes) - 1); @@ -1978,30 +2124,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public AlignFrame newView(String viewtitle) { AlignmentI newal; - if (viewport.hasHiddenRows) + if (viewport.hasHiddenRows()) { newal = new Alignment(viewport.getAlignment().getHiddenSequences() .getFullAlignment().getSequencesArray()); } else { - newal = new Alignment(viewport.alignment.getSequencesArray()); + newal = new Alignment(viewport.getAlignment().getSequencesArray()); } - if (viewport.alignment.getAlignmentAnnotation() != null) + if (viewport.getAlignment().getAlignmentAnnotation() != null) { - for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) + for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++) { - if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) + if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated) { - newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); + newal.addAnnotation(viewport.getAlignment() + .getAlignmentAnnotation()[i]); } } } AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); - newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId()); PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av.getSequenceSetId()); @@ -2146,11 +2293,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, overview.getPreferredSize().height + 50); frame.pack(); + final AlignmentPanel ap = alignPanel; frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { - alignPanel.setOverviewPanel(null); + if (ap != null) + { + ap.setOverviewPanel(null); + } }; }); @@ -2181,13 +2333,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.getConservationSelected()) { - Alignment al = (Alignment) viewport.alignment; + Alignment al = (Alignment) viewport.getAlignment(); Conservation c = new Conservation("All", ResidueProperties.propHash, 3, al.getSequences(), 0, al.getWidth() - 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); @@ -2200,82 +2352,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cs.setConservation(null); } - cs.setConsensus(viewport.hconsensus); + cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (cs == null) - { - sg.cs = null; - continue; - } - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), - sg.getWidth()); - } - else - { - try - { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); - } catch (Exception ex) - { - ex.printStackTrace(); - sg.cs = cs; - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), 0, - sg.getWidth())); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport.hiddenRepSequences), 0, - viewport.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - } - } - if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged( - alignPanel); + .getStructureSelectionManager(viewport.applet) + .sequenceColoursChanged(alignPanel); alignPanel.paintAlignment(true); } @@ -2283,7 +2372,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); @@ -2294,10 +2383,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } @@ -2333,7 +2422,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2341,7 +2430,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2350,7 +2440,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2359,7 +2449,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2384,7 +2474,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void PCAMenuItem_actionPerformed() { // are the sequences aligned? - if (!viewport.alignment.isAligned(false)) + if (!viewport.getAlignment().isAligned(false)) { SequenceI current; int Width = viewport.getAlignment().getWidth(); @@ -2441,7 +2531,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, void NewTreePanel(String type, String pwType, String title) { // are the sequences aligned? - if (!viewport.alignment.isAligned(false)) + if (!viewport.getAlignment().isAligned(false)) { SequenceI current; int Width = viewport.getAlignment().getWidth(); @@ -2461,8 +2551,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if ((viewport.getSelectionGroup() != null && viewport .getSelectionGroup().getSize() > 1) - || (viewport.getSelectionGroup() == null && viewport.alignment - .getHeight() > 1)) + || (viewport.getAlignment().getHeight() > 1)) { final TreePanel tp = new TreePanel(alignPanel, type, pwType); @@ -2505,7 +2594,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); addHistoryItem(new OrderCommand("Order by " + title, oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2523,6 +2612,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { sortByTree(treePanel, title); // treePanel.getTitle()); @@ -2531,6 +2621,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, treePanel.addWindowListener(new WindowAdapter() { + @Override public void windowOpened(WindowEvent e) { if (viewport.sortByTree) @@ -2540,31 +2631,35 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, super.windowOpened(e); } + @Override public void windowClosing(WindowEvent e) { sortByTreeMenu.remove(item); }; }); } + public boolean sortBy(AlignmentOrder alorder, String undoname) { - SequenceI[] oldOrder = viewport.getAlignment() - .getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); if (viewport.applet.debug) { - System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'"); + System.err.println("Sorting " + alorder.getOrder().size() + + " in alignment '" + getTitle() + "'"); } AlignmentSorter.sortBy(viewport.getAlignment(), alorder); - if (undoname!=null) + if (undoname != null) { - addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.getAlignment())); } alignPanel.paintAlignment(true); return true; } + protected void documentation_actionPerformed() { - showURL("http://www.jalview.org/help.html", "HELP"); + alignPanel.av.applet.openJalviewHelpUrl(); } protected void about_actionPerformed() @@ -2582,6 +2677,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.builddate = builddate; } + @Override public void paint(Graphics g) { g.setColor(Color.white); @@ -2599,9 +2695,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, g.drawString("Build date: " + builddate, x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g.drawString( - "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,", + "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,", x, y += fh * 1.5); - g.drawString("David Martin & Geoff Barton.", x + 50, y += fh); + g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8); g.drawString( "Development managed by The Barton Group, University of Dundee, Scotland, UK.", x, y += fh); @@ -2635,44 +2731,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - try - { - if (url.indexOf(":") == -1) - { - // TODO: verify (Bas Vroling bug) prepend codebase or server URL to - // form valid URL - if (url.indexOf("/") == 0) - { - String codebase = viewport.applet.getCodeBase().toString(); - url = codebase.substring(0, codebase.length() - - viewport.applet.getCodeBase().getFile().length()) - + url; - } - else - { - url = viewport.applet.getCodeBase() + url; - } - System.out.println("Show url (prepended codebase): " + url); - } - else - { - System.out.println("Show url: " + url); - } - if (url.indexOf("javascript:") == 0) - { - // no target for the javascript context - viewport.applet.getAppletContext().showDocument( - new java.net.URL(url)); - } - else - { - viewport.applet.getAppletContext().showDocument( - new java.net.URL(url), target); - } - } catch (Exception ex) - { - ex.printStackTrace(); - } + viewport.applet.showURL(url, target); } } @@ -2761,12 +2820,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem buriedColour = new MenuItem(); + MenuItem purinePyrimidineColour = new MenuItem(); + + MenuItem RNAHelixColour = new MenuItem(); + MenuItem userDefinedColour = new MenuItem(); MenuItem PIDColour = new MenuItem(); MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem tcoffeeColour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); @@ -2832,6 +2897,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem autoCalculate = new CheckboxMenuItem( "Autocalculate Consensus", true); + CheckboxMenuItem sortByTree = new CheckboxMenuItem( + "Sort Alignment With New Tree", true); + Menu sortByTreeMenu = new Menu(); Menu sort = new Menu(); @@ -2849,15 +2917,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem seqLimits = new CheckboxMenuItem(); CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); - + CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); - Menu autoAnnMenu=new Menu(); - CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem(); + + Menu autoAnnMenu = new Menu(); + + CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem(); + CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); + CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); + CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); + CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); + CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem(); + private void jbInit() throws Exception { @@ -2874,6 +2950,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -2946,12 +3023,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, turnColour.addActionListener(this); buriedColour.setLabel("Buried Index"); buriedColour.addActionListener(this); + purinePyrimidineColour.setLabel("Purine/Pyrimidine"); + purinePyrimidineColour.addActionListener(this); + RNAHelixColour.setLabel("by RNA Helices"); + RNAHelixColour.addActionListener(this); userDefinedColour.setLabel("User Defined..."); userDefinedColour.addActionListener(this); PIDColour.setLabel("Percentage Identity"); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(this); + tcoffeeColour.setLabel("T-Coffee Scores"); + tcoffeeColour.setEnabled(false); // it will enabled only if a score file is + // provided + tcoffeeColour.addActionListener(this); avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62"); avDistanceTreeBlosumMenuItem.addActionListener(this); @@ -3027,6 +3112,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); autoCalculate.addItemListener(this); + sortByTree.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); centreColumnLabelFlag.setLabel("Centre column labels"); @@ -3064,10 +3150,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, showGroupConservation.setLabel("Group Conservation"); showConsensusHistogram.setLabel("Show Consensus Histogram"); showSequenceLogo.setLabel("Show Consensus Logo"); + normSequenceLogo.setLabel("Normalise Consensus Logo"); applyAutoAnnotationSettings.setLabel("Apply to all groups"); applyAutoAnnotationSettings.setState(true); autoAnnMenu.setLabel("Autocalculated Annotation"); - + invertColSel.addActionListener(this); showColumns.addActionListener(this); showSeqs.addActionListener(this); @@ -3080,6 +3167,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, showGroupConservation.addItemListener(this); showConsensusHistogram.addItemListener(this); showSequenceLogo.addItemListener(this); + normSequenceLogo.addItemListener(this); + applyAutoAnnotationSettings.addItemListener(this); formatMenu.setLabel("Format"); selectMenu.setLabel("Select"); @@ -3133,6 +3222,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normSequenceLogo); autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); @@ -3158,6 +3248,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); + colourMenu.add(tcoffeeColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -3165,12 +3257,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); + colourMenu.add(RNAHelixColour); calculateMenu.add(sort); calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.add(autoCalculate); + calculateMenu.add(sortByTree); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); @@ -3279,14 +3373,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, final AlignFrame me = this; viewport.applet.addFocusListener(new FocusListener() { - + @Override public void focusLost(FocusEvent e) { - if (me.viewport.applet.currentAlignFrame==me) { - me.viewport.applet.currentAlignFrame = null; - }} - + if (me.viewport.applet.currentAlignFrame == me) + { + me.viewport.applet.currentAlignFrame = null; + } + } + @Override public void focusGained(FocusEvent e) { @@ -3379,12 +3475,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // TODO: search for a jmv that involves viewer if (jmv == null) { // create a new viewer/jalview binding. - jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs}); + jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] + { seqs }); } return jmv; } + /** + * bind a pdb file to a sequence in the current view + * + * @param sequenceId + * - sequenceId within the dataset. + * @param pdbEntryString + * - the short name for the PDB file + * @param pdbFile + * - pdb file - either a URL or a valid PDB file. + * @return true if binding was as success TODO: consider making an exception + * structure for indicating when PDB parsing or sequenceId location + * fails. + */ public boolean addPdbFile(String sequenceId, String pdbEntryString, String pdbFile) { @@ -3489,6 +3599,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return; } } + if (applet.useXtrnalSviewer) + { + // register the association(s) and quit, don't create any windows. + if (StructureSelectionManager.getStructureSelectionManager(applet) + .setMapping(seqs, chains, pdb.getFile(), protocol) == null) + { + System.err.println("Failed to map " + pdb.getFile() + " (" + + protocol + ") to any sequences"); + } + return; + } if (applet.isAlignPdbStructures() && applet.jmolAvailable) { // can only do alignments with Jmol @@ -3537,12 +3658,96 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } /** - * modify the current selection, providing the user has not made a selection already. - * @param sel - sequences from this alignment - * @param csel - columns to be selected on the alignment + * modify the current selection, providing the user has not made a selection + * already. + * + * @param sel + * - sequences from this alignment + * @param csel + * - columns to be selected on the alignment */ public void select(SequenceGroup sel, ColumnSelection csel) { alignPanel.seqPanel.selection(sel, csel, null); } + + public void scrollTo(int row, int column) + { + alignPanel.seqPanel.scrollTo(row, column); + } + + public void scrollToRow(int row) + { + alignPanel.seqPanel.scrollToRow(row); + } + + public void scrollToColumn(int column) + { + alignPanel.seqPanel.scrollToColumn(column); + } + + /** + * @return the alignments unique ID. + */ + public String getSequenceSetId() + { + return viewport.getSequenceSetId(); + } + + /** + * Load the (T-Coffee) score file from the specified url + * + * @param source + * File/URL/T-COFFEE score file contents + * @throws IOException + * @return true if alignment was annotated with data from source + */ + public boolean loadScoreFile(String source) throws IOException + { + + TCoffeeScoreFile file = new TCoffeeScoreFile(source, + AppletFormatAdapter.checkProtocol(source)); + if (!file.isValid()) + { + // TODO: raise dialog for gui + System.err.println("Problems parsing T-Coffee scores: " + + file.getWarningMessage()); + System.err.println("Origin was:\n" + source); + return false; + } + + /* + * check that the score matrix matches the alignment dimensions + */ + AlignmentI aln; + if ((aln = viewport.getAlignment()) != null + && (aln.getHeight() != file.getHeight() || aln.getWidth() != file + .getWidth())) + { + // TODO: raise a dialog box here rather than bomb out. + System.err + .println("The scores matrix does not match the alignment dimensions"); + + } + + // TODO add parameter to indicate if matching should be done + if (file.annotateAlignment(alignPanel.getAlignment(), false)) + { + alignPanel.fontChanged(); + tcoffeeColour.setEnabled(true); + // switch to this color + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + return true; + } + else + { + System.err.println("Problems resolving T-Coffee scores:"); + if (file.getWarningMessage() != null) + { + System.err.println(file.getWarningMessage()); + } + } + return false; + } + }