X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ab99e065edd79a2053a65ca1de46f243d9e88ccc;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=c5f37fd2faaa68e175cb4ee3d8a3a0f061036ef3;hpb=05c04b298565cdc668027027e13d0ac6f8bc8517;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java old mode 100755 new mode 100644 index c5f37fd..ab99e06 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,39 +1,94 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * 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 * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.io.*; -import java.net.*; -import java.util.*; - -import java.applet.Applet; -import java.awt.*; -import java.awt.event.*; - -import org.jmol.api.JmolViewer; - -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 @@ -51,7 +106,6 @@ 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"); @@ -72,7 +126,13 @@ 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.isShowGroupConsensus()); + showGroupConservation.setState(viewport.isShowGroupConservation()); + showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); + showSequenceLogo.setState(viewport.isShowSequenceLogo()); + normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); seqLimits.setState(viewport.showJVSuffix); @@ -129,7 +189,23 @@ 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 @@ -138,8 +214,13 @@ 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); } @@ -154,22 +235,46 @@ 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); + .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureColours, featureLinks, + true, viewport.applet.getDefaultParameter( + "relaxedidmatch", false)); } catch (Exception ex) { ex.printStackTrace(); @@ -181,17 +286,22 @@ 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 @@ -205,6 +315,8 @@ 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()) @@ -464,8 +576,9 @@ 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())) { @@ -488,12 +601,13 @@ 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(); } @@ -501,12 +615,12 @@ 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) @@ -516,14 +630,17 @@ 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) @@ -590,7 +707,11 @@ 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) { @@ -600,7 +721,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { mouseOverFlag_stateChanged(); } - + else if (evt.getSource() == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (evt.getSource() == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (evt.getSource() == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (evt.getSource() == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } alignPanel.paintAlignment(true); } @@ -617,6 +761,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.alignPanel.annotationPanel.repaint(); } + @Override public void actionPerformed(ActionEvent evt) { Object source = evt.getSource(); @@ -790,44 +935,38 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); } + else if (source == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (source == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (source == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (source == normSequenceLogo) + { + normSequenceLogo_actionPerformed(); + } + else if (source == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (source == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } else if (source == featureSettings) { new FeatureSettings(alignPanel); } else if (source == alProperties) { - StringBuffer contents = new StringBuffer(); - - float avg = 0; - int min = Integer.MAX_VALUE, max = 0; - for (int i = 0; i < viewport.alignment.getHeight(); i++) - { - int size = viewport.alignment.getSequenceAt(i).getEnd() - - viewport.alignment.getSequenceAt(i).getStart(); - avg += size; - if (size > max) - max = size; - if (size < min) - min = size; - } - avg = avg / (float) viewport.alignment.getHeight(); - - contents.append("\nSequences: " + viewport.alignment.getHeight()); - contents.append("\nMinimum Sequence Length: " + min); - contents.append("\nMaximum Sequence Length: " + max); - contents.append("\nAverage Length: " + (int) avg); - - if (((Alignment) viewport.alignment).alignmentProperties != null) - { - Hashtable props = ((Alignment) viewport.alignment).alignmentProperties; - Enumeration en = props.keys(); - while (en.hasMoreElements()) - { - String key = en.nextElement().toString(); - contents.append("\n" + key + "\t" + props.get(key)); - } - } - + StringBuffer contents = new jalview.io.AlignmentProperties( + viewport.getAlignment()).formatAsString(); CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); cap.setText(contents.toString()); Frame frame = new Frame(); @@ -846,9 +985,7 @@ 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) { @@ -882,6 +1019,14 @@ 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(); @@ -902,6 +1047,10 @@ 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); @@ -984,7 +1133,7 @@ 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); @@ -995,10 +1144,10 @@ 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) { @@ -1014,7 +1163,8 @@ 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(); @@ -1034,26 +1184,40 @@ 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; } @@ -1152,19 +1316,30 @@ 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() { @@ -1195,6 +1370,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } + /** + * TODO: JAL-1104 + */ public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1202,12 +1380,12 @@ 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! @@ -1224,15 +1402,22 @@ 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! @@ -1249,11 +1434,19 @@ 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) @@ -1273,7 +1466,7 @@ 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; @@ -1288,7 +1481,7 @@ 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; @@ -1304,65 +1497,25 @@ 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) @@ -1370,21 +1523,20 @@ 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) @@ -1450,14 +1602,14 @@ 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(); @@ -1604,17 +1756,18 @@ 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()); } @@ -1642,7 +1795,7 @@ 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); @@ -1659,10 +1812,10 @@ 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()); @@ -1671,6 +1824,66 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { this.setVisible(false); } + viewport.sendSelection(); + } + + /** + * group consensus toggled + * + */ + protected void showGroupConsensus_actionPerformed() + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /** + * group conservation toggled. + */ + protected void showGroupConservation_actionPerformed() + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed() + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showSequenceLogo_actionPerformed() + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + 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()); } protected void makeGrpsFromSelection_actionPerformed() @@ -1680,9 +1893,9 @@ 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 @@ -1690,24 +1903,22 @@ 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(); + alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } } protected void deleteGroups_actionPerformed() { - viewport.alignment.deleteAllGroups(); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); @@ -1721,10 +1932,11 @@ 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()); + viewport.sendSelection(); } public void deselectAllSequenceMenuItem_actionPerformed() @@ -1741,6 +1953,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void invertSequenceMenuItem_actionPerformed() @@ -1752,6 +1965,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void invertColSel_actionPerformed() @@ -1759,6 +1973,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.invertColumnSelection(); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } void trimAlignment(boolean trimLeft) @@ -1781,11 +1996,11 @@ 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; @@ -1793,32 +2008,28 @@ 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); } } @@ -1829,23 +2040,24 @@ 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); @@ -1854,7 +2066,7 @@ 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()); @@ -1869,28 +2081,28 @@ 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); @@ -1913,30 +2125,31 @@ 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()); @@ -2081,11 +2294,16 @@ 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); + } }; }); @@ -2116,13 +2334,13 @@ 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); @@ -2135,82 +2353,19 @@ 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); } @@ -2218,7 +2373,7 @@ 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"); @@ -2229,10 +2384,10 @@ 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(); } } @@ -2268,7 +2423,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2276,7 +2431,8 @@ 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); } @@ -2285,7 +2441,7 @@ 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); } @@ -2294,7 +2450,7 @@ 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); } @@ -2319,7 +2475,7 @@ 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(); @@ -2376,7 +2532,7 @@ 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(); @@ -2396,10 +2552,9 @@ 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(viewport, type, pwType); + final TreePanel tp = new TreePanel(alignPanel, type, pwType); addTreeMenuItem(tp, title); @@ -2419,7 +2574,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void loadTree(jalview.io.NewickFile tree, String treeFile) { - TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree); + TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } @@ -2440,7 +2595,7 @@ 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); } @@ -2458,6 +2613,7 @@ 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()); @@ -2466,6 +2622,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, treePanel.addWindowListener(new WindowAdapter() { + @Override public void windowOpened(WindowEvent e) { if (viewport.sortByTree) @@ -2475,6 +2632,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, super.windowOpened(e); } + @Override public void windowClosing(WindowEvent e) { sortByTreeMenu.remove(item); @@ -2482,9 +2640,27 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, }); } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + if (viewport.applet.debug) + { + System.err.println("Sorting " + alorder.getOrder().size() + + " in alignment '" + getTitle() + "'"); + } + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + 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() @@ -2502,6 +2678,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.builddate = builddate; } + @Override public void paint(Graphics g) { g.setColor(Color.white); @@ -2519,9 +2696,9 @@ 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: Andrew Waterhouse, Jim Procter, 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); @@ -2555,44 +2732,7 @@ 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); } } @@ -2681,12 +2821,18 @@ 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(); @@ -2752,6 +2898,9 @@ 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(); @@ -2772,6 +2921,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CheckboxMenuItem followMouseOverFlag = 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 { @@ -2788,6 +2951,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -2860,12 +3024,20 @@ 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); @@ -2941,6 +3113,7 @@ 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"); @@ -2974,6 +3147,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)"); hideAllSelection.setLabel("Selected Region"); showAllHidden.setLabel("All Sequences and Columns"); + showGroupConsensus.setLabel("Group Consensus"); + 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); @@ -2982,6 +3164,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hideAllButSelection.addActionListener(this); hideAllSelection.addActionListener(this); showAllHidden.addActionListener(this); + showGroupConsensus.addItemListener(this); + showGroupConservation.addItemListener(this); + showConsensusHistogram.addItemListener(this); + showSequenceLogo.addItemListener(this); + normSequenceLogo.addItemListener(this); + + applyAutoAnnotationSettings.addItemListener(this); formatMenu.setLabel("Format"); selectMenu.setLabel("Select"); newView.setLabel("New View"); @@ -3031,6 +3220,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewMenu.addSeparator(); viewMenu.add(followMouseOverFlag); viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); viewMenu.add(featureSettings); @@ -3052,6 +3249,8 @@ 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); @@ -3059,12 +3258,14 @@ 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); @@ -3170,6 +3371,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.applet.getSize().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); viewport.applet.add(alignPanel, BorderLayout.CENTER); + 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; + } + } + + @Override + public void focusGained(FocusEvent e) + { + me.viewport.applet.currentAlignFrame = me; + } + }); viewport.applet.validate(); } else @@ -3195,61 +3415,87 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * create a new binding between structures in an existing jmol viewer instance * and an alignpanel with sequences that have existing PDBFile entries. Note, * this does not open a new Jmol window, or modify the display of the - * structures in the original jmol window. Note + * structures in the original jmol window. Note This method doesn't work + * without an additional javascript library to exchange messages between the + * distinct applets. See http://issues.jalview.org/browse/JAL-621 * * @param viewer * JmolViewer instance * @param sequenceIds * - sequence Ids to search for associations - * This method doesn't work. See http://issues.jalview.org/browse/JAL-621 - * - public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds) + */ + public SequenceStructureBinding addStructureViewInstance( + Object jmolviewer, String[] sequenceIds) { - org.jmol.api.JmolViewer viewer=null; - try { + org.jmol.api.JmolViewer viewer = null; + try + { viewer = (org.jmol.api.JmolViewer) jmolviewer; - } - catch (ClassCastException ex) { - System.err.println("Unsupported viewer object :"+jmolviewer.getClass()); + } catch (ClassCastException ex) + { + System.err.println("Unsupported viewer object :" + + jmolviewer.getClass()); } - if (viewer==null) + if (viewer == null) { - System.err.println("Can't use this object as a structure viewer:"+jmolviewer.getClass()); + System.err.println("Can't use this object as a structure viewer:" + + jmolviewer.getClass()); return null; } - SequenceI[] seqs=null; - if (sequenceIds==null || sequenceIds.length==0) + SequenceI[] seqs = null; + if (sequenceIds == null || sequenceIds.length == 0) { seqs = viewport.getAlignment().getSequencesArray(); - } else { - Vector sqi=new Vector(); + } + else + { + Vector sqi = new Vector(); AlignmentI al = viewport.getAlignment(); - for (int sid=0;sid0) { + if (sqi.size() > 0) + { seqs = new SequenceI[sqi.size()]; - for (int sid=0,sSize=sqi.size();sid