X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=efb0f4c8ef979f6fcf1aecae963375d602c40551;hb=ef23315db576f5451de0fcb850f645c5db222b20;hp=759075a46a1b723a133a69bc0879f81f9a1f49b5;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 759075a..efb0f4c 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -17,23 +17,80 @@ */ package jalview.appletgui; -import java.net.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; +import jalview.analysis.AAFrequency; +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; -public class AlignFrame extends EmbmenuFrame implements ActionListener, - ItemListener, KeyListener +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.io.InputStreamReader; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; + +public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener { public AlignmentPanel alignPanel; @@ -44,11 +101,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, int DEFAULT_HEIGHT = 500; String jalviewServletURL; + - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, - String title, boolean embedded) + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded) { - if (applet != null) { jalviewServletURL = applet.getParameter("APPLICATION_URL"); @@ -69,12 +125,12 @@ 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()); seqLimits.setState(viewport.showJVSuffix); @@ -131,7 +187,20 @@ 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 @@ -161,20 +230,32 @@ 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) { + 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 + */ + public void parseFeaturesFile(String file, String type, boolean autoenabledisplay) + { Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try { featuresFile = new jalview.io.FeaturesFile(file, type) - .parse(viewport.alignment, + .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false)); } catch (Exception ex) @@ -188,8 +269,11 @@ 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(); @@ -473,7 +557,7 @@ 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 + if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection() .getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) @@ -497,12 +581,12 @@ 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(); } @@ -510,12 +594,12 @@ 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) @@ -599,7 +683,7 @@ 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) { @@ -669,6 +753,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { loadAnnotations(); } + else if( source == loadScores ) { + loadScores(); + } else if (source == outputAnnotations) { outputAnnotations(true); @@ -849,7 +936,7 @@ 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(); @@ -869,8 +956,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { abovePIDThreshold.setState(false); changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), - viewport.alignment.getWidth())); + viewport.getAlignment().getSequences(), + viewport.getAlignment().getWidth())); } else if (source == zappoColour) { @@ -904,6 +991,14 @@ 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(); @@ -924,6 +1019,9 @@ 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); @@ -1013,14 +1111,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300); } + + public void loadScores() { + //TODO + + } public String outputAnnotations(boolean displayTextbox) { String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport.getAlignment() .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + ((Alignment) viewport.getAlignment()).alignmentProperties); if (displayTextbox) { @@ -1057,13 +1160,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (format.equalsIgnoreCase("Jalview")) { features = new FeaturesFile().printJalviewFormat( - viewport.alignment.getSequencesArray(), + viewport.getAlignment().getSequencesArray(), getDisplayedFeatureCols()); } else { features = new FeaturesFile().printGFFFormat( - viewport.alignment.getSequencesArray(), + viewport.getAlignment().getSequencesArray(), getDisplayedFeatureCols()); } @@ -1201,7 +1304,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } /** - * DOCUMENT ME! + * TODO: JAL-1104 */ void updateEditMenuBar() { @@ -1232,6 +1335,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } + /** + * TODO: JAL-1104 + */ public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -1239,11 +1345,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.historyList.push(command); viewport.redoList.removeAllElements(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + viewport.updateHiddenColumns(); } } /** + * TODO: JAL-1104 * DOCUMENT ME! * * @param e @@ -1261,14 +1368,18 @@ 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.getAlignment().getSequences()); } /** + * TODO: JAL-1104 * DOCUMENT ME! * * @param e @@ -1286,11 +1397,15 @@ 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.getAlignment().getSequences()); } AlignViewport getOriginatingSource(CommandI command) @@ -1310,7 +1425,7 @@ 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; @@ -1325,7 +1440,7 @@ 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; @@ -1344,42 +1459,42 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (up) { - for (int i = 1; i < viewport.alignment.getHeight(); i++) + for (int i = 1; i < viewport.getAlignment().getHeight(); i++) { - SequenceI seq = viewport.alignment.getSequenceAt(i); + SequenceI seq = viewport.getAlignment().getSequenceAt(i); if (!sg.getSequences(null).contains(seq)) { continue; } - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1); if (sg.getSequences(null).contains(temp)) { continue; } - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); + viewport.getAlignment().getSequences().setElementAt(temp, i); + viewport.getAlignment().getSequences().setElementAt(seq, i - 1); } } else { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--) { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) + SequenceI seq = viewport.getAlignment().getSequenceAt(i); + if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq)) { continue; } - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) + SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1); + if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp)) { continue; } - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); + viewport.getAlignment().getSequences().setElementAt(temp, i); + viewport.getAlignment().getSequences().setElementAt(seq, i + 1); } } @@ -1391,15 +1506,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Vector sg = new Vector(); if (viewport.cursorMode) { - sg.addElement(viewport.alignment + sg.addElement(viewport.getAlignment() .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport.alignment + && viewport.getSelectionGroup().getSize() != viewport.getAlignment() .getHeight()) { sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1409,10 +1524,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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()]; @@ -1487,14 +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(); @@ -1641,17 +1756,17 @@ 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.setEndSeq(viewport.getAlignment().getHeight()); + viewport.getAlignment().getWidth(); viewport.firePropertyChange("alignment", null, - viewport.alignment.getSequences()); + viewport.getAlignment().getSequences()); } @@ -1679,7 +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); @@ -1696,10 +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()); @@ -1769,8 +1884,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.getSequenceSelection(), viewport.getAlignmentView(true).getSequenceStrings( viewport.getGapCharacter()), - viewport.alignment.getGroups()); - viewport.alignment.deleteAllGroups(); + viewport.getAlignment().getGroups()); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); // set view properties for each group @@ -1778,7 +1893,7 @@ 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(); @@ -1795,7 +1910,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void deleteGroups_actionPerformed() { - viewport.alignment.deleteAllGroups(); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); @@ -1809,7 +1924,7 @@ 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()); @@ -1873,11 +1988,11 @@ 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; @@ -1885,23 +2000,23 @@ 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(); + Vector groups = viewport.getAlignment().getGroups(); for (int i = 0; i < groups.size(); i++) { @@ -1910,7 +2025,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } @@ -1921,23 +2036,23 @@ 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); @@ -1946,7 +2061,7 @@ 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()); @@ -1961,28 +2076,28 @@ 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); @@ -2005,30 +2120,30 @@ 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()); @@ -2208,13 +2323,13 @@ 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); @@ -2227,14 +2342,14 @@ 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(); + Vector groups = viewport.getAlignment().getGroups(); for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); @@ -2247,14 +2362,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (cs instanceof ClustalxColourScheme) { sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), + sg.getSequences(viewport.getHiddenRepSequences()), sg.getWidth()); } else { try { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + sg.cs = cs.getClass().newInstance(); } catch (Exception ex) { ex.printStackTrace(); @@ -2268,7 +2383,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), 0, + sg.getSequences(viewport.getHiddenRepSequences()), 0, sg.getWidth())); } else @@ -2280,10 +2395,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(viewport.hiddenRepSequences), 0, - viewport.alignment.getWidth() - 1); + sg.getSequences(viewport.getHiddenRepSequences()), 0, + viewport.getAlignment().getWidth() - 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); sg.cs.setConservation(c); } else @@ -2310,7 +2425,7 @@ 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"); @@ -2321,10 +2436,10 @@ 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(); } } @@ -2360,7 +2475,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2368,7 +2483,7 @@ 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); } @@ -2377,7 +2492,7 @@ 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); } @@ -2386,7 +2501,7 @@ 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); } @@ -2411,7 +2526,7 @@ 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(); @@ -2468,7 +2583,7 @@ 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(); @@ -2488,7 +2603,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if ((viewport.getSelectionGroup() != null && viewport .getSelectionGroup().getSize() > 1) - || (viewport.getSelectionGroup() == null && viewport.alignment + || (viewport.getSelectionGroup() == null && viewport.getAlignment() .getHeight() > 1)) { final TreePanel tp = new TreePanel(alignPanel, type, pwType); @@ -2532,7 +2647,7 @@ 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); } @@ -2584,7 +2699,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, AlignmentSorter.sortBy(viewport.getAlignment(), alorder); if (undoname!=null) { - addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } alignPanel.paintAlignment(true); return true; @@ -2679,6 +2794,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem loadTree = new MenuItem("Load Associated Tree ..."); MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); + + MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ..."); MenuItem outputFeatures = new MenuItem("Export Features ..."); @@ -2752,11 +2869,16 @@ 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(); @@ -2881,6 +3003,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, loadTree.addActionListener(this); loadAnnotations.addActionListener(this); + loadScores.addActionListener(this); outputFeatures.addActionListener(this); outputAnnotations.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); @@ -2940,14 +3063,20 @@ 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); - avDistanceTreeBlosumMenuItem - .setLabel("Average Distance Using BLOSUM62"); + 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); njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); njTreeBlosumMenuItem.addActionListener(this); @@ -3092,7 +3221,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, fileMenu.add(inputText); fileMenu.add(loadTree); fileMenu.add(loadAnnotations); - + fileMenu.add(loadScores); + fileMenu.addSeparator(); fileMenu.add(outputTextboxMenu); fileMenu.add(outputFeatures); @@ -3153,6 +3283,8 @@ 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); @@ -3160,6 +3292,7 @@ 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(); @@ -3580,4 +3713,41 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public String getSequenceSetId() { return viewport.getSequenceSetId(); } + + + /** + * Load the (T-Coffee) score file from the specified url + * + * @param url The absolute path from where download and read the score file + * @throws IOException + */ + public void loadScoreFile( URL url ) throws IOException { + // TODO: refactor to string/standard jalview data importer + TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) ); + if( file == null ) { + // TODO: raise a dialog box here rather than bomb out. + + throw new RuntimeException("The file provided does not match the T-Coffee scores file format"); + } + + /* + * 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. + throw new RuntimeException("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)) + { + tcoffeeColour.setEnabled(true); + // switch to this color + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } + } + + }