X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=a44afa372af83745880ba19391ad06a606d8b2e6;hb=1a699d598db807829bbf3e4d9dcd7f7e6c373f76;hp=cfffbb9e1bbb57a3746a8c8e5eec82cbab0680d7;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index cfffbb9..a44afa3 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,4 +1,21 @@ /* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * 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 . + */ +/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * @@ -23,72 +40,122 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; + import jalview.bin.*; + import jalview.datamodel.*; + import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class AlignViewport +public class AlignViewport implements SelectionSource { + private static final int RIGHT_JUSTIFY = 1; + int startRes; + int endRes; + int startSeq; + int endSeq; + boolean showJVSuffix = true; + boolean showText = true; + boolean showColourText = false; + boolean showBoxes = true; + boolean wrapAlignment = false; + boolean renderGaps = true; + boolean showSequenceFeatures = false; + boolean showAnnotation = true; + boolean colourAppliesToAllGroups = true; + ColourSchemeI globalColourScheme = null; + boolean conservationColourSelected = false; + boolean abovePIDThreshold = false; + SequenceGroup selectionGroup; + int charHeight; + int charWidth; + boolean validCharWidth; + int wrappedWidth; + Font font; + boolean seqNameItalics; + AlignmentI alignment; + ColumnSelection colSel = new ColumnSelection(); + int threshold; + int increment; + NJTree currentTree = null; + boolean scaleAboveWrapped = false; + boolean scaleLeftWrapped = true; + boolean scaleRightWrapped = true; + boolean hasHiddenColumns = false; + boolean hasHiddenRows = false; + boolean showHiddenMarkers = true; boolean cursorMode = false; - // The following vector holds the features which are - // currently visible, in the correct order or rendering + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ Hashtable featuresDisplayed = null; /** DOCUMENT ME!! */ public Hashtable[] hconsensus; + AlignmentAnnotation consensus; + AlignmentAnnotation conservation; + AlignmentAnnotation quality; + + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + boolean autoCalculateConsensus = true; /** DOCUMENT ME!! */ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans. - PropertyChangeSupport(this); + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); boolean ignoreGapsInConsensusCalculation = false; @@ -107,22 +174,28 @@ public class AlignViewport boolean gatherViewsHere = false; Stack historyList = new Stack(); + Stack redoList = new Stack(); Hashtable sequenceColours; int thresholdTextColour = 0; + Color textColour = Color.black; + Color textColour2 = Color.white; boolean rightAlignIds = false; Hashtable hiddenRepSequences; + boolean sortByTree; + /** * Creates a new AlignViewport object. - * - * @param al DOCUMENT ME! + * + * @param al + * alignment to view */ public AlignViewport(AlignmentI al) { @@ -131,9 +204,42 @@ public class AlignViewport } /** + * Create a new AlignViewport object with a specific sequence set ID + * + * @param al + * @param seqsetid + * (may be null - but potential for ambiguous constructor exception) + */ + public AlignViewport(AlignmentI al, String seqsetid) + { + this(al, seqsetid, null); + } + + public AlignViewport(AlignmentI al, String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + init(); + } + + /** * Create a new AlignViewport with hidden regions - * @param al AlignmentI - * @param hiddenColumns ColumnSelection + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection */ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) { @@ -141,10 +247,71 @@ public class AlignViewport if (hiddenColumns != null) { this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + init(); + } + + /** + * New viewport with hidden columns and an existing sequence set id + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) + { + this(al, hiddenColumns, seqsetid, null); + } + + /** + * New viewport with hidden columns and an existing sequence set id and viewid + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; } + else + { + hasHiddenColumns = false; + } } init(); } @@ -162,10 +329,12 @@ public class AlignViewport showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); - + centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); padGaps = Cache.getDefault("PAD_GAPS", true); + shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); + showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); @@ -186,7 +355,8 @@ public class AlignViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + alignment + .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); // We must set conservation and consensus before setting colour, // as Blosum and Clustal require this to be done @@ -195,11 +365,9 @@ public class AlignViewport if (!alignment.isNucleotide()) { conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - new Annotation[1], 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); + "Conservation of total alignment less than " + ConsPercGaps + + "% gaps", new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; @@ -211,21 +379,29 @@ public class AlignViewport if (Cache.getDefault("SHOW_QUALITY", true)) { quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], - 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); quality.hasText = true; quality.autoCalculated = true; alignment.addAnnotation(quality); } - } + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); + + { + } + } + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); + // TODO: add menu option action that nulls or creates consensus object + // depending on if the user wants to see the annotation or not in a + // specific alignment consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; consensus.autoCalculated = true; @@ -238,13 +414,13 @@ public class AlignViewport if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) { globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); if (globalColourScheme instanceof UserColourScheme) { globalColourScheme = UserDefinedColours.loadDefaultColours(); - ( (UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); } if (globalColourScheme != null) @@ -254,12 +430,18 @@ public class AlignViewport } wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); + showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", + false); + sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); + // disabled by default for 2.5.1 release + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", false); } /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * set the flag + * + * @param b + * features are displayed if true */ public void setShowSequenceFeatures(boolean b) { @@ -271,166 +453,6 @@ public class AlignViewport return showSequenceFeatures; } - class ConservationThread - extends Thread - { - AlignmentPanel ap; - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - try - { - updatingConservation = true; - - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.repaint(); - } - Thread.sleep(200); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSERVATION = true; - - int alWidth = alignment.getWidth(); - if (alWidth < 0) - { - return; - } - - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alWidth - 1); - - cons.calculate(); - cons.verdict(false, ConsPercGaps); - - if (quality != null) - { - cons.findQuality(); - } - - char[] sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and Quality - - float min = 0f; - float max = 11f; - float qmin = 0f; - float qmax = 0f; - - char c; - - conservation.annotations = new Annotation[alWidth]; - - if (quality != null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - value = 11; - } - else if (c == '+') - { - value = 10; - } - - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = - new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - if (quality != null) - { - value = ( (Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String.valueOf(value), - ' ', - value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - } - } - } - catch (OutOfMemoryError error) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating conservation!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - - conservation = null; - quality = null; - - System.out.println("Conservation calculation: " + error); - System.gc(); - - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.repaint(); - } - - } - } - ConservationThread conservationThread; ConsensusThread consensusThread; @@ -446,32 +468,54 @@ public class AlignViewport boolean updatingConservation = false; /** - * DOCUMENT ME! + * centre columnar annotation labels in displayed alignment annotation TODO: + * add to jalviewXML and annotation display settings + */ + boolean centreColumnLabels = false; + + private boolean showdbrefs; + + private boolean shownpfeats; + + /** + * consensus annotation includes all percentage for all symbols in column + */ + private boolean includeAllConsensusSymbols = true; + + /** + * trigger update of conservation annotation */ public void updateConservation(final AlignmentPanel ap) { - if (alignment.isNucleotide() || conservation == null) + // see note in mantis : issue number 8585 + if (alignment.isNucleotide() || conservation == null + || !autoCalculateConsensus) { return; } - conservationThread = new ConservationThread(ap); + conservationThread = new ConservationThread(this, ap); conservationThread.start(); } /** - * DOCUMENT ME! + * trigger update of consensus annotation */ public void updateConsensus(final AlignmentPanel ap) { + // see note in mantis : issue number 8585 + if (consensus == null || !autoCalculateConsensus) + { + return; + } consensusThread = new ConsensusThread(ap); consensusThread.start(); } - class ConsensusThread - extends Thread + class ConsensusThread extends Thread { AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) { this.ap = ap; @@ -486,12 +530,11 @@ public class AlignViewport { if (ap != null) { - ap.repaint(); + ap.paintAlignment(false); } Thread.sleep(200); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -501,7 +544,10 @@ public class AlignViewport try { - int aWidth = alignment.getWidth(); + int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null + // pointer + // possibility + // here. if (aWidth < 0) { return; @@ -511,79 +557,39 @@ public class AlignViewport consensus.annotations = new Annotation[aWidth]; hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). - floatValue(); - } - else - { - value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). - floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ( (int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } + AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment + .getWidth(), hconsensus, includeAllConsensusSymbols); + AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth, + ignoreGapsInConsensusCalculation, + includeAllConsensusSymbols); if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); } - } - catch (OutOfMemoryError error) + } catch (OutOfMemoryError error) { alignment.deleteAnnotation(consensus); consensus = null; hconsensus = null; - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating consensus!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - - System.out.println("Consensus calculation: " + error); - System.gc(); + new OOMWarning("calculating consensus", error); } UPDATING_CONSENSUS = false; updatingConsensus = false; if (ap != null) { - ap.repaint(); + ap.paintAlignment(true); } } } /** - * get the consensus sequence as displayed under the PID consensus annotation row. + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * * @return consensus sequence as a new sequence object */ public SequenceI getConsensusSeq() @@ -613,15 +619,14 @@ public class AlignViewport } SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " + - ( (ignoreGapsInConsensusCalculation) ? " without gaps" : - "")); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); return sq; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public SequenceGroup getSelectionGroup() @@ -631,8 +636,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param sg DOCUMENT ME! + * + * @param sg + * DOCUMENT ME! */ public void setSelectionGroup(SequenceGroup sg) { @@ -641,7 +647,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getConservationSelected() @@ -651,8 +657,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setConservationSelected(boolean b) { @@ -661,7 +668,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getAbovePIDThreshold() @@ -671,8 +678,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setAbovePIDThreshold(boolean b) { @@ -681,7 +689,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getStartRes() @@ -691,7 +699,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getEndRes() @@ -701,7 +709,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getStartSeq() @@ -711,8 +719,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param cs DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! */ public void setGlobalColourScheme(ColourSchemeI cs) { @@ -721,7 +730,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public ColourSchemeI getGlobalColourScheme() @@ -731,8 +740,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param res DOCUMENT ME! + * + * @param res + * DOCUMENT ME! */ public void setStartRes(int res) { @@ -741,8 +751,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param seq DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! */ public void setStartSeq(int seq) { @@ -751,14 +762,16 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param res DOCUMENT ME! + * + * @param res + * DOCUMENT ME! */ public void setEndRes(int res) { if (res > (alignment.getWidth() - 1)) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); res = alignment.getWidth() - 1; } @@ -772,8 +785,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param seq DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -792,7 +806,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getEndSeq() @@ -802,8 +816,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param f DOCUMENT ME! + * + * @param f + * DOCUMENT ME! */ public void setFont(Font f) { @@ -819,7 +834,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public Font getFont() @@ -829,8 +844,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param w DOCUMENT ME! + * + * @param w + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -839,7 +855,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getCharWidth() @@ -849,8 +865,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param h DOCUMENT ME! + * + * @param h + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -859,7 +876,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getCharHeight() @@ -869,8 +886,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param w DOCUMENT ME! + * + * @param w + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -879,7 +897,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getWrappedWidth() @@ -889,7 +907,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public AlignmentI getAlignment() @@ -899,18 +917,30 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param align DOCUMENT ME! + * + * @param align + * DOCUMENT ME! */ public void setAlignment(AlignmentI align) { + if (alignment != null && alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager() + .removeMappings(alignment.getCodonFrames()); + } this.alignment = align; + if (alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager().addMappings( + alignment.getCodonFrames()); + } } /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -919,8 +949,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -929,8 +960,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -939,7 +971,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getColourText() @@ -949,8 +981,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -959,8 +992,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -969,7 +1003,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getWrapAlignment() @@ -979,7 +1013,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowText() @@ -989,7 +1023,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowBoxes() @@ -999,7 +1033,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public char getGapCharacter() @@ -1009,8 +1043,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param gap DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -1022,8 +1057,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param thresh DOCUMENT ME! + * + * @param thresh + * DOCUMENT ME! */ public void setThreshold(int thresh) { @@ -1032,7 +1068,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getThreshold() @@ -1042,8 +1078,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param inc DOCUMENT ME! + * + * @param inc + * DOCUMENT ME! */ public void setIncrement(int inc) { @@ -1052,7 +1089,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getIncrement() @@ -1062,7 +1099,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public ColumnSelection getColumnSelection() @@ -1072,8 +1109,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param tree DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1082,7 +1120,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public NJTree getCurrentTree() @@ -1092,8 +1130,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setColourAppliesToAllGroups(boolean b) { @@ -1102,7 +1141,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getColourAppliesToAllGroups() @@ -1112,7 +1151,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowJVSuffix() @@ -1122,8 +1161,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1132,7 +1172,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowAnnotation() @@ -1142,8 +1182,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1152,7 +1193,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getScaleAboveWrapped() @@ -1162,7 +1203,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getScaleLeftWrapped() @@ -1172,7 +1213,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getScaleRightWrapped() @@ -1182,8 +1223,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1192,8 +1234,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1202,8 +1245,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setScaleRightWrapped(boolean b) { @@ -1212,34 +1256,40 @@ public class AlignViewport /** * Property change listener for changes in alignment - * - * @param listener DOCUMENT ME! + * + * @param listener + * DOCUMENT ME! */ public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) + java.beans.PropertyChangeListener listener) { changeSupport.addPropertyChangeListener(listener); } /** * DOCUMENT ME! - * - * @param listener DOCUMENT ME! + * + * @param listener + * DOCUMENT ME! */ public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) + java.beans.PropertyChangeListener listener) { changeSupport.removePropertyChangeListener(listener); } /** * Property change listener for changes in alignment - * - * @param prop DOCUMENT ME! - * @param oldvalue DOCUMENT ME! - * @param newvalue DOCUMENT ME! + * + * @param prop + * DOCUMENT ME! + * @param oldvalue + * DOCUMENT ME! + * @param newvalue + * DOCUMENT ME! */ - public void firePropertyChange(String prop, Object oldvalue, Object newvalue) + public void firePropertyChange(String prop, Object oldvalue, + Object newvalue) { changeSupport.firePropertyChange(prop, oldvalue, newvalue); } @@ -1251,7 +1301,7 @@ public class AlignViewport if (globalColourScheme != null) { globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); + ignoreGapsInConsensusCalculation); } } @@ -1312,7 +1362,7 @@ public class AlignViewport hiddenRepSequences.put(repSequence, sg); - //Hide all sequences except the repSequence + // Hide all sequences except the repSequence SequenceI[] seqs = new SequenceI[sSize - 1]; int index = 0; for (int i = 0; i < sSize; i++) @@ -1327,14 +1377,15 @@ public class AlignViewport seqs[index++] = sg.getSequenceAt(i); } } - + sg.setSeqrep(repSequence); + sg.setHidereps(true); hideSequence(seqs); } public void hideAllSelectedSeqs() { - if (selectionGroup == null) + if (selectionGroup == null || selectionGroup.getSize() < 1) { return; } @@ -1361,8 +1412,8 @@ public class AlignViewport public void showSequence(int index) { - Vector tmp = alignment.getHiddenSequences().showSequence(index - , hiddenRepSequences); + Vector tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -1373,11 +1424,10 @@ public class AlignViewport for (int t = 0; t < tmp.size(); t++) { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); } firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); } if (alignment.getHiddenSequences().getSize() < 1) @@ -1410,14 +1460,14 @@ public class AlignViewport selectionGroup = new SequenceGroup(); selectionGroup.setEndRes(alignment.getWidth() - 1); } - Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences); + Vector tmp = alignment.getHiddenSequences().showAll( + hiddenRepSequences); for (int t = 0; t < tmp.size(); t++) { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); } firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); hasHiddenRows = false; hiddenRepSequences = null; } @@ -1425,31 +1475,23 @@ public class AlignViewport public void invertColumnSelection() { - for (int i = 0; i < alignment.getWidth(); i++) - { - if (colSel.contains(i)) - { - colSel.removeElement(i); - } - else - { - if (!hasHiddenColumns || colSel.isVisible(i)) - { - colSel.addElement(i); - } - } - } + colSel.invertColumnSelection(0, alignment.getWidth()); } public int adjustForHiddenSeqs(int alignmentIndex) { - return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex); + return alignment.getHiddenSequences().adjustForHiddenSeqs( + alignmentIndex); } /** - * This method returns the a new SequenceI [] with - * the selection sequence and start and end points adjusted - * @return String[] + * This method returns an array of new SequenceI objects derived from the + * whole alignment or just the current selection with start and end points + * adjusted + * + * @note if you need references to the actual SequenceI objects in the + * alignment or currently selected then use getSequenceSelection() + * @return selection as new sequenceI objects */ public SequenceI[] getSelectionAsNewSequence() { @@ -1458,6 +1500,14 @@ public class AlignViewport if (selectionGroup == null) { sequences = alignment.getSequencesArray(); + AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); + for (int i = 0; i < sequences.length; i++) + { + sequences[i] = new Sequence(sequences[i], annots); // construct new + // sequence with + // subset of visible + // annotation + } } else { @@ -1468,15 +1518,35 @@ public class AlignViewport } /** - * This method returns the visible alignment as text, as - * seen on the GUI, ie if columns are hidden they will not - * be returned in the result. - * Use this for calculating trees, PCA, redundancy etc on views - * which contain hidden columns. + * get the currently selected sequence objects or all the sequences in the + * alignment. + * + * @return array of references to sequence objects + */ + public SequenceI[] getSequenceSelection() + { + SequenceI[] sequences = null; + if (selectionGroup != null) + { + sequences = selectionGroup.getSequencesInOrder(alignment); + } + if (sequences == null) + { + sequences = alignment.getSequencesArray(); + } + return sequences; + } + + /** + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * * @return String[] */ - public jalview.datamodel.CigarArray getViewAsCigars(boolean - selectedRegionOnly) + public jalview.datamodel.CigarArray getViewAsCigars( + boolean selectedRegionOnly) { CigarArray selection = null; SequenceI[] seqs = null; @@ -1487,7 +1557,8 @@ public class AlignViewport iSize = selectionGroup.getSize(); seqs = selectionGroup.getSequencesInOrder(alignment); start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor + end = selectionGroup.getEndRes(); // inclusive for start and end in + // SeqCigar constructor } else { @@ -1564,33 +1635,36 @@ public class AlignViewport } /** - * return a compact representation of the current alignment selection to - * pass to an analysis function - * @param selectedOnly boolean true to just return the selected view + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view * @return AlignmentView */ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) { // JBPNote: - // this is here because the AlignmentView constructor modifies the CigarArray + // this is here because the AlignmentView constructor modifies the + // CigarArray // object. Refactoring of Cigar and alignment view representation should // be done to remove redundancy. CigarArray aligview = getViewAsCigars(selectedOnly); if (aligview != null) { return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? - selectionGroup.getStartRes() : 0); + (selectedOnly && selectionGroup != null) ? selectionGroup + .getStartRes() : 0); } return null; } /** - * This method returns the visible alignment as text, as - * seen on the GUI, ie if columns are hidden they will not - * be returned in the result. - * Use this for calculating trees, PCA, redundancy etc on views - * which contain hidden columns. + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * * @return String[] */ public String[] getViewAsString(boolean selectedRegionOnly) @@ -1629,6 +1703,50 @@ public class AlignViewport return selection; } + public int[][] getVisibleRegionBoundaries(int min, int max) + { + Vector regions = new Vector(); + int start = min; + int end = max; + + do + { + if (hasHiddenColumns) + { + if (start == 0) + { + start = colSel.adjustForHiddenColumns(start); + } + + end = colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = max; + } + if (end > max) + { + end = max; + } + } + + regions.addElement(new int[] + { start, end }); + + if (hasHiddenColumns) + { + start = colSel.adjustForHiddenColumns(end); + start = colSel.getHiddenBoundaryLeft(start) + 1; + } + } while (end < max); + + int[][] startEnd = new int[regions.size()][2]; + + regions.copyInto(startEnd); + + return startEnd; + + } + public boolean getShowHiddenMarkers() { return showHiddenMarkers; @@ -1649,20 +1767,37 @@ public class AlignViewport return sequenceSetID; } + /** + * unique viewId for synchronizing state with stored Jalview Project + * + */ + private String viewId = null; + + public String getViewId() + { + if (viewId == null) + { + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; + } + return viewId; + } + public void alignmentChanged(AlignmentPanel ap) { if (padGaps) { alignment.padGaps(); } - if (hconsensus != null && autoCalculateConsensus) { - updateConsensus(ap); updateConservation(ap); } + if (autoCalculateConsensus) + { + updateConsensus(ap); + } - //Reset endRes of groups if beyond alignment width + // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); Vector groups = alignment.getGroups(); if (groups != null) @@ -1694,9 +1829,8 @@ public class AlignViewport { if (cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) cs). - resetClustalX(alignment.getSequences(), - alignment.getWidth()); + ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), + alignment.getWidth()); } cs.setConsensus(hconsensus); @@ -1704,9 +1838,8 @@ public class AlignViewport { Alignment al = (Alignment) alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, al + .getWidth() - 1); c.calculate(); c.verdict(false, ConsPercGaps); @@ -1720,8 +1853,8 @@ public class AlignViewport SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) sg.cs).resetClustalX( - sg.getSequences(hiddenRepSequences), sg.getWidth()); + ((ClustalxColourScheme) sg.cs).resetClustalX(sg + .getSequences(hiddenRepSequences), sg.getWidth()); } sg.recalcConservation(); } @@ -1756,4 +1889,428 @@ public class AlignViewport } } + /** + * returns the visible column regions of the alignment + * + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return + */ + public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + { + int[] viscontigs = null; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + end = alignment.getWidth(); + } + viscontigs = colSel.getVisibleContigs(start, end); + return viscontigs; + } + + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() + { + if (historyList == null || redoList == null) + return new long[] + { -1, -1 }; + return new long[] + { historyList.hashCode(), this.redoList.hashCode() }; + } + + /** + * test if a particular set of hashcodes are different to the hashcodes for + * the undo and redo list. + * + * @param undoredo + * the stored set of hashcodes as returned by getUndoRedoHash + * @return true if the hashcodes differ (ie the alignment has been edited) or + * the stored hashcode array differs in size + */ + public boolean isUndoRedoHashModified(long[] undoredo) + { + if (undoredo == null) + { + return true; + } + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) + { + return true; + } + + for (int i = 0; i < cstate.length; i++) + { + if (cstate[i] != undoredo[i]) + { + return true; + } + } + return false; + } + + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } + + public void setCentreColumnLabels(boolean centrecolumnlabels) + { + centreColumnLabels = centrecolumnlabels; + } + + public void updateSequenceIdColours() + { + Vector groups = alignment.getGroups(); + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); + if (sg.idColour != null) + { + Vector sqs = sg.getSequences(hiddenRepSequences); + for (int s = 0, sSize = sqs.size(); s < sSize; s++) + { + sequenceColours.put(sqs.elementAt(s), sg.idColour); + } + } + } + } + + /** + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ + public void setShowDbRefs(boolean show) + { + showdbrefs = show; + } + + /** + * + * @return true if Database References are to be displayed on tooltips. + */ + public boolean isShowDbRefs() + { + return showdbrefs; + } + + /** + * + * @return true if Non-positional features are to be displayed on tooltips. + */ + public boolean isShowNpFeats() + { + return shownpfeats; + } + + /** + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show + */ + public void setShowNpFeats(boolean show) + { + shownpfeats = show; + } + + /** + * + * @return true if view has hidden rows + */ + public boolean hasHiddenRows() + { + return hasHiddenRows; + } + + /** + * + * @return true if view has hidden columns + */ + public boolean hasHiddenColumns() + { + return hasHiddenColumns; + } + + /** + * when set, view will scroll to show the highlighted position + */ + public boolean followHighlight = true; + + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + public boolean getFollowHighlight() + { + return followHighlight; + } + + public boolean followSelection = true; + + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } + + private long sgrouphash = -1, colselhash = -1; + + boolean showSeqFeaturesHeight; + + /** + * checks current SelectionGroup against record of last hash value, and + * updates record. + * + * @return true if SelectionGroup changed since last call + */ + boolean isSelectionGroupChanged() + { + int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); + if (hc != sgrouphash) + { + sgrouphash = hc; + return true; + } + return false; + } + + /** + * checks current colsel against record of last hash value, and updates + * record. + * + * @return true if colsel changed since last call + */ + boolean isColSelChanged() + { + int hc = (colSel == null) ? -1 : colSel.hashCode(); + if (hc != colselhash) + { + colselhash = hc; + return true; + } + return false; + } + + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + public void setShowSequenceFeaturesHeight(boolean selected) + { + showSeqFeaturesHeight = selected; + } + + public boolean getShowSequenceFeaturesHeight() + { + return showSeqFeaturesHeight; + } + + boolean showUnconserved = false; + + public boolean getShowUnconserved() + { + return showUnconserved; + } + + public void setShowUnconserved(boolean showunconserved) + { + showUnconserved = showunconserved; + } + + /** + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. + * + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference + */ + public AlignmentPanel getAlignPanel() + { + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + AlignmentPanel ap = null; + for (int p = 0; aps != null && p < aps.length; p++) + { + if (aps[p].av == this) + { + return aps[p]; + } + } + return null; + } + + public boolean getSortByTree() + { + return sortByTree; + } + + public void setSortByTree(boolean sort) + { + sortByTree = sort; + } + + /** + * should conservation rows be shown for groups + */ + boolean showGroupConservation = false; + + /** + * should consensus rows be shown for groups + */ + boolean showGroupConsensus = false; + + /** + * should consensus profile be rendered by default + */ + public boolean showSequenceLogo = false; + + /** + * should consensus histograms be rendered by default + */ + public boolean showConsensusHistogram = true; + + /** + * @return the showConsensusProfile + */ + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + /** + * @param showSequenceLogo + * the new value + */ + public void setShowSequenceLogo(boolean showSequenceLogo) + { + this.showSequenceLogo = showSequenceLogo; + } + + /** + * @param showConsensusHistogram + * the showConsensusHistogram to set + */ + public void setShowConsensusHistogram(boolean showConsensusHistogram) + { + this.showConsensusHistogram = showConsensusHistogram; + } + + /** + * @return the showGroupConservation + */ + public boolean isShowGroupConservation() + { + return showGroupConservation; + } + + /** + * @param showGroupConservation + * the showGroupConservation to set + */ + public void setShowGroupConservation(boolean showGroupConservation) + { + this.showGroupConservation = showGroupConservation; + } + + /** + * @return the showGroupConsensus + */ + public boolean isShowGroupConsensus() + { + return showGroupConsensus; + } + + /** + * @param showGroupConsensus + * the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + + /** + * @return the includeAllConsensusSymbols + */ + public boolean isIncludeAllConsensusSymbols() + { + return includeAllConsensusSymbols; + } + + /** + * @param includeAllConsensusSymbols + * the includeAllConsensusSymbols to set + */ + public void setIncludeAllConsensusSymbols( + boolean includeAllConsensusSymbols) + { + this.includeAllConsensusSymbols = includeAllConsensusSymbols; + } + + /** + * + * @return flag to indicate if the consensus histogram should be rendered by + * default + */ + public boolean isShowConsensusHistogram() + { + return this.showConsensusHistogram; + } + + /** + * synthesize a column selection if none exists so it covers the given + * selection group. if wholewidth is false, no column selection is made if the + * selection group covers the whole alignment width. + * + * @param sg + * @param wholewidth + */ + public void expandColSelection(SequenceGroup sg, boolean wholewidth) + { + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } + } }