X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=1c6a94e154b0d89ed1e65600eaf40d0f6cd5d96f;hb=298c2b85845dbaabda7e3304751cc856e7b0ad30;hp=cbb19fb99f2a23ecbd585b9613130f6cc878892a;hpb=fd618c7346eab858aa0039376872820aca37783a;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index cbb19fb..1c6a94e --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,4 +1,21 @@ - /* +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 * @@ -23,1653 +40,1769 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.AlignViewportI; import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; /** * DOCUMENT ME! - * + * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport +public class AlignViewport implements SelectionSource, VamsasSource, AlignViewportI { - 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 - Hashtable featuresDisplayed = null; - - - /** DOCUMENT ME!! */ - public Hashtable [] hconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; - 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 static final int RIGHT_JUSTIFY = 1; - boolean ignoreGapsInConsensusCalculation = false; + int startRes; - boolean isDataset = false; + int endRes; - boolean antiAlias = false; + int startSeq; - boolean padGaps = false; + int endSeq; - Rectangle explodedPosition; + boolean showJVSuffix = true; - String viewName; + boolean showText = true; - String sequenceSetID; + boolean showColourText = false; - boolean gatherViewsHere = false; + boolean showBoxes = true; - Stack historyList = new Stack(); - Stack redoList = new Stack(); + boolean wrapAlignment = false; - Hashtable sequenceColours; + boolean renderGaps = true; - int thresholdTextColour = 0; - Color textColour = Color.black; - Color textColour2 = Color.white; + boolean showSequenceFeatures = false; - boolean rightAlignIds = false; + boolean showAnnotation = true; - Hashtable hiddenRepSequences; + boolean colourAppliesToAllGroups = true; + ColourSchemeI globalColourScheme = null; - /** - * Creates a new AlignViewport object. - * - * @param al DOCUMENT ME! - */ - public AlignViewport(AlignmentI al) - { - setAlignment(al); - init(); - } - /** - * Create a new AlignViewport with hidden regions - * @param al AlignmentI - * @param hiddenColumns ColumnSelection - */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) - { - setAlignment(al); - if (hiddenColumns != null) - { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) - { - hasHiddenColumns = true; - } - } - init(); - } - - void init() - { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; + boolean conservationColourSelected = false; - antiAlias = Cache.getDefault("ANTI_ALIAS", false); + boolean abovePIDThreshold = false; - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); - showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + SequenceGroup selectionGroup; - rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); + int charHeight; - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + int charWidth; - padGaps = Cache.getDefault("PAD_GAPS", true); + boolean validCharWidth; - String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); - String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ; - String fontSize = Cache.getDefault("FONT_SIZE", "10"); + int wrappedWidth; - seqNameItalics = Cache.getDefault("ID_ITALICS", true); + Font font; - int style = 0; + boolean seqNameItalics; - if (fontStyle.equals("bold")) - { - style = 1; - } - else if (fontStyle.equals("italic")) - { - style = 2; - } + AlignmentI alignment; - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + ColumnSelection colSel = new ColumnSelection(); - alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) ); + int threshold; + int increment; - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - if(hconsensus==null && !isDataset) - { - if(!alignment.isNucleotide()) - { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - new Annotation[1], 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); - conservation.hasText = true; - conservation.autoCalculated=true; - - - if (Cache.getDefault("SHOW_CONSERVATION", true)) - { - alignment.addAnnotation(conservation); - } - - if (Cache.getDefault("SHOW_QUALITY", true)) - { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], - 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated=true; - - alignment.addAnnotation(quality); - } - } + NJTree currentTree = null; - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated=true; + boolean scaleAboveWrapped = false; - if (Cache.getDefault("SHOW_IDENTITY", true)) - { - alignment.addAnnotation(consensus); - } - } + boolean scaleLeftWrapped = true; - if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + boolean scaleRightWrapped = true; - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ( (UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); - } - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - } + boolean hasHiddenColumns = false; - wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); - } + boolean hasHiddenRows = false; + boolean showHiddenMarkers = true; + boolean cursorMode = false; - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ + Hashtable featuresDisplayed = null; - public boolean getShowSequenceFeatures() - { - return showSequenceFeatures; - } + /** DOCUMENT ME!! */ + public Hashtable[] hconsensus; - class ConservationThread - extends Thread - { - AlignmentPanel ap; - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } + public Hashtable[] hStrucConsensus; - public void run() - { - try - { - updatingConservation = true; + AlignmentAnnotation consensus; - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } - Thread.sleep(200); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + AlignmentAnnotation strucConsensus; - UPDATING_CONSERVATION = true; + AlignmentAnnotation conservation; + AlignmentAnnotation quality; - int alWidth = alignment.getWidth(); - if(alWidth<0) - { - return; - } + AlignmentAnnotation[] groupConsensus; - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alWidth -1); + AlignmentAnnotation[] groupConservation; - cons.calculate(); - cons.verdict(false, ConsPercGaps); + boolean autoCalculateConsensus = true; - if (quality!=null) - { - cons.findQuality(); - } + boolean autoCalculateStrucConsensus = true; - 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(); - } + /** DOCUMENT ME!! */ + public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - for (int i = 0; i < alWidth; i++) - { - float value = 0; + // JBPNote Prolly only need this in the applet version. + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); - c = sequence[i]; + boolean ignoreGapsInConsensusCalculation = false; - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - value = 11; - } - else if (c == '+') - { - value = 10; - } + boolean isDataset = false; - 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() - { + boolean antiAlias = false; + boolean padGaps = false; - 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); - } - }); + Rectangle explodedPosition; - conservation = null; - quality = null; + String viewName; - System.out.println("Conservation calculation: " + error); - System.gc(); + String sequenceSetID; - } + boolean gatherViewsHere = false; - UPDATING_CONSERVATION = false; - updatingConservation = false; + Stack historyList = new Stack(); - if(ap!=null) - { - ap.paintAlignment(true); - } + Stack redoList = new Stack(); - } - } + Hashtable sequenceColours; + int thresholdTextColour = 0; - ConservationThread conservationThread; + Color textColour = Color.black; - ConsensusThread consensusThread; + Color textColour2 = Color.white; - boolean consUpdateNeeded = false; + boolean rightAlignIds = false; - static boolean UPDATING_CONSENSUS = false; + Hashtable hiddenRepSequences; - static boolean UPDATING_CONSERVATION = false; + boolean sortByTree; - boolean updatingConsensus = false; + /** + * Creates a new AlignViewport object. + * + * @param al + * alignment to view + */ + public AlignViewport(AlignmentI al) + { + setAlignment(al); + init(); + } - boolean updatingConservation = false; + /** + * 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); + } - /** - * DOCUMENT ME! - */ - public void updateConservation(final AlignmentPanel ap) + 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) { - if (alignment.isNucleotide() || conservation==null) + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) { - return; + Cache.log.debug("Setting viewport's view id : " + viewId); } + setAlignment(al); + init(); + } - conservationThread = new ConservationThread(ap); - conservationThread.start(); + /** + * Create a new AlignViewport with hidden regions + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + { + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } } + init(); + } - /** - * DOCUMENT ME! - */ - public void updateConsensus(final AlignmentPanel ap) + /** + * 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) { - consensusThread = new ConsensusThread(ap); - consensusThread.start(); + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); } - - class ConsensusThread - extends Thread + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + if (hiddenColumns != null) { - AlignmentPanel ap; - public ConsensusThread(AlignmentPanel ap) + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { - this.ap = ap; + hasHiddenColumns = true; } - public void run() + else { - updatingConsensus = true; - while (UPDATING_CONSENSUS) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } + hasHiddenColumns = false; + } + } + init(); + } - Thread.sleep(200); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + antiAlias = Cache.getDefault("ANTI_ALIAS", false); - UPDATING_CONSENSUS = true; + showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); + showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); - try - { - int aWidth = alignment.getWidth(); - if(aWidth<0) - { - return; - } + rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); + centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; + 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 + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); + seqNameItalics = Cache.getDefault("ID_ITALICS", true); - 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(); - } + int style = 0; - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + if (fontStyle.equals("bold")) + { + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } + setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - mouseOver += ( (int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } + 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 + if (hconsensus == null && !isDataset) + { + if (!alignment.isNucleotide()) + { + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + ConsPercGaps + + "% gaps", new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; - if (globalColourScheme != null) + if (Cache.getDefault("SHOW_CONSERVATION", true)) { - globalColourScheme.setConsensus(hconsensus); + alignment.addAnnotation(conservation); } - } - catch (OutOfMemoryError error) + if (Cache.getDefault("SHOW_QUALITY", true)) { - alignment.deleteAnnotation(consensus); + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; - 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(); + alignment.addAnnotation(quality); } - UPDATING_CONSENSUS = false; - updatingConsensus = false; + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); - if (ap != null) { - ap.paintAlignment(true); + } } - } - /** - * get the consensus sequence as displayed under the PID consensus annotation row. - * @return consensus sequence as a new sequence object - */ - public SequenceI getConsensusSeq() - { - if (consensus==null) - { - updateConsensus(null); - } - if (consensus==null) - { - return null; - } - StringBuffer seqs=new StringBuffer(); - for (int i = 0; i < consensus.annotations.length; i++) - { - if (consensus.annotations[i] != null) + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + normaliseSequenceLogo = Cache.getDefault("NORMALISE_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); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (alignment.isNucleotide() && alignment.hasRNAStructure()) { - if (consensus.annotations[i].description.charAt(0) == '[') - { - seqs.append(consensus.annotations[i].description.charAt(1)); - } - else + strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + strucConsensus.hasText = true; + strucConsensus.autoCalculated = true; + } + + if (Cache.getDefault("SHOW_IDENTITY", true)) + { + alignment.addAnnotation(consensus); + // TODO: Make own if for structure + if (alignment.isNucleotide() && alignment.hasRNAStructure()) { - seqs.append(consensus.annotations[i].displayCharacter); + alignment.addAnnotation(strucConsensus); } } - } - SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " + - ( (ignoreGapsInConsensusCalculation) ? " without gaps" : - "")); - return sq; - } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceGroup getSelectionGroup() - { - return selectionGroup; } - /** - * DOCUMENT ME! - * - * @param sg DOCUMENT ME! - */ - public void setSelectionGroup(SequenceGroup sg) + if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) { - selectionGroup = sg; - } + globalColourScheme = ColourSchemeProperty.getColour(alignment, + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getConservationSelected() - { - return conservationColourSelected; - } + if (globalColourScheme instanceof UserColourScheme) + { + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } + 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); + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", + true); + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } + /** + * set the flag + * + * @param b + * features are displayed if true + */ + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartRes() - { - return startRes; - } + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndRes() - { - return endRes; - } + ConservationThread conservationThread; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartSeq() - { - return startSeq; - } + ConsensusThread consensusThread; - /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! - */ - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } + StrucConsensusThread strucConsensusThread; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColourSchemeI getGlobalColourScheme() + boolean consUpdateNeeded = false; + + static boolean UPDATING_CONSENSUS = false; + + static boolean UPDATING_STRUC_CONSENSUS = false; + + static boolean UPDATING_CONSERVATION = false; + + boolean updatingConsensus = false; + + boolean updatingStrucConsensus = false; + + boolean updatingConservation = false; + + /** + * 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; + + /** + * trigger update of conservation annotation + */ + public void updateConservation(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (alignment.isNucleotide() || conservation == null + || !autoCalculateConsensus) { - return globalColourScheme; + return; } - /** - * DOCUMENT ME! - * - * @param res DOCUMENT ME! - */ - public void setStartRes(int res) + conservationThread = new ConservationThread(this, ap); + conservationThread.start(); + } + + /** + * trigger update of consensus annotation + */ + public void updateConsensus(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (consensus == null || !autoCalculateConsensus) { - this.startRes = res; + return; } + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + } - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setStartSeq(int seq) + class ConsensusThread extends Thread + { + AlignmentPanel ap; + + public ConsensusThread(AlignmentPanel ap) { - this.startSeq = seq; + this.ap = ap; } - /** - * DOCUMENT ME! - * - * @param res DOCUMENT ME! - */ - public void setEndRes(int res) + public void run() { - if (res > (alignment.getWidth() - 1)) + updatingConsensus = true; + while (UPDATING_CONSENSUS) + { + try { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; - } + if (ap != null) + { + ap.paintAlignment(false); + } - if (res < 0) + Thread.sleep(200); + } catch (Exception ex) { - res = 0; + ex.printStackTrace(); } + } - this.endRes = res; - } + UPDATING_CONSENSUS = true; - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) { - seq = alignment.getHeight(); + updatingConsensus = false; + UPDATING_CONSENSUS = false; + return; } - if (seq < 0) + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; + + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment + .getWidth(), hconsensus, true); + updateAnnotation(true); + if (globalColourScheme != null) { - seq = 0; + globalColourScheme.setConsensus(hconsensus); } - this.endSeq = seq; + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(consensus); + + consensus = null; + hconsensus = null; + new OOMWarning("calculating consensus", error); + } + UPDATING_CONSENSUS = false; + updatingConsensus = false; + + if (ap != null) + { + ap.paintAlignment(true); + } } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * update the consensus annotation from the sequence profile data using + * current visualization settings. */ - public int getEndSeq() + public void updateAnnotation() { - return endSeq; + updateAnnotation(false); } - /** - * DOCUMENT ME! - * - * @param f DOCUMENT ME! - */ - public void setFont(Font f) + protected void updateAnnotation(boolean immediate) { - font = f; - - Container c = new Container(); - - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. + if (immediate + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + AAFrequency.completeConsensus(consensus, hconsensus, 0, + hconsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() + // --------START Structure Conservation + public void updateStrucConsensus(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (strucConsensus == null || !autoCalculateStrucConsensus) { - return font; + return; } + strucConsensusThread = new StrucConsensusThread(ap); + strucConsensusThread.start(); + } - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setCharWidth(int w) - { - this.charWidth = w; - } + class StrucConsensusThread extends Thread + { + AlignmentPanel ap; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() + public StrucConsensusThread(AlignmentPanel ap) { - return charWidth; + this.ap = ap; } - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setCharHeight(int h) + public void run() { - this.charHeight = h; - } + updatingStrucConsensus = true; + while (UPDATING_STRUC_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() - { - return charHeight; - } + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setWrappedWidth(int w) - { - this.wrappedWidth = w; - } + UPDATING_STRUC_CONSENSUS = true; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() - { - return wrappedWidth; - } + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) + { + updatingStrucConsensus = false; + UPDATING_STRUC_CONSENSUS = false; + return; + } + strucConsensus.annotations = null; + strucConsensus.annotations = new Annotation[aWidth]; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public AlignmentI getAlignment() - { - return alignment; - } + hStrucConsensus = new Hashtable[aWidth]; - /** - * DOCUMENT ME! - * - * @param align DOCUMENT ME! - */ - public void setAlignment(AlignmentI align) - { - this.alignment = align; - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation rnaStruc = null; + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + rnaStruc = aa[i]; + break; + } + } - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowText(boolean state) - { - showText = state; - } + AlignmentAnnotation rna = ap.av.getAlignment() + .getAlignmentAnnotation()[0]; + StructureFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hStrucConsensus, true, rnaStruc); + // TODO AlignmentAnnotation rnaStruc!!! + updateAnnotation(true); + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hStrucConsensus); + } - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setRenderGaps(boolean state) - { - renderGaps = state; - } + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(strucConsensus); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() - { - return showColourText; - } + strucConsensus = null; + hStrucConsensus = null; + new OOMWarning("calculating structure consensus", error); + } + UPDATING_STRUC_CONSENSUS = false; + updatingStrucConsensus = false; - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setColourText(boolean state) - { - showColourText = state; + if (ap != null) + { + ap.paintAlignment(true); + } } /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * update the consensus annotation from the sequence profile data using + * current visualization settings. */ - public void setShowBoxes(boolean state) + public void updateAnnotation() { - showBoxes = state; + updateAnnotation(false); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getWrapAlignment() + protected void updateAnnotation(boolean immediate) { - return wrapAlignment; + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. + if (immediate + || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null)) + { + StructureFrequency.completeConsensus(strucConsensus, + hStrucConsensus, 0, hStrucConsensus.length, false, + showSequenceLogo); + } } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowText() - { - return showText; - } + // --------END Structure Conservation - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowBoxes() + /** + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * + * @return consensus sequence as a new sequence object + */ + public SequenceI getConsensusSeq() + { + if (consensus == null) { - return showBoxes; + updateConsensus(null); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getGapCharacter() + if (consensus == null) { - return getAlignment().getGapCharacter(); + return null; } - - /** - * DOCUMENT ME! - * - * @param gap DOCUMENT ME! - */ - public void setGapCharacter(char gap) + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) { - if (getAlignment() != null) + if (consensus.annotations[i] != null) + { + if (consensus.annotations[i].description.charAt(0) == '[') { - getAlignment().setGapCharacter(gap); + seqs.append(consensus.annotations[i].description.charAt(1)); } + else + { + seqs.append(consensus.annotations[i].displayCharacter); + } + } } - /** - * DOCUMENT ME! - * - * @param thresh DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; - } + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); + return sq; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; - } + /** + * + * + * @return null or the currently selected sequence region + */ + public SequenceGroup getSelectionGroup() + { + return selectionGroup; + } - /** - * DOCUMENT ME! - * - * @param inc DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } + /** + * Set the selection group for this window. + * + * @param sg + * - group holding references to sequences in this alignment view + * + */ + public void setSelectionGroup(SequenceGroup sg) + { + selectionGroup = sg; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() - { - return increment; - } + /** + * GUI state + * + * @return true if conservation based shading is enabled + */ + public boolean getConservationSelected() + { + return conservationColourSelected; + } + /** + * GUI state + * + * @param b + * enable conservation based shading + */ + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColumnSelection getColumnSelection() - { - return colSel; - } + /** + * GUI state + * + * @return true if percent identity threshold is applied to shading + */ + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + /** + * GUI state + * + * + * @param b + * indicate if percent identity threshold is applied to shading + */ + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartRes() + { + return startRes; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() - { - return currentTree; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndRes() + { + return endRes; + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartSeq() + { + return startSeq; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } + /** + * DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! + */ + public void setGlobalColourScheme(ColourSchemeI cs) + { + globalColourScheme = cs; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() - { - return showJVSuffix; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColourSchemeI getGlobalColourScheme() + { + return globalColourScheme; + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowJVSuffix(boolean b) - { - showJVSuffix = b; - } + /** + * DOCUMENT ME! + * + * @param res + * DOCUMENT ME! + */ + public void setStartRes(int res) + { + this.startRes = res; + } + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + public void setStartSeq(int seq) + { + this.startSeq = seq; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() + /** + * DOCUMENT ME! + * + * @param res + * DOCUMENT ME! + */ + public void setEndRes(int res) + { + if (res > (alignment.getWidth() - 1)) { - return showAnnotation; + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); + res = alignment.getWidth() - 1; } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) + if (res < 0) { - showAnnotation = b; + res = 0; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() - { - return scaleAboveWrapped; - } + this.endRes = res; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) { - return scaleLeftWrapped; + seq = alignment.getHeight(); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() + if (seq < 0) { - return scaleRightWrapped; + seq = 0; } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleAboveWrapped(boolean b) - { - scaleAboveWrapped = b; - } + this.endSeq = seq; + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndSeq() + { + return endSeq; + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) - { - scaleRightWrapped = b; - } + /** + * DOCUMENT ME! + * + * @param f + * DOCUMENT ME! + */ + public void setFont(Font f) + { + font = f; - /** - * Property change listener for changes in alignment - * - * @param listener DOCUMENT ME! - */ - public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } + Container c = new Container(); - /** - * DOCUMENT ME! - * - * @param listener DOCUMENT ME! - */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(listener); - } + java.awt.FontMetrics fm = c.getFontMetrics(font); + setCharHeight(fm.getHeight()); + setCharWidth(fm.charWidth('M')); + validCharWidth = true; + } - /** - * Property change listener for changes in alignment - * - * @param prop DOCUMENT ME! - * @param oldvalue DOCUMENT ME! - * @param newvalue DOCUMENT ME! - */ - public void firePropertyChange(String prop, Object oldvalue, Object newvalue) - { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); - } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Font getFont() + { + return font; + } - public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(ap); - if(globalColourScheme!=null) - { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); - } - } + /** + * DOCUMENT ME! + * + * @param w + * DOCUMENT ME! + */ + public void setCharWidth(int w) + { + this.charWidth = w; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getCharWidth() + { + return charWidth; + } + + /** + * DOCUMENT ME! + * + * @param h + * DOCUMENT ME! + */ + public void setCharHeight(int h) + { + this.charHeight = h; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getCharHeight() + { + return charHeight; + } + + /** + * DOCUMENT ME! + * + * @param w + * DOCUMENT ME! + */ + public void setWrappedWidth(int w) + { + this.wrappedWidth = w; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedWidth() + { + return wrappedWidth; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public AlignmentI getAlignment() + { + return alignment; + } - public boolean getIgnoreGapsConsensus() + /** + * DOCUMENT ME! + * + * @param align + * DOCUMENT ME! + */ + public void setAlignment(AlignmentI align) + { + if (alignment != null && alignment.getCodonFrames() != null) { - return ignoreGapsInConsensusCalculation; + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).removeMappings(alignment.getCodonFrames()); } - - public void setDataset(boolean b) + this.alignment = align; + if (alignment.getCodonFrames() != null) { - isDataset = b; + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); } + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setWrapAlignment(boolean state) + { + wrapAlignment = state; + } - public boolean isDataset() + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowText(boolean state) + { + showText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setRenderGaps(boolean state) + { + renderGaps = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourText() + { + return showColourText; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setColourText(boolean state) + { + showColourText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowBoxes(boolean state) + { + showBoxes = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getWrapAlignment() + { + return wrapAlignment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowText() + { + return showText; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowBoxes() + { + return showBoxes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } + + /** + * DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! + */ + public void setGapCharacter(char gap) + { + if (getAlignment() != null) { - return isDataset; + getAlignment().setGapCharacter(gap); } + } + /** + * DOCUMENT ME! + * + * @param thresh + * DOCUMENT ME! + */ + public void setThreshold(int thresh) + { + threshold = thresh; + } - public void hideSelectedColumns() - { - if (colSel.size() < 1) + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getThreshold() + { + return threshold; + } + + /** + * DOCUMENT ME! + * + * @param inc + * DOCUMENT ME! + */ + public void setIncrement(int inc) + { + increment = inc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getIncrement() + { + return increment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColumnSelection getColumnSelection() + { + return colSel; + } + + /** + * DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! + */ + public void setCurrentTree(NJTree tree) + { + currentTree = tree; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public NJTree getCurrentTree() + { + return currentTree; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setColourAppliesToAllGroups(boolean b) + { + colourAppliesToAllGroups = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourAppliesToAllGroups() + { + return colourAppliesToAllGroups; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowJVSuffix() + { + return showJVSuffix; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowJVSuffix(boolean b) + { + showJVSuffix = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowAnnotation() + { + return showAnnotation; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleAboveWrapped() + { + return scaleAboveWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleLeftWrapped() + { + return scaleLeftWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleRightWrapped() + { + return scaleRightWrapped; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleAboveWrapped(boolean b) + { + scaleAboveWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleLeftWrapped(boolean b) + { + scaleLeftWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleRightWrapped(boolean b) + { + scaleRightWrapped = b; + } + + /** + * Property change listener for changes in alignment + * + * @param listener + * DOCUMENT ME! + */ + public void addPropertyChangeListener( + java.beans.PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /** + * DOCUMENT ME! + * + * @param listener + * DOCUMENT ME! + */ + public void removePropertyChangeListener( + 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! + */ + public void firePropertyChange(String prop, Object oldvalue, + Object newvalue) + { + changeSupport.firePropertyChange(prop, oldvalue, newvalue); + } + + public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) + { + ignoreGapsInConsensusCalculation = b; + updateConsensus(ap); + if (globalColourScheme != null) { - return; + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + ignoreGapsInConsensusCalculation); } + } - colSel.hideSelectedColumns(); - setSelectionGroup(null); + public boolean getIgnoreGapsConsensus() + { + return ignoreGapsInConsensusCalculation; + } - hasHiddenColumns = true; - } + public void setDataset(boolean b) + { + isDataset = b; + } + public boolean isDataset() + { + return isDataset; + } - public void hideColumns(int start, int end) + public void hideSelectedColumns() + { + if (colSel.size() < 1) { - if(start==end) + return; + } + + colSel.hideSelectedColumns(); + setSelectionGroup(null); + + hasHiddenColumns = true; + } + + public void hideColumns(int start, int end) + { + if (start == end) { - colSel.hideColumns(start); + colSel.hideColumns(start); } - else + else { - colSel.hideColumns(start, end); + colSel.hideColumns(start, end); } - hasHiddenColumns = true; - } + hasHiddenColumns = true; + } - public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) - { - int sSize = sg.getSize(); - if(sSize < 2) + public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) + { + int sSize = sg.getSize(); + if (sSize < 2) { - return; + return; } - if(hiddenRepSequences==null) + if (hiddenRepSequences == null) { - hiddenRepSequences = new Hashtable(); + hiddenRepSequences = new Hashtable(); } - hiddenRepSequences.put(repSequence, sg); + hiddenRepSequences.put(repSequence, sg); - //Hide all sequences except the repSequence - SequenceI [] seqs = new SequenceI[sSize-1]; - int index = 0; - for(int i=0; i 0) { - Vector tmp = alignment.getHiddenSequences().showSequence(index - , hiddenRepSequences); - if(tmp.size()>0) + if (selectionGroup == null) { - if(selectionGroup==null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); - } - - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); - } - firePropertyChange("alignment", null, alignment.getSequences()); + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); } - if(alignment.getHiddenSequences().getSize()<1) - { - hasHiddenRows = false; + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); } - } - public void showColumn(int col) - { - colSel.revealHiddenColumns(col); - if(colSel.getHiddenColumns()==null) + if (alignment.getHiddenSequences().getSize() < 1) { - hasHiddenColumns = false; + hasHiddenRows = false; } } - public void showAllHiddenColumns() + public void showColumn(int col) + { + colSel.revealHiddenColumns(col); + if (colSel.getHiddenColumns() == null) { - colSel.revealAllHiddenColumns(); hasHiddenColumns = false; } + } - public void showAllHiddenSeqs() + public void showAllHiddenColumns() + { + colSel.revealAllHiddenColumns(); + hasHiddenColumns = false; + } + + public void showAllHiddenSeqs() + { + if (alignment.getHiddenSequences().getSize() > 0) { - if(alignment.getHiddenSequences().getSize()>0) + if (selectionGroup == null) { - if(selectionGroup==null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); - } - Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences); - for(int t=0; t