X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=fb77cf32ebdd7e369d85cf2162d558abd7f90dc1;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=cef87f7ca9b76497471470ebd6fca82a902742c9;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index cef87f7..fb77cf3 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,505 +1,1692 @@ -package jalview.appletgui; - -import java.awt.*; -import jalview.bin.*; -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import java.util.*; - -public class AlignViewport -{ - int startRes; - int endRes; - - int startSeq; - int endSeq; - - boolean showFullId = true; - boolean showText=true; - boolean showColourText=false; - boolean showBoxes=true; - boolean wrapAlignment=false; - boolean renderGaps = true; - boolean showSequenceFeatures = false; - boolean showAnnotation = true; - boolean showConservation = true; - boolean showQuality = true; - boolean showConsensus = true; - - boolean colourAppliesToAllGroups = true; - ColourSchemeI globalColourScheme = null; - boolean conservationColourSelected = false; - boolean abovePIDThreshold = false; - - SequenceGroup selectionGroup = new SequenceGroup(); - - int charHeight; - int charWidth; - int chunkWidth; - int chunkHeight; - - Font font = new Font("SansSerif",Font.PLAIN,10); - AlignmentI alignment; - - ColumnSelection colSel = new ColumnSelection(); - - int threshold; - int increment; - - NJTree currentTree = null; - - boolean scaleAboveWrapped = true; - boolean scaleLeftWrapped = true; - boolean scaleRightWrapped = true; - - public AlignViewport(AlignmentI al, JalviewLite applet) - { - setAlignment(al); - this.startRes = 0; - this.endRes = al.getWidth()-1; - this.startSeq = 0; - this.endSeq = al.getHeight()-1; - setFont(font); - - - if(applet!=null) - { - String param = applet.getParameter("showFullId"); - if (param != null) - showFullId = Boolean.valueOf(param).booleanValue(); - - param = applet.getParameter("showAnnotation"); - if (param != null) - showAnnotation = Boolean.valueOf(param).booleanValue(); - - param = applet.getParameter("showConservation"); - if (param != null) - showConservation = Boolean.valueOf(param).booleanValue(); - - param = applet.getParameter("showQuality"); - if (param != null) - showQuality = Boolean.valueOf(param).booleanValue(); - - param = applet.getParameter("showConsensus"); - if (param != null) - showConsensus = Boolean.valueOf(param).booleanValue(); - } - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - updateConservation(); - updateConsensus(); - - if(applet!=null && applet.getParameter("defaultColour")!=null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - applet.getParameter("defaultColour")); - if(globalColourScheme!=null) - globalColourScheme.setConsensus( vconsensus ); - } - } - - - public void showSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - public Vector vconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; - - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - public void updateConservation() - { - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, - alignment.getWidth()-1); - cons.calculate(); - cons.verdict(false, ConsPercGaps); - cons.findQuality(); - int alWidth = alignment.getWidth(); - Annotation [] annotations = new Annotation[alWidth]; - Annotation [] qannotations = new Annotation[alWidth]; - String sequence = cons.getConsSequence().getSequence(); - float minR,minG,minB, maxR,maxG,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 = cons.qualityRange[0].floatValue(); - float qmax = cons.qualityRange[1].floatValue(); - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - try - { - value = Integer.parseInt(sequence.charAt(i) + ""); - } - catch (Exception ex) - { - if (sequence.charAt(i) == '*') value = 11; - if (sequence.charAt(i) == '+') value = 10; - } - float vprop = value-min; - vprop/=max; - annotations[i] = new Annotation(sequence.charAt(i) + "", - "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop)); - // Quality calc - value = ((Double) cons.quality.elementAt(i)).floatValue(); - vprop = value - qmin; - vprop/=qmax; - qannotations[i] = new Annotation(" ", - String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop)); - } - - if(conservation==null) - { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than "+ConsPercGaps+"% gaps", - annotations, - 0f, // cons.qualityRange[0].floatValue(), - 11f, // cons.qualityRange[1].floatValue() - 1); - if(showConservation) - alignment.addAnnotation(conservation); - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), - 1); - if(showQuality) - alignment.addAnnotation(quality); - } - else { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); - } - - - } - - public void updateConsensus() - { - Annotation [] annotations = new Annotation[alignment.getWidth()]; - - // this routine prevents vconsensus becoming a new object each time - // consenus is calculated. Important for speed of Blosum62 - // and PID colouring of alignment - if(vconsensus == null) - vconsensus = alignment.getAAFrequency(); - else - { - Vector temp = alignment.getAAFrequency(); - vconsensus.removeAllElements(); - Enumeration e = temp.elements(); - while(e.hasMoreElements()) - { - vconsensus.addElement(e.nextElement()); - } - } - Hashtable hash = null; - for (int i = 0; i2) - { - mouseOver = "["+maxRes+"] "; - maxRes = "+ "; - } - - mouseOver += (int)value+"%"; - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - - } - - if(consensus==null) - { - consensus = new AlignmentAnnotation("Consensus", - "PID", annotations, 0f, 100f, 1); - if(showConsensus) - alignment.addAnnotation(consensus); - } - else - consensus.annotations = annotations; - - } - - - public SequenceGroup getSelectionGroup() - { - return selectionGroup; - } - - public void setSelectionGroup(SequenceGroup sg) - { - selectionGroup = sg; - } - - - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - - public int getStartRes() { - return startRes; - } - - public int getEndRes() { - return endRes; - } - - public int getStartSeq() { - return startSeq; - } - - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } - - public ColourSchemeI getGlobalColourScheme() - { - return globalColourScheme; - } - - - public void setStartRes(int res) { - this.startRes = res; - } - public void setStartSeq(int seq) { - this.startSeq = seq; - } - public void setEndRes(int res) { - if (res > alignment.getWidth()-1) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); - res = alignment.getWidth()-1; - } - if (res < 0) { - res = 0; - } - this.endRes = res; - } - public void setEndSeq(int seq) { - if (seq > alignment.getHeight()) { - seq = alignment.getHeight(); - } - if (seq < 0) { - seq = 0; - } - this.endSeq = seq; - } - public int getEndSeq() { - return endSeq; - } - - public void setFont(Font f) { - font = f; - java.awt.Frame temp = new java.awt.Frame(); - temp.addNotify(); - java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - } - - public Font getFont() { - return font; - } - public void setCharWidth(int w) { - this.charWidth = w; - } - public int getCharWidth() { - return charWidth; - } - public void setCharHeight(int h) { - this.charHeight = h; - } - public int getCharHeight() { - return charHeight; - } - public void setChunkWidth(int w) { - this.chunkWidth = w; - } - public int getChunkWidth() { - return chunkWidth; - } - public void setChunkHeight(int h) { - this.chunkHeight = h; - } - public int getChunkHeight() { - return chunkHeight; - } - public AlignmentI getAlignment() { - return alignment; - } - public void setAlignment(AlignmentI align) { - this.alignment = align; - } - - public void setWrapAlignment(boolean state) { - wrapAlignment = state; - } - public void setShowText(boolean state) { - showText = state; - } - - public void setRenderGaps(boolean state){ - renderGaps = state; - } - - - public boolean getColourText() - { - return showColourText; - } - - public void setColourText(boolean state) - { - showColourText = state; - } - - public void setShowBoxes(boolean state) { - showBoxes = state; - } - - public boolean getWrapAlignment() { - return wrapAlignment; - } - public boolean getShowText() { - return showText; - } - public boolean getShowBoxes() { - return showBoxes; - } - - public char getGapCharacter() { - return getAlignment().getGapCharacter(); - } - public void setGapCharacter(char gap) { - if (getAlignment() != null) { - getAlignment().setGapCharacter(gap); - } - } - public void setThreshold(int thresh) { - threshold = thresh; - } - public int getThreshold() { - return threshold; - } - public void setIncrement(int inc) { - increment = inc; - } - public int getIncrement() { - return increment; - } - public int getIndex(int y) { - int y1 = 0; - int starty = getStartSeq(); - int endy = getEndSeq(); - - for (int i = starty; i <= endy; i++) { - if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) { - int y2 = y1 + getCharHeight(); - - if (y>=y1 && y <=y2) { - return i; - } - y1 = y2; - } else { - return -1; - } - } - return -1; - } - - public ColumnSelection getColumnSelection() { - return colSel; - } - - public void resetSeqLimits(int height) { - setEndSeq(height/getCharHeight()); - } - public void setCurrentTree(NJTree tree) { - currentTree = tree; - } - public NJTree getCurrentTree() { - return currentTree; - } - - - public void setColourAppliesToAllGroups(boolean b) - { colourAppliesToAllGroups = b; } - - public boolean getColourAppliesToAllGroups() - {return colourAppliesToAllGroups; } - - public boolean getShowFullId() - { - return showFullId; - } - - public void setShowFullId(boolean b) - { - showFullId = b; - } - - public boolean getShowAnnotation() - { - return showAnnotation; - } - - public void setShowAnnotation(boolean b) - { - showAnnotation = b; - } - - public boolean getScaleAboveWrapped() - { return scaleAboveWrapped;} - - public boolean getScaleLeftWrapped() - { return scaleLeftWrapped; } - - public boolean getScaleRightWrapped() - { return scaleRightWrapped; } - - public void setScaleAboveWrapped(boolean b) - { scaleAboveWrapped = b; } - - public void setScaleLeftWrapped(boolean b) - { scaleLeftWrapped = b; } - - public void setScaleRightWrapped(boolean b) - { scaleRightWrapped = b; } - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * 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 . + */ +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; + +import jalview.analysis.*; +import jalview.bin.*; +import jalview.datamodel.*; +import jalview.schemes.*; + +public class AlignViewport +{ + int startRes; + + int endRes; + + int startSeq; + + int endSeq; + + boolean cursorMode = false; + + 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 showConservation = true; + + boolean showQuality = true; + + boolean showConsensus = true; + + boolean upperCasebold = false; + + boolean colourAppliesToAllGroups = true; + + ColourSchemeI globalColourScheme = null; + + boolean conservationColourSelected = false; + + boolean abovePIDThreshold = false; + + SequenceGroup selectionGroup; + + int charHeight; + + int charWidth; + + int wrappedWidth; + + Font font = new Font("SansSerif", Font.PLAIN, 10); + + boolean validCharWidth = true; + + AlignmentI alignment; + + ColumnSelection colSel = new ColumnSelection(); + + int threshold; + + int increment; + + NJTree currentTree = null; + + boolean scaleAboveWrapped = true; + + boolean scaleLeftWrapped = true; + + boolean scaleRightWrapped = true; + + // The following vector holds the features which are + // currently visible, in the correct order or rendering + public Hashtable featuresDisplayed; + + boolean hasHiddenColumns = false; + + boolean hasHiddenRows = false; + + boolean showHiddenMarkers = true; + + public Hashtable[] hconsensus; + + AlignmentAnnotation consensus; + + AlignmentAnnotation conservation; + + AlignmentAnnotation quality; + + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + + boolean autocalculateConsensus = true; + + public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! + + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); + + boolean ignoreGapsInConsensusCalculation = false; + + jalview.bin.JalviewLite applet; + + Hashtable sequenceColours; + + boolean MAC = false; + + Stack historyList = new Stack(); + + Stack redoList = new Stack(); + + String sequenceSetID; + + Hashtable hiddenRepSequences; + + public AlignViewport(AlignmentI al, JalviewLite applet) + { + this.applet = applet; + setAlignment(al); + this.startRes = 0; + this.endRes = al.getWidth() - 1; + this.startSeq = 0; + this.endSeq = al.getHeight() - 1; + if (applet != null) + { + // get the width and height scaling factors if they were specified + String param = applet.getParameter("widthScale"); + if (param != null) + { + try + { + widthScale = new Float(param).floatValue(); + } catch (Exception e) + { + } + if (widthScale <= 1.0) + { + System.err + .println("Invalid alignment character width scaling factor (" + + widthScale + "). Ignoring."); + widthScale = 1; + } + if (applet.debug) + { + System.err + .println("Alignment character width scaling factor is now " + + widthScale); + } + } + param = applet.getParameter("heightScale"); + if (param != null) + { + try + { + heightScale = new Float(param).floatValue(); + } catch (Exception e) + { + } + if (heightScale <= 1.0) + { + System.err + .println("Invalid alignment character height scaling factor (" + + heightScale + "). Ignoring."); + heightScale = 1; + } + if (applet.debug) + { + System.err + .println("Alignment character height scaling factor is now " + + heightScale); + } + } + } + setFont(font); + + MAC = new jalview.util.Platform().isAMac(); + + if (applet != null) + { + String param = applet.getParameter("showFullId"); + if (param != null) + { + showJVSuffix = Boolean.valueOf(param).booleanValue(); + } + + param = applet.getParameter("showAnnotation"); + if (param != null) + { + showAnnotation = Boolean.valueOf(param).booleanValue(); + } + + param = applet.getParameter("showConservation"); + if (param != null) + { + showConservation = Boolean.valueOf(param).booleanValue(); + } + + param = applet.getParameter("showQuality"); + if (param != null) + { + showQuality = Boolean.valueOf(param).booleanValue(); + } + + param = applet.getParameter("showConsensus"); + if (param != null) + { + showConsensus = Boolean.valueOf(param).booleanValue(); + } + + param = applet.getParameter("showUnconserved"); + if (param != null) + { + this.showUnconserved = Boolean.valueOf(param).booleanValue(); + } + + param = applet.getParameter("upperCase"); + if (param != null) + { + if (param.equalsIgnoreCase("bold")) + { + upperCasebold = true; + } + } + param = applet.getParameter("sortByTree"); + if (param != null) + { + sortByTree = Boolean.valueOf(param).booleanValue(); + } + + } + + if (applet != null) + { + String colour = applet.getParameter("defaultColour"); + + if (colour == null) + { + colour = applet.getParameter("userDefinedColour"); + if (colour != null) + { + colour = "User Defined"; + } + } + + if (colour != null) + { + globalColourScheme = ColourSchemeProperty.getColour(alignment, + colour); + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + } + + if (applet.getParameter("userDefinedColour") != null) + { + ((UserColourScheme) globalColourScheme).parseAppletParameter(applet + .getParameter("userDefinedColour")); + } + } + if (hconsensus == null) + { + 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 (showConservation) + { + alignment.addAnnotation(conservation); + } + + if (showQuality) + { + 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); + } + } + + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (showConsensus) + { + alignment.addAnnotation(consensus); + } + } + + } + + public void showSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + + public boolean getShowSequenceFeatures() + { + 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.paintAlignment(false); + } + 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; + } + // TODO - refactor to use a graduatedColorScheme to calculate the + // histogram colors. + 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.elementAt(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) + { + System.out.println("Out of memory calculating conservation!!"); + conservation = null; + quality = null; + System.gc(); + } + + UPDATING_CONSERVATION = false; + updatingConservation = false; + + if (ap != null) + { + ap.paintAlignment(true); + } + + } + } + + ConservationThread conservationThread; + + ConsensusThread consensusThread; + + boolean consUpdateNeeded = false; + + static boolean UPDATING_CONSENSUS = false; + + static boolean UPDATING_CONSERVATION = false; + + boolean updatingConsensus = false; + + boolean updatingConservation = false; + + /** + * DOCUMENT ME! + */ + public void updateConservation(final AlignmentPanel ap) + { + if (alignment.isNucleotide() || conservation == null) + { + return; + } + + conservationThread = new ConservationThread(ap); + conservationThread.start(); + } + + /** + * DOCUMENT ME! + */ + public void updateConsensus(final AlignmentPanel ap) + { + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + } + + class ConsensusThread extends Thread + { + AlignmentPanel ap; + + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + updatingConsensus = true; + while (UPDATING_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_CONSENSUS = true; + + try + { + int aWidth = alignment.getWidth(); + if (aWidth < 0) + { + return; + } + + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; + + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment + .getWidth(), hconsensus, true); // always calculate the full profile + AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth, + ignoreGapsInConsensusCalculation, + includeAllConsensusSymbols); + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(consensus); + + consensus = null; + hconsensus = null; + System.out.println("Out of memory calculating consensus!!"); + System.gc(); + } + UPDATING_CONSENSUS = false; + updatingConsensus = 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) + { + return null; + } + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) + { + if (consensus.annotations[i] != null) + { + if (consensus.annotations[i].description.charAt(0) == '[') + { + seqs.append(consensus.annotations[i].description.charAt(1)); + } + else + { + seqs.append(consensus.annotations[i].displayCharacter); + } + } + } + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); + return sq; + } + + public SequenceGroup getSelectionGroup() + { + return selectionGroup; + } + + public void setSelectionGroup(SequenceGroup sg) + { + selectionGroup = sg; + } + + public boolean getConservationSelected() + { + return conservationColourSelected; + } + + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } + + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } + + public int getStartRes() + { + return startRes; + } + + public int getEndRes() + { + return endRes; + } + + public int getStartSeq() + { + return startSeq; + } + + public void setGlobalColourScheme(ColourSchemeI cs) + { + globalColourScheme = cs; + } + + public ColourSchemeI getGlobalColourScheme() + { + return globalColourScheme; + } + + public void setStartRes(int res) + { + this.startRes = res; + } + + public void setStartSeq(int seq) + { + this.startSeq = seq; + } + + public void setEndRes(int res) + { + if (res > alignment.getWidth() - 1) + { + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); + res = alignment.getWidth() - 1; + } + if (res < 0) + { + res = 0; + } + this.endRes = res; + } + + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) + { + seq = alignment.getHeight(); + } + if (seq < 0) + { + seq = 0; + } + this.endSeq = seq; + } + + public int getEndSeq() + { + return endSeq; + } + + java.awt.Frame nullFrame; + + protected FeatureSettings featureSettings = null; + + private float heightScale = 1, widthScale = 1; + + public void setFont(Font f) + { + font = f; + if (nullFrame == null) + { + nullFrame = new java.awt.Frame(); + nullFrame.addNotify(); + } + + java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); + setCharHeight((int) (heightScale * fm.getHeight())); + charWidth = (int) (widthScale * fm.charWidth('M')); + + if (upperCasebold) + { + Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); + fm = nullFrame.getGraphics().getFontMetrics(f2); + charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)); + } + } + + public Font getFont() + { + return font; + } + + public int getCharWidth() + { + return charWidth; + } + + public void setCharHeight(int h) + { + this.charHeight = h; + } + + public int getCharHeight() + { + return charHeight; + } + + public void setWrappedWidth(int w) + { + this.wrappedWidth = w; + } + + public int getwrappedWidth() + { + return wrappedWidth; + } + + public AlignmentI getAlignment() + { + return alignment; + } + + public void setAlignment(AlignmentI align) + { + this.alignment = align; + } + + public void setWrapAlignment(boolean state) + { + wrapAlignment = state; + } + + public void setShowText(boolean state) + { + showText = state; + } + + public void setRenderGaps(boolean state) + { + renderGaps = state; + } + + public boolean getColourText() + { + return showColourText; + } + + public void setColourText(boolean state) + { + showColourText = state; + } + + public void setShowBoxes(boolean state) + { + showBoxes = state; + } + + public boolean getWrapAlignment() + { + return wrapAlignment; + } + + public boolean getShowText() + { + return showText; + } + + public boolean getShowBoxes() + { + return showBoxes; + } + + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } + + public void setGapCharacter(char gap) + { + if (getAlignment() != null) + { + getAlignment().setGapCharacter(gap); + } + } + + public void setThreshold(int thresh) + { + threshold = thresh; + } + + public int getThreshold() + { + return threshold; + } + + public void setIncrement(int inc) + { + increment = inc; + } + + public int getIncrement() + { + return increment; + } + + public void setHiddenColumns(ColumnSelection colsel) + { + this.colSel = colsel; + if (colSel.getHiddenColumns() != null) + { + hasHiddenColumns = true; + } + } + + public ColumnSelection getColumnSelection() + { + return colSel; + } + + public void resetSeqLimits(int height) + { + setEndSeq(height / getCharHeight()); + } + + public void setCurrentTree(NJTree tree) + { + currentTree = tree; + } + + public NJTree getCurrentTree() + { + return currentTree; + } + + public void setColourAppliesToAllGroups(boolean b) + { + colourAppliesToAllGroups = b; + } + + public boolean getColourAppliesToAllGroups() + { + return colourAppliesToAllGroups; + } + + public boolean getShowJVSuffix() + { + return showJVSuffix; + } + + public void setShowJVSuffix(boolean b) + { + showJVSuffix = b; + } + + public boolean getShowAnnotation() + { + return showAnnotation; + } + + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + public boolean getScaleAboveWrapped() + { + return scaleAboveWrapped; + } + + public boolean getScaleLeftWrapped() + { + return scaleLeftWrapped; + } + + public boolean getScaleRightWrapped() + { + return scaleRightWrapped; + } + + public void setScaleAboveWrapped(boolean b) + { + scaleAboveWrapped = b; + } + + public void setScaleLeftWrapped(boolean b) + { + scaleLeftWrapped = b; + } + + public void setScaleRightWrapped(boolean b) + { + scaleRightWrapped = b; + } + + public void setIgnoreGapsConsensus(boolean b) + { + ignoreGapsInConsensusCalculation = b; + updateConsensus(null); + if (globalColourScheme != null) + { + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + ignoreGapsInConsensusCalculation); + + } + } + + /** + * 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 boolean getIgnoreGapsConsensus() + { + return ignoreGapsInConsensusCalculation; + } + + public void hideSelectedColumns() + { + if (colSel.size() < 1) + { + return; + } + + colSel.hideSelectedColumns(); + setSelectionGroup(null); + + hasHiddenColumns = true; + } + + 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); + } + } + } + } + + public void hideColumns(int start, int end) + { + if (start == end) + { + colSel.hideColumns(start); + } + else + { + colSel.hideColumns(start, end); + } + + hasHiddenColumns = true; + } + + public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) + { + int sSize = sg.getSize(); + if (sSize < 2) + { + return; + } + + if (hiddenRepSequences == null) + { + hiddenRepSequences = new Hashtable(); + } + + hiddenRepSequences.put(repSequence, sg); + + // Hide all sequences except the repSequence + SequenceI[] seqs = new SequenceI[sSize - 1]; + int index = 0; + for (int i = 0; i < sSize; i++) + { + if (sg.getSequenceAt(i) != repSequence) + { + if (index == sSize - 1) + { + return; + } + + seqs[index++] = sg.getSequenceAt(i); + } + } + + hideSequence(seqs); + + } + + public void hideAllSelectedSeqs() + { + if (selectionGroup == null || selectionGroup.getSize() < 1) + { + return; + } + + SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); + + hideSequence(seqs); + + setSelectionGroup(null); + } + + public void hideSequence(SequenceI[] seq) + { + if (seq != null) + { + for (int i = 0; i < seq.length; i++) + { + alignment.getHiddenSequences().hideSequence(seq[i]); + } + + hasHiddenRows = true; + firePropertyChange("alignment", null, alignment.getSequences()); + } + } + + public void showColumn(int col) + { + colSel.revealHiddenColumns(col); + if (colSel.getHiddenColumns() == null) + { + hasHiddenColumns = false; + } + } + + public void showAllHiddenColumns() + { + colSel.revealAllHiddenColumns(); + hasHiddenColumns = false; + } + + public void showAllHiddenSeqs() + { + if (alignment.getHiddenSequences().getSize() > 0) + { + if (selectionGroup == null) + { + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); + } + Vector tmp = alignment.getHiddenSequences().showAll( + hiddenRepSequences); + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + hasHiddenRows = false; + hiddenRepSequences = null; + } + } + + public int adjustForHiddenSeqs(int 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[] + */ + public SequenceI[] getSelectionAsNewSequence() + { + SequenceI[] sequences; + + if (selectionGroup == null) + { + sequences = alignment.getSequencesArray(); + } + else + { + sequences = selectionGroup.getSelectionAsNewSequences(alignment); + } + + return sequences; + } + + /** + * 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) + { + CigarArray selection = null; + SequenceI[] seqs = null; + int i, iSize; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + iSize = selectionGroup.getSize(); + seqs = selectionGroup.getSequencesInOrder(alignment); + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes(); // inclusive for start and end in + // SeqCigar constructor + } + else + { + iSize = alignment.getHeight(); + seqs = alignment.getSequencesArray(); + end = alignment.getWidth() - 1; + } + SeqCigar[] selseqs = new SeqCigar[iSize]; + for (i = 0; i < iSize; i++) + { + selseqs[i] = new SeqCigar(seqs[i], start, end); + } + selection = new CigarArray(selseqs); + // now construct the CigarArray operations + if (hasHiddenColumns) + { + Vector regions = colSel.getHiddenColumns(); + int[] region; + int hideStart, hideEnd; + int last = start; + for (int j = 0; last < end & j < regions.size(); j++) + { + region = (int[]) regions.elementAt(j); + hideStart = region[0]; + hideEnd = region[1]; + // edit hidden regions to selection range + if (hideStart < last) + { + if (hideEnd > last) + { + hideStart = last; + } + else + { + continue; + } + } + + if (hideStart > end) + { + break; + } + + if (hideEnd > end) + { + hideEnd = end; + } + + if (hideStart > hideEnd) + { + break; + } + /** + * form operations... + */ + if (last < hideStart) + { + selection.addOperation(CigarArray.M, hideStart - last); + } + selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); + last = hideEnd + 1; + } + // Final match if necessary. + if (last < end) + { + selection.addOperation(CigarArray.M, end - last + 1); + } + } + else + { + selection.addOperation(CigarArray.M, end - start + 1); + } + return selection; + } + + /** + * 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 + // 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); + } + 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. + * + * @return String[] + */ + public String[] getViewAsString(boolean selectedRegionOnly) + { + String[] selection = null; + SequenceI[] seqs = null; + int i, iSize; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + iSize = selectionGroup.getSize(); + seqs = selectionGroup.getSequencesInOrder(alignment); + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + iSize = alignment.getHeight(); + seqs = alignment.getSequencesArray(); + end = alignment.getWidth(); + } + + selection = new String[iSize]; + + for (i = 0; i < iSize; i++) + { + if (hasHiddenColumns) + { + StringBuffer visibleSeq = new StringBuffer(); + Vector regions = colSel.getHiddenColumns(); + + int blockStart = start, blockEnd = end; + int[] region; + int hideStart, hideEnd; + + for (int j = 0; j < regions.size(); j++) + { + region = (int[]) regions.elementAt(j); + hideStart = region[0]; + hideEnd = region[1]; + + if (hideStart < start) + { + continue; + } + + blockStart = Math.min(blockStart, hideEnd + 1); + blockEnd = Math.min(blockEnd, hideStart); + + if (blockStart > blockEnd) + { + break; + } + + visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd)); + + blockStart = hideEnd + 1; + blockEnd = end; + } + + if (end > blockStart) + { + visibleSeq.append(seqs[i].getSequence(blockStart, end)); + } + + selection[i] = visibleSeq.toString(); + } + else + { + selection[i] = seqs[i].getSequenceAsString(start, end); + } + } + + return selection; + } + + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } + + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; + } + + public Color getSequenceColour(SequenceI seq) + { + if (sequenceColours == null || !sequenceColours.containsKey(seq)) + { + return Color.white; + } + else + { + return (Color) sequenceColours.get(seq); + } + } + + public void setSequenceColour(SequenceI seq, Color col) + { + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + + if (col == null) + { + sequenceColours.remove(seq); + } + else + { + sequenceColours.put(seq, col); + } + } + + public String getSequenceSetId() + { + if (sequenceSetID == null) + { + sequenceSetID = alignment.hashCode() + ""; + } + + return sequenceSetID; + } + + public void alignmentChanged(AlignmentPanel ap) + { + alignment.padGaps(); + + if (hconsensus != null && autocalculateConsensus) + { + updateConsensus(ap); + updateConservation(ap); + } + + // Reset endRes of groups if beyond alignment width + int alWidth = alignment.getWidth(); + Vector groups = alignment.getGroups(); + if (groups != null) + { + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (sg.getEndRes() > alWidth) + { + sg.setEndRes(alWidth - 1); + } + } + } + + if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) + { + selectionGroup.setEndRes(alWidth - 1); + } + + resetAllColourSchemes(); + + // AW alignment.adjustSequenceAnnotations(); + } + + void resetAllColourSchemes() + { + ColourSchemeI cs = globalColourScheme; + if (cs != null) + { + if (cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), + alignment.getWidth()); + } + + cs.setConsensus(hconsensus); + if (cs.conservationApplied()) + { + Alignment al = (Alignment) alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, al.getSequences(), 0, al + .getWidth() - 1); + c.calculate(); + c.verdict(false, ConsPercGaps); + + cs.setConservation(c); + } + } + + int s, sSize = alignment.getGroups().size(); + for (s = 0; s < sSize; s++) + { + SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); + if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) sg.cs).resetClustalX(sg + .getSequences(hiddenRepSequences), sg.getWidth()); + } + sg.recalcConservation(); + } + } + + boolean centreColumnLabels; + + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } + + public void updateSequenceIdColours() + { + Vector groups = alignment.getGroups(); + 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++) + { + this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour); + } + } + } + } + + public boolean followHighlight = false; + + public boolean getFollowHighlight() + { + return followHighlight; + } + + /** + * show non-conserved residues only + */ + public boolean showUnconserved = false; + + /** + * when set, alignment should be reordered according to a newly opened tree + */ + public boolean sortByTree = false; + + /** + * @return the showUnconserved + */ + public boolean getShowunconserved() + { + return showUnconserved; + } + + /** + * @param showNonconserved + * the showUnconserved to set + */ + public void setShowunconserved(boolean displayNonconserved) + { + this.showUnconserved = displayNonconserved; + } + + /** + * consensus annotation includes all percentage for all symbols in column + * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 + * compatible) + */ + private boolean includeAllConsensusSymbols = false; + + /** + * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug + * 62446) + */ + boolean showGroupConservation = false; + + /** + * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug + * 62446) + */ + boolean showGroupConsensus = false; + + /** + * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE + * (bug #60064 logo rendering is not AWT 1.1 compatible) + */ + 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 showGroupConsensus + * the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + + /** + * @return the includeAllConsensusSymbols + */ + public boolean isIncludeAllConsensusSymbols() + { + return false; + } + + /** + * + * @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); + } + } + } + +}