X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=4e1da95a47cbb7e8163c7b073a671de971ea6158;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=bdc2359c0a92fa45b95ad9e241c5aaf4d6bf4894;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index bdc2359..4e1da95 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,30 +1,32 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.appletgui; +import java.util.*; + import java.awt.*; -import jalview.bin.*; + import jalview.analysis.*; +import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; -import java.util.*; public class AlignViewport { @@ -34,32 +36,35 @@ public class AlignViewport int startSeq; int endSeq; - boolean showFullId = true; - boolean showText=true; - boolean showColourText=false; - boolean showBoxes=true; - boolean wrapAlignment=false; + 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 = new SequenceGroup(); + SequenceGroup selectionGroup; - int charHeight; - int charWidth; - int chunkWidth; - int chunkHeight; + int charHeight; + int charWidth; + int wrappedWidth; - Font font = new Font("SansSerif",Font.PLAIN,10); - AlignmentI alignment; + Font font = new Font("SansSerif", Font.PLAIN, 10); + boolean validCharWidth = true; + AlignmentI alignment; ColumnSelection colSel = new ColumnSelection(); @@ -69,196 +74,504 @@ public class AlignViewport NJTree currentTree = null; boolean scaleAboveWrapped = true; - boolean scaleLeftWrapped = 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; + + 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.endRes = al.getWidth() - 1; this.startSeq = 0; - this.endSeq = al.getHeight()-1; + this.endSeq = al.getHeight() - 1; setFont(font); + if (System.getProperty("os.name").startsWith("Mac")) + { + MAC = true; + } - if(applet!=null) + if (applet != null) { String param = applet.getParameter("showFullId"); if (param != null) - showFullId = Boolean.valueOf(param).booleanValue(); + { + 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("upperCase"); + if (param != null) + { + if (param.equalsIgnoreCase("bold")) + { + upperCasebold = true; + } + } + } - // 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) + if (applet != null) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - applet.getParameter("defaultColour")); - if(globalColourScheme!=null) - globalColourScheme.setConsensus( vconsensus ); - } - } + String colour = applet.getParameter("defaultColour"); + if (colour == null) + { + colour = applet.getParameter("userDefinedColour"); + if (colour != null) + { + colour = "User Defined"; + } + } - public void showSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } + if (colour != null) + { + globalColourScheme = ColourSchemeProperty.getColour(alignment, colour); + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + } - public Vector vconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; + if (applet.getParameter("userDefinedColour") != null) + { + ( (UserColourScheme) globalColourScheme).parseAppletParameter( + applet.getParameter("userDefinedColour")); + } - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! + 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; - public void updateConservation() + if (showConsensus) + { + alignment.addAnnotation(consensus); + } + } + } + } + + public void showSequenceFeatures(boolean b) { - 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; + 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) { - value = Integer.parseInt(sequence.charAt(i) + ""); + try + { + if (ap != null) + { + ap.repaint(); + } + Thread.sleep(200); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } - catch (Exception ex) + + UPDATING_CONSERVATION = true; + + int alWidth = alignment.getWidth(); + if (alWidth < 0) { - if (sequence.charAt(i) == '*') value = 11; - if (sequence.charAt(i) == '+') value = 10; + return; } - float vprop = value-min; - vprop/=max; - annotations[i] = new Annotation(sequence.charAt(i) + "", - "", ' ', 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)); + Conservation cons = new jalview.analysis.Conservation("All", + jalview.schemes.ResidueProperties.propHash, 3, + alignment.getSequences(), 0, alWidth - 1); + + cons.calculate(); + cons.verdict(false, ConsPercGaps); + + if (quality != null) + { + cons.findQuality(); + } + + char[] sequence = cons.getConsSequence().getSequence(); + float minR; + float minG; + float minB; + float maxR; + float maxG; + float maxB; + minR = 0.3f; + minG = 0.0f; + minB = 0f; + maxR = 1.0f - minR; + maxG = 0.9f - minG; + maxB = 0f - minB; // scalable range for colouring both Conservation and Quality + + float min = 0f; + float max = 11f; + float qmin = 0f; + float qmax = 0f; + + char c; + + conservation.annotations = new Annotation[alWidth]; + + if (quality != null) + { + quality.graphMax = cons.qualityRange[1].floatValue(); + quality.annotations = new Annotation[alWidth]; + qmin = cons.qualityRange[0].floatValue(); + qmax = cons.qualityRange[1].floatValue(); + } + + for (int i = 0; i < alWidth; i++) + { + float value = 0; + + c = sequence[i]; + + if (Character.isDigit(c)) + { + value = (int) (c - '0'); + } + else if (c == '*') + { + value = 11; + } + else if (c == '+') + { + value = 10; + } + + float vprop = value - min; + vprop /= max; + conservation.annotations[i] = + new Annotation(String.valueOf(c), + String.valueOf(value), ' ', value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); + + // Quality calc + if (quality != null) + { + value = ( (Double) cons.quality.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.repaint(); + } + } + } + + ConservationThread conservationThread; + + ConsensusThread consensusThread; + + boolean consUpdateNeeded = false; + + static boolean UPDATING_CONSENSUS = false; + + static boolean UPDATING_CONSERVATION = false; + + boolean updatingConsensus = false; + + boolean updatingConservation = false; - if(conservation==null) + /** + * DOCUMENT ME! + */ + public void updateConservation(final AlignmentPanel ap) + { + if (alignment.isNucleotide() || 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(); + return; } + conservationThread = new ConservationThread(ap); + conservationThread.start(); + } + /** + * DOCUMENT ME! + */ + public void updateConsensus(final AlignmentPanel ap) + { + consensusThread = new ConsensusThread(ap); + consensusThread.start(); } - public void updateConsensus() + class ConsensusThread + extends Thread { - Annotation [] annotations = new Annotation[alignment.getWidth()]; + AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } - // 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 + public void run() { - Vector temp = alignment.getAAFrequency(); - vconsensus.removeAllElements(); - Enumeration e = temp.elements(); - while(e.hasMoreElements()) + updatingConsensus = true; + while (UPDATING_CONSENSUS) + { + try { - vconsensus.addElement(e.nextElement()); + if (ap != null) + { + ap.repaint(); + } + + Thread.sleep(200); } - } - Hashtable hash = null; - for (int i = 0; i2) + try + { + int aWidth = alignment.getWidth(); + if (aWidth < 0) { - mouseOver = "["+maxRes+"] "; - maxRes = "+ "; + return; } - mouseOver += (int)value+"%"; - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; - } + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), + 0, + alignment.getWidth(), + hconsensus); - if(consensus==null) - { - consensus = new AlignmentAnnotation("Consensus", - "PID", annotations, 0f, 100f, 1); - if(showConsensus) - alignment.addAnnotation(consensus); - } - else - consensus.annotations = annotations; + for (int i = 0; i < aWidth; i++) + { + float value = 0; + if (ignoreGapsInConsensusCalculation) + { + value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). + floatValue(); + } + else + { + value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). + floatValue(); + } + + String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); + String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + + if (maxRes.length() > 1) + { + mouseOver = "[" + maxRes + "] "; + maxRes = "+"; + } + + mouseOver += ( (int) value + "%"); + consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', + value); + } + + 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.repaint(); + } + } } + /** + * get the consensus sequence as displayed under the PID consensus annotation row. + * @return consensus sequence as a new sequence object + */ + /** + * 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() { @@ -270,42 +583,44 @@ public class AlignViewport selectionGroup = sg; } + public boolean getConservationSelected() + { + return conservationColourSelected; + } - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } - public int getStartRes() { + public int getStartRes() + { return startRes; } - public int getEndRes() { + public int getEndRes() + { return endRes; } - public int getStartSeq() { + public int getStartSeq() + { return startSeq; } public void setGlobalColourScheme(ColourSchemeI cs) { - globalColourScheme = cs; + globalColourScheme = cs; } public ColourSchemeI getGlobalColourScheme() @@ -313,91 +628,125 @@ public class AlignViewport return globalColourScheme; } - - public void setStartRes(int res) { + public void setStartRes(int res) + { this.startRes = res; } - public void setStartSeq(int seq) { + + public void setStartSeq(int seq) + { this.startSeq = seq; } - public void setEndRes(int res) { - if (res > alignment.getWidth()-1) { + + 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; + res = alignment.getWidth() - 1; } - if (res < 0) { + if (res < 0) + { res = 0; } this.endRes = res; } - public void setEndSeq(int seq) { - if (seq > alignment.getHeight()) { + + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) + { seq = alignment.getHeight(); } - if (seq < 0) { + if (seq < 0) + { seq = 0; } this.endSeq = seq; } - public int getEndSeq() { + + public int getEndSeq() + { return endSeq; } - public void setFont(Font f) { + java.awt.Frame nullFrame; + 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); + if (nullFrame == null) + { + nullFrame = new java.awt.Frame(); + nullFrame.addNotify(); + } + + java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); + charWidth = fm.charWidth('M'); + + if (upperCasebold) + { + Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); + fm = nullFrame.getGraphics().getFontMetrics(f2); + charWidth = fm.stringWidth("MMMMMMMMMMM") / 10; + } } - public Font getFont() { + public Font getFont() + { return font; } - public void setCharWidth(int w) { - this.charWidth = w; - } - public int getCharWidth() { + + public int getCharWidth() + { return charWidth; } - public void setCharHeight(int h) { + + public void setCharHeight(int h) + { this.charHeight = h; } - public int getCharHeight() { + + 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 void setWrappedWidth(int w) + { + this.wrappedWidth = w; } - public int getChunkHeight() { - return chunkHeight; + + public int getwrappedWidth() + { + return wrappedWidth; } - public AlignmentI getAlignment() { + + public AlignmentI getAlignment() + { return alignment; } - public void setAlignment(AlignmentI align) { + + public void setAlignment(AlignmentI align) + { this.alignment = align; } - public void setWrapAlignment(boolean state) { + public void setWrapAlignment(boolean state) + { wrapAlignment = state; } - public void setShowText(boolean state) { + + public void setShowText(boolean state) + { showText = state; } - public void setRenderGaps(boolean state){ + public void setRenderGaps(boolean state) + { renderGaps = state; } - public boolean getColourText() { return showColourText; @@ -408,89 +757,106 @@ public class AlignViewport showColourText = state; } - public void setShowBoxes(boolean state) { + public void setShowBoxes(boolean state) + { showBoxes = state; } - public boolean getWrapAlignment() { - return wrapAlignment; + public boolean getWrapAlignment() + { + return wrapAlignment; } - public boolean getShowText() { + + public boolean getShowText() + { return showText; } - public boolean getShowBoxes() { + + public boolean getShowBoxes() + { return showBoxes; } - public char getGapCharacter() { + public char getGapCharacter() + { return getAlignment().getGapCharacter(); } - public void setGapCharacter(char gap) { - if (getAlignment() != null) { + + public void setGapCharacter(char gap) + { + if (getAlignment() != null) + { getAlignment().setGapCharacter(gap); } } - public void setThreshold(int thresh) { + + public void setThreshold(int thresh) + { threshold = thresh; } - public int getThreshold() { + + public int getThreshold() + { return threshold; } - public void setIncrement(int inc) { + + public void setIncrement(int inc) + { increment = inc; } - public int getIncrement() { + + 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; - } + public void setHiddenColumns(ColumnSelection colsel) + { + this.colSel = colsel; + if (colSel.getHiddenColumns() != null) + { + hasHiddenColumns = true; } - return -1; } - public ColumnSelection getColumnSelection() { + public ColumnSelection getColumnSelection() + { return colSel; } - public void resetSeqLimits(int height) { - setEndSeq(height/getCharHeight()); + public void resetSeqLimits(int height) + { + setEndSeq(height / getCharHeight()); } - public void setCurrentTree(NJTree tree) { - currentTree = tree; + + public void setCurrentTree(NJTree tree) + { + currentTree = tree; } - public NJTree getCurrentTree() { + + public NJTree getCurrentTree() + { return currentTree; } - public void setColourAppliesToAllGroups(boolean b) - { colourAppliesToAllGroups = b; } + { + colourAppliesToAllGroups = b; + } public boolean getColourAppliesToAllGroups() - {return colourAppliesToAllGroups; } + { + return colourAppliesToAllGroups; + } - public boolean getShowFullId() + public boolean getShowJVSuffix() { - return showFullId; + return showJVSuffix; } - public void setShowFullId(boolean b) + public void setShowJVSuffix(boolean b) { - showFullId = b; + showJVSuffix = b; } public boolean getShowAnnotation() @@ -504,22 +870,579 @@ public class AlignViewport } public boolean getScaleAboveWrapped() - { return scaleAboveWrapped;} + { + return scaleAboveWrapped; + } public boolean getScaleLeftWrapped() - { return scaleLeftWrapped; } + { + return scaleLeftWrapped; + } public boolean getScaleRightWrapped() - { return scaleRightWrapped; } + { + return scaleRightWrapped; + } public void setScaleAboveWrapped(boolean b) - { scaleAboveWrapped = b; } + { + scaleAboveWrapped = b; + } public void setScaleLeftWrapped(boolean b) - { scaleLeftWrapped = b; } + { + scaleLeftWrapped = b; + } public void setScaleRightWrapped(boolean b) - { scaleRightWrapped = 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) + { + 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; + } + + /** + * 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(); + } + } }