-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import jalview.io.*;\r
-import jalview.analysis.NJTree;\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-\r
-public class AlignViewport\r
-{\r
- int startRes;\r
- int endRes;\r
-\r
- int startSeq;\r
- int endSeq;\r
-\r
- boolean showScores=false;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\r
- boolean renderGaps = false;\r
-\r
- boolean groupEdit = false;\r
-\r
- RendererI renderer = new SequenceRenderer();\r
-\r
- int charHeight;\r
- double charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
-\r
- Color backgroundColour;\r
-\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
-\r
- Selection sel = new Selection();\r
- ColumnSelection colSel = new ColumnSelection();\r
-\r
- OutputGenerator og;\r
-\r
- String visibleConsensus;\r
-\r
- int threshold;\r
- int increment;\r
-\r
- NJTree currentTree = null;\r
-\r
- int window = 50;\r
- int baseline = 30;\r
-\r
- Vector kmers;\r
-\r
- public AlignViewport(AlignmentI da,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
- this(0,da.getWidth()-1,0,da.getHeight()-1,showScores,\r
- showText,\r
- showBoxes,\r
- wrapAlignment);\r
-\r
- setAlignment(da);\r
- }\r
-\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
-\r
- this.startRes = startRes;\r
- this.endRes = endRes;\r
- this.startSeq = startSeq;\r
- this.endSeq = endSeq;\r
-\r
- this.showScores = showScores;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
- this.wrapAlignment = wrapAlignment;\r
-\r
- // og = new AlignmentOutputGenerator(this);\r
-\r
- setFont( font );\r
- }\r
-\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment,\r
- Color backgroundColour) {\r
- this(startRes,endRes,startSeq,endSeq,showScores,showText,showBoxes,wrapAlignment);\r
-\r
- this.backgroundColour = backgroundColour;\r
- }\r
-\r
-\r
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\r
- }\r
-\r
- Vector consensus = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
- {\r
- if(recalculate || consensus.size()<1)\r
- {\r
- consensus = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensus.size(); i++)\r
- {\r
- hash = (Hashtable) consensus.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
- }\r
- visibleConsensus = sb.toString();\r
- }\r
-\r
-\r
- return consensus;\r
- }\r
-\r
-\r
- public int getStartRes() {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes() {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq() {\r
- return startSeq;\r
- }\r
-\r
-\r
- public void setStartRes(int res) {\r
- this.startRes = res;\r
- }\r
- public void setStartSeq(int seq) {\r
- this.startSeq = seq;\r
- }\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
- System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() -1;\r
- }\r
- if (res < 0) {\r
- res = 0;\r
- }\r
- this.endRes = res;\r
- }\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
- seq = alignment.getHeight();\r
- }\r
- if (seq < 0) {\r
- seq = 0;\r
- }\r
- this.endSeq = seq;\r
- }\r
- public int getEndSeq() {\r
- return endSeq;\r
- }\r
-\r
- public void setFont(Font f) {\r
- font = f;\r
- javax.swing.JFrame temp = new javax.swing.JFrame();\r
- temp.addNotify();\r
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
- setCharHeight(fm.getHeight());\r
- setCharWidth(fm.charWidth('M'));\r
- }\r
-\r
- public Font getFont() {\r
- return font;\r
- }\r
- public void setCharWidth(double w) {\r
- this.charWidth = w;\r
- }\r
- public double getCharWidth() {\r
- return charWidth;\r
- }\r
- public void setCharHeight(int h) {\r
- this.charHeight = h;\r
- }\r
- public int getCharHeight() {\r
- return charHeight;\r
- }\r
- public void setChunkWidth(int w) {\r
- this.chunkWidth = w;\r
- }\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
- public void setChunkHeight(int h) {\r
- this.chunkHeight = h;\r
- }\r
- public int getChunkHeight() {\r
- return chunkHeight;\r
- }\r
- public AlignmentI getAlignment() {\r
- return alignment;\r
- }\r
- public void setAlignment(AlignmentI align) {\r
- this.alignment = align;\r
- }\r
- public void setShowScores(boolean state) {\r
- showScores = state;\r
- }\r
- public void setWrapAlignment(boolean state) {\r
- wrapAlignment = state;\r
- }\r
- public void setShowText(boolean state) {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state){\r
- renderGaps = state;\r
- if(renderer instanceof SequenceRenderer)\r
- {\r
- SequenceRenderer sr = (SequenceRenderer)renderer;\r
- sr.renderGaps(state);\r
- }\r
- }\r
-\r
-\r
- public boolean getColourText()\r
- {\r
- return showColourText;\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- showColourText = state;\r
- }\r
-\r
- public void setShowBoxes(boolean state) {\r
- showBoxes = state;\r
- }\r
- public boolean getShowScores() {\r
- return showScores;\r
- }\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
- }\r
- public boolean getShowText() {\r
- return showText;\r
- }\r
- public boolean getShowBoxes() {\r
- return showBoxes;\r
- }\r
- // public CommandParser getCommandLog() {\r
- /// return log;\r
- // }\r
- public boolean getGroupEdit() {\r
- return groupEdit;\r
- }\r
- public void setGroupEdit(boolean state) {\r
- groupEdit = state;\r
- }\r
- public char getGapCharacter() {\r
- return getAlignment().getGapCharacter();\r
- }\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
- public void setThreshold(int thresh) {\r
- threshold = thresh;\r
- }\r
- public int getThreshold() {\r
- return threshold;\r
- }\r
- public void setIncrement(int inc) {\r
- increment = inc;\r
- }\r
- public int getIncrement() {\r
- return increment;\r
- }\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
- int starty = getStartSeq();\r
- int endy = getEndSeq();\r
-\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
- int y2 = y1 + getCharHeight();\r
-\r
- if (y>=y1 && y <=y2) {\r
- return i;\r
- }\r
- y1 = y2;\r
- } else {\r
- return -1;\r
- }\r
- }\r
- return -1;\r
- }\r
- public Selection getSelection() {\r
- return sel;\r
- }\r
- public ColumnSelection getColumnSelection() {\r
- return colSel;\r
- }\r
- public OutputGenerator getOutputGenerator() {\r
- return og;\r
- }\r
- public void resetSeqLimits(int height) {\r
- setStartSeq(0);\r
- setEndSeq(height/getCharHeight());\r
- }\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
- }\r
- public NJTree getCurrentTree() {\r
- return currentTree;\r
- }\r
-\r
- public void setRenderer(RendererI rend) {\r
- this.renderer = rend;\r
- }\r
-\r
- public RendererI getRenderer() {\r
- return renderer;\r
- }\r
- public int getPIDWindow() {\r
- return window;\r
- }\r
- public void setPIDWindow(int window) {\r
- this.window = window;\r
- }\r
-\r
- public int getPIDBaseline() {\r
- return baseline;\r
- }\r
- public void setPIDBaseline(int baseline) {\r
- this.baseline = baseline;\r
- }\r
-\r
- public void setKmers(Vector kmers) {\r
- this.kmers = kmers;\r
- }\r
-\r
- public Vector getKmers() {\r
- return this.kmers;\r
- }\r
-\r
-\r
-}\r
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.gui;
+
+import jalview.analysis.*;
+
+import jalview.bin.*;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignViewport
+{
+ 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;
+ 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);
+
+ boolean ignoreGapsInConsensusCalculation = false;
+
+ boolean isDataset = false;
+
+ boolean antiAlias = false;
+
+ boolean padGaps = false;
+
+ Rectangle explodedPosition;
+
+ String viewName;
+
+ String sequenceSetID;
+
+ boolean gatherViewsHere = false;
+
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+
+ Hashtable sequenceColours;
+
+ int thresholdTextColour = 0;
+ Color textColour = Color.black;
+ Color textColour2 = Color.white;
+
+ boolean rightAlignIds = false;
+
+
+ /**
+ * 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;
+
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+ showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+
+ rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ padGaps = Cache.getDefault("PAD_GAPS", true);
+
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+ int style = 0;
+
+ if (fontStyle.equals("bold"))
+ {
+ style = 1;
+ }
+ else if (fontStyle.equals("italic"))
+ {
+ style = 2;
+ }
+
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+
+ 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;
+
+
+ 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;
+
+ alignment.addAnnotation(quality);
+ }
+ }
+
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+
+ if (Cache.getDefault("SHOW_IDENTITY", true))
+ {
+ alignment.addAnnotation(consensus);
+ }
+ }
+
+ if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+
+ if (globalColourScheme instanceof UserColourScheme)
+ {
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
+ ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
+ }
+
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+ }
+
+ wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setShowSequenceFeatures(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.repaint();
+ }
+ Thread.sleep(200);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ UPDATING_CONSERVATION = true;
+
+
+ int alWidth = alignment.getWidth();
+ if(alWidth<0)
+ return;
+
+ Conservation cons = new jalview.analysis.Conservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth -1);
+
+ cons.calculate();
+ cons.verdict(false, ConsPercGaps);
+
+ if (quality!=null)
+ {
+ cons.findQuality();
+ }
+
+ String 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.charAt(i);
+
+ if (Character.isDigit(c))
+ value = (int) (c - '0');
+ else if (c == '*')
+ value = 11;
+ else if (c == '+')
+ value = 10;
+
+ float vprop = value - min;
+ vprop /= max;
+ conservation.annotations[i] =
+ new Annotation(String.valueOf(c),
+ String.valueOf(value), ' ', value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+
+ // Quality calc
+ if (quality!=null)
+ {
+ value = ( (Double) cons.quality.get(i)).floatValue();
+ vprop = value - qmin;
+ vprop /= qmax;
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+ value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+ }
+ }
+ }
+ catch (OutOfMemoryError error)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+
+
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory calculating conservation!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ conservation = null;
+ quality = null;
+
+ System.out.println("Conservation calculation: " + error);
+ System.gc();
+
+ }
+
+ UPDATING_CONSERVATION = false;
+ updatingConservation = false;
+
+ if(ap!=null)
+ {
+ ap.repaint();
+ }
+
+ }
+ }
+
+
+ ConservationThread conservationThread;
+
+ ConsensusThread consensusThread;
+
+ 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.repaint();
+ }
+
+ 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);
+
+ 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;
+ 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();
+ }
+ 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
+ */
+ 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) {
+ 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;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sg DOCUMENT ME!
+ */
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs DOCUMENT ME!
+ */
+ public void setGlobalColourScheme(ColourSchemeI cs)
+ {
+ globalColourScheme = cs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColourSchemeI getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ /**
+ * 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!
+ *
+ * @param res DOCUMENT ME!
+ */
+ public void setEndRes(int res)
+ {
+ if (res > (alignment.getWidth() - 1))
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ this.endRes = res;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+
+ this.endSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f DOCUMENT ME!
+ */
+ public void setFont(Font f)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ setCharHeight(fm.getHeight());
+ setCharWidth(fm.charWidth('M'));
+ validCharWidth = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh DOCUMENT ME!
+ */
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * 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)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
+ }
+ }
+
+ public boolean getIgnoreGapsConsensus()
+ {
+ return ignoreGapsInConsensusCalculation;
+ }
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+
+ public void hideSelectedColumns()
+ {
+ if (colSel.size() < 1)
+ return;
+
+ colSel.hideSelectedColumns();
+ setSelectionGroup(null);
+
+ hasHiddenColumns = true;
+ }
+
+
+ public void hideColumns(int start, int end)
+ {
+ if(start==end)
+ colSel.hideColumns(start);
+ else
+ colSel.hideColumns(start, end);
+
+ hasHiddenColumns = true;
+ }
+
+ 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 showSequence(int index)
+ {
+ Vector tmp = alignment.getHiddenSequences().showSequence(index);
+ if(tmp.size()>0)
+ {
+ 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());
+ }
+
+ if(alignment.getHiddenSequences().getSize()<1)
+ hasHiddenRows = false;
+ }
+
+ 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();
+ for(int t=0; t<tmp.size(); t++)
+ {
+ selectionGroup.addSequence(
+ (SequenceI)tmp.elementAt(t), false
+ );
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ hasHiddenRows = false;
+ }
+ }
+
+ 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 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(false);
+ 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(false);
+ 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];
+ if (hasHiddenColumns) {
+ selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+ } else {
+ for(i=0; i<iSize; i++)
+ {
+ selection[i] = seqs[i].getSequence(start, end);
+ }
+
+ }
+ return selection;
+ }
+
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
+
+ public String getSequenceSetId()
+ {
+ if(sequenceSetID==null)
+ sequenceSetID = alignment.hashCode()+"";
+
+ return sequenceSetID;
+ }
+
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ if (padGaps)
+ 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();
+
+ 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(true), sg.getWidth());
+ }
+ sg.recalcConservation();
+ }
+ }
+
+
+ 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);
+ }
+
+
+}