-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-public class AlignViewport\r
-{\r
- int startRes;\r
- int endRes;\r
-\r
- int startSeq;\r
- int endSeq;\r
-\r
- boolean cursorMode = false;\r
-\r
- boolean showJVSuffix = true;\r
- boolean showText = true;\r
- boolean showColourText = false;\r
- boolean showBoxes = true;\r
- boolean wrapAlignment = false;\r
- boolean renderGaps = true;\r
- boolean showSequenceFeatures = false;\r
- boolean showAnnotation = true;\r
- boolean showConservation = true;\r
- boolean showQuality = true;\r
- boolean showConsensus = true;\r
- boolean upperCasebold = false;\r
-\r
- boolean colourAppliesToAllGroups = true;\r
- ColourSchemeI globalColourScheme = null;\r
- boolean conservationColourSelected = false;\r
- boolean abovePIDThreshold = false;\r
-\r
- SequenceGroup selectionGroup;\r
-\r
- int charHeight;\r
- int charWidth;\r
- int wrappedWidth;\r
-\r
- Font font = new Font("SansSerif", Font.PLAIN, 10);\r
- boolean validCharWidth = true;\r
- AlignmentI alignment;\r
-\r
- ColumnSelection colSel = new ColumnSelection();\r
-\r
- int threshold;\r
- int increment;\r
-\r
- NJTree currentTree = null;\r
-\r
- boolean scaleAboveWrapped = true;\r
- boolean scaleLeftWrapped = true;\r
- boolean scaleRightWrapped = true;\r
-\r
- // The following vector holds the features which are\r
- // currently visible, in the correct order or rendering\r
- public Hashtable featuresDisplayed;\r
-\r
- boolean hasHiddenColumns = false;\r
- boolean hasHiddenRows = false;\r
- boolean showHiddenMarkers = true;\r
-\r
- public Hashtable[] hconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\r
-\r
- boolean autocalculateConsensus = true;\r
-\r
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
-\r
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.\r
- PropertyChangeSupport(this);\r
-\r
- boolean ignoreGapsInConsensusCalculation = false;\r
-\r
- jalview.bin.JalviewLite applet;\r
-\r
- Hashtable sequenceColours;\r
-\r
- boolean MAC = false;\r
-\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
-\r
- String sequenceSetID;\r
-\r
- Hashtable hiddenRepSequences;\r
-\r
- public AlignViewport(AlignmentI al, JalviewLite applet)\r
- {\r
- this.applet = applet;\r
- setAlignment(al);\r
- this.startRes = 0;\r
- this.endRes = al.getWidth() - 1;\r
- this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
- setFont(font);\r
-\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- MAC = true;\r
- }\r
-\r
- if (applet != null)\r
- {\r
- String param = applet.getParameter("showFullId");\r
- if (param != null)\r
- {\r
- showJVSuffix = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showAnnotation");\r
- if (param != null)\r
- {\r
- showAnnotation = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showConservation");\r
- if (param != null)\r
- {\r
- showConservation = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showQuality");\r
- if (param != null)\r
- {\r
- showQuality = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showConsensus");\r
- if (param != null)\r
- {\r
- showConsensus = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("upperCase");\r
- if (param != null)\r
- {\r
- if (param.equalsIgnoreCase("bold"))\r
- {\r
- upperCasebold = true;\r
- }\r
- }\r
-\r
- }\r
-\r
- if (applet != null)\r
- {\r
- String colour = applet.getParameter("defaultColour");\r
-\r
- if (colour == null)\r
- {\r
- colour = applet.getParameter("userDefinedColour");\r
- if (colour != null)\r
- {\r
- colour = "User Defined";\r
- }\r
- }\r
-\r
- if (colour != null)\r
- {\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
- if (globalColourScheme != null)\r
- {\r
- globalColourScheme.setConsensus(hconsensus);\r
- }\r
- }\r
-\r
- if (applet.getParameter("userDefinedColour") != null)\r
- {\r
- ( (UserColourScheme) globalColourScheme).parseAppletParameter(\r
- applet.getParameter("userDefinedColour"));\r
- }\r
-\r
- if (hconsensus == null)\r
- {\r
- if (!alignment.isNucleotide())\r
- {\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than " +\r
- ConsPercGaps + "% gaps",\r
- new Annotation[1], 0f,\r
- 11f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
- conservation.hasText = true;\r
- conservation.autoCalculated = true;\r
-\r
- if (showConservation)\r
- {\r
- alignment.addAnnotation(conservation);\r
- }\r
-\r
- if (showQuality)\r
- {\r
- quality = new AlignmentAnnotation("Quality",\r
- "Alignment Quality based on Blosum62 scores",\r
- new Annotation[1],\r
- 0f,\r
- 11f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
- quality.hasText = true;\r
- quality.autoCalculated = true;\r
-\r
- alignment.addAnnotation(quality);\r
- }\r
- }\r
-\r
- consensus = new AlignmentAnnotation("Consensus", "PID",\r
- new Annotation[1], 0f, 100f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
- consensus.hasText = true;\r
- consensus.autoCalculated = true;\r
-\r
- if (showConsensus)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public boolean getShowSequenceFeatures()\r
- {\r
- return showSequenceFeatures;\r
- }\r
-\r
- class ConservationThread\r
- extends Thread\r
- {\r
- AlignmentPanel ap;\r
- public ConservationThread(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- }\r
-\r
- public void run()\r
- {\r
- try\r
- {\r
- updatingConservation = true;\r
-\r
- while (UPDATING_CONSERVATION)\r
- {\r
- try\r
- {\r
- if (ap != null)\r
- {\r
- ap.paintAlignment(true);\r
- }\r
- Thread.sleep(200);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- UPDATING_CONSERVATION = true;\r
-\r
- int alWidth = alignment.getWidth();\r
- if (alWidth < 0)\r
- {\r
- return;\r
- }\r
-\r
- Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0, alWidth - 1);\r
-\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
-\r
- if (quality != null)\r
- {\r
- cons.findQuality();\r
- }\r
-\r
- char[] sequence = cons.getConsSequence().getSequence();\r
- float minR;\r
- float minG;\r
- float minB;\r
- float maxR;\r
- float maxG;\r
- float maxB;\r
- minR = 0.3f;\r
- minG = 0.0f;\r
- minB = 0f;\r
- maxR = 1.0f - minR;\r
- maxG = 0.9f - minG;\r
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
-\r
- float min = 0f;\r
- float max = 11f;\r
- float qmin = 0f;\r
- float qmax = 0f;\r
-\r
- char c;\r
-\r
- conservation.annotations = new Annotation[alWidth];\r
-\r
- if (quality != null)\r
- {\r
- quality.graphMax = cons.qualityRange[1].floatValue();\r
- quality.annotations = new Annotation[alWidth];\r
- qmin = cons.qualityRange[0].floatValue();\r
- qmax = cons.qualityRange[1].floatValue();\r
- }\r
-\r
- for (int i = 0; i < alWidth; i++)\r
- {\r
- float value = 0;\r
-\r
- c = sequence[i];\r
-\r
- if (Character.isDigit(c))\r
- {\r
- value = (int) (c - '0');\r
- }\r
- else if (c == '*')\r
- {\r
- value = 11;\r
- }\r
- else if (c == '+')\r
- {\r
- value = 10;\r
- }\r
-\r
- float vprop = value - min;\r
- vprop /= max;\r
- conservation.annotations[i] =\r
- new Annotation(String.valueOf(c),\r
- String.valueOf(value), ' ', value,\r
- new Color(minR + (maxR * vprop),\r
- minG + (maxG * vprop),\r
- minB + (maxB * vprop)));\r
-\r
- // Quality calc\r
- if (quality != null)\r
- {\r
- value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop /= qmax;\r
- quality.annotations[i] = new Annotation(" ", String.valueOf(value),\r
- ' ',\r
- value,\r
- new Color(minR + (maxR * vprop),\r
- minG + (maxG * vprop),\r
- minB + (maxB * vprop)));\r
- }\r
- }\r
- }\r
- catch (OutOfMemoryError error)\r
- {\r
- System.out.println("Out of memory calculating conservation!!");\r
- conservation = null;\r
- quality = null;\r
- System.gc();\r
- }\r
-\r
- UPDATING_CONSERVATION = false;\r
- updatingConservation = false;\r
-\r
- if (ap != null)\r
- {\r
- ap.paintAlignment(true);\r
- }\r
-\r
- }\r
- }\r
-\r
- ConservationThread conservationThread;\r
-\r
- ConsensusThread consensusThread;\r
-\r
- boolean consUpdateNeeded = false;\r
-\r
- static boolean UPDATING_CONSENSUS = false;\r
-\r
- static boolean UPDATING_CONSERVATION = false;\r
-\r
- boolean updatingConsensus = false;\r
-\r
- boolean updatingConservation = false;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateConservation(final AlignmentPanel ap)\r
- {\r
- if (alignment.isNucleotide() || conservation == null)\r
- {\r
- return;\r
- }\r
-\r
- conservationThread = new ConservationThread(ap);\r
- conservationThread.start();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateConsensus(final AlignmentPanel ap)\r
- {\r
- consensusThread = new ConsensusThread(ap);\r
- consensusThread.start();\r
- }\r
-\r
- class ConsensusThread\r
- extends Thread\r
- {\r
- AlignmentPanel ap;\r
- public ConsensusThread(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- }\r
-\r
- public void run()\r
- {\r
- updatingConsensus = true;\r
- while (UPDATING_CONSENSUS)\r
- {\r
- try\r
- {\r
- if (ap != null)\r
- {\r
- ap.paintAlignment(true);\r
- }\r
-\r
- Thread.sleep(200);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- UPDATING_CONSENSUS = true;\r
-\r
- try\r
- {\r
- int aWidth = alignment.getWidth();\r
- if (aWidth < 0)\r
- {\r
- return;\r
- }\r
-\r
- consensus.annotations = null;\r
- consensus.annotations = new Annotation[aWidth];\r
-\r
- hconsensus = new Hashtable[aWidth];\r
- AAFrequency.calculate(alignment.getSequencesArray(),\r
- 0,\r
- alignment.getWidth(),\r
- hconsensus);\r
-\r
- for (int i = 0; i < aWidth; i++)\r
- {\r
- float value = 0;\r
- if (ignoreGapsInConsensusCalculation)\r
- {\r
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).\r
- floatValue();\r
- }\r
- else\r
- {\r
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).\r
- floatValue();\r
- }\r
-\r
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";\r
-\r
- if (maxRes.length() > 1)\r
- {\r
- mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+";\r
- }\r
-\r
- mouseOver += ( (int) value + "%");\r
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',\r
- value);\r
- }\r
-\r
- if (globalColourScheme != null)\r
- {\r
- globalColourScheme.setConsensus(hconsensus);\r
- }\r
-\r
- }\r
- catch (OutOfMemoryError error)\r
- {\r
- alignment.deleteAnnotation(consensus);\r
-\r
- consensus = null;\r
- hconsensus = null;\r
- System.out.println("Out of memory calculating consensus!!");\r
- System.gc();\r
- }\r
- UPDATING_CONSENSUS = false;\r
- updatingConsensus = false;\r
-\r
- if (ap != null)\r
- {\r
- ap.paintAlignment(true);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * get the consensus sequence as displayed under the PID consensus annotation row.\r
- * @return consensus sequence as a new sequence object\r
- */\r
- /**\r
- * get the consensus sequence as displayed under the PID consensus annotation row.\r
- * @return consensus sequence as a new sequence object\r
- */\r
- public SequenceI getConsensusSeq()\r
- {\r
- if (consensus == null)\r
- {\r
- return null;\r
- }\r
- StringBuffer seqs = new StringBuffer();\r
- for (int i = 0; i < consensus.annotations.length; i++)\r
- {\r
- if (consensus.annotations[i] != null)\r
- {\r
- if (consensus.annotations[i].description.charAt(0) == '[')\r
- {\r
- seqs.append(consensus.annotations[i].description.charAt(1));\r
- }\r
- else\r
- {\r
- seqs.append(consensus.annotations[i].displayCharacter);\r
- }\r
- }\r
- }\r
- SequenceI sq = new Sequence("Consensus", seqs.toString());\r
- sq.setDescription("Percentage Identity Consensus " +\r
- ( (ignoreGapsInConsensusCalculation) ? " without gaps" :\r
- ""));\r
- return sq;\r
- }\r
-\r
- public SequenceGroup getSelectionGroup()\r
- {\r
- return selectionGroup;\r
- }\r
-\r
- public void setSelectionGroup(SequenceGroup sg)\r
- {\r
- selectionGroup = sg;\r
- }\r
-\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
-\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
-\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
-\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq()\r
- {\r
- return startSeq;\r
- }\r
-\r
- public void setGlobalColourScheme(ColourSchemeI cs)\r
- {\r
- globalColourScheme = cs;\r
- }\r
-\r
- public ColourSchemeI getGlobalColourScheme()\r
- {\r
- return globalColourScheme;\r
- }\r
-\r
- public void setStartRes(int res)\r
- {\r
- this.startRes = res;\r
- }\r
-\r
- public void setStartSeq(int seq)\r
- {\r
- this.startSeq = seq;\r
- }\r
-\r
- public void setEndRes(int res)\r
- {\r
- if (res > alignment.getWidth() - 1)\r
- {\r
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() - 1;\r
- }\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
- this.endRes = res;\r
- }\r
-\r
- public void setEndSeq(int seq)\r
- {\r
- if (seq > alignment.getHeight())\r
- {\r
- seq = alignment.getHeight();\r
- }\r
- if (seq < 0)\r
- {\r
- seq = 0;\r
- }\r
- this.endSeq = seq;\r
- }\r
-\r
- public int getEndSeq()\r
- {\r
- return endSeq;\r
- }\r
-\r
- java.awt.Frame nullFrame;\r
- public void setFont(Font f)\r
- {\r
- font = f;\r
- if (nullFrame == null)\r
- {\r
- nullFrame = new java.awt.Frame();\r
- nullFrame.addNotify();\r
- }\r
-\r
- java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);\r
- setCharHeight(fm.getHeight());\r
- charWidth = fm.charWidth('M');\r
-\r
- if (upperCasebold)\r
- {\r
- Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());\r
- fm = nullFrame.getGraphics().getFontMetrics(f2);\r
- charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;\r
- }\r
- }\r
-\r
- public Font getFont()\r
- {\r
- return font;\r
- }\r
-\r
- public int getCharWidth()\r
- {\r
- return charWidth;\r
- }\r
-\r
- public void setCharHeight(int h)\r
- {\r
- this.charHeight = h;\r
- }\r
-\r
- public int getCharHeight()\r
- {\r
- return charHeight;\r
- }\r
-\r
- public void setWrappedWidth(int w)\r
- {\r
- this.wrappedWidth = w;\r
- }\r
-\r
- public int getwrappedWidth()\r
- {\r
- return wrappedWidth;\r
- }\r
-\r
- public AlignmentI getAlignment()\r
- {\r
- return alignment;\r
- }\r
-\r
- public void setAlignment(AlignmentI align)\r
- {\r
- this.alignment = align;\r
- }\r
-\r
- public void setWrapAlignment(boolean state)\r
- {\r
- wrapAlignment = state;\r
- }\r
-\r
- public void setShowText(boolean state)\r
- {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state)\r
- {\r
- renderGaps = state;\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
- {\r
- showBoxes = state;\r
- }\r
-\r
- public boolean getWrapAlignment()\r
- {\r
- return wrapAlignment;\r
- }\r
-\r
- public boolean getShowText()\r
- {\r
- return showText;\r
- }\r
-\r
- public boolean getShowBoxes()\r
- {\r
- return showBoxes;\r
- }\r
-\r
- public char getGapCharacter()\r
- {\r
- return getAlignment().getGapCharacter();\r
- }\r
-\r
- public void setGapCharacter(char gap)\r
- {\r
- if (getAlignment() != null)\r
- {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
-\r
- public void setThreshold(int thresh)\r
- {\r
- threshold = thresh;\r
- }\r
-\r
- public int getThreshold()\r
- {\r
- return threshold;\r
- }\r
-\r
- public void setIncrement(int inc)\r
- {\r
- increment = inc;\r
- }\r
-\r
- public int getIncrement()\r
- {\r
- return increment;\r
- }\r
-\r
- public void setHiddenColumns(ColumnSelection colsel)\r
- {\r
- this.colSel = colsel;\r
- if (colSel.getHiddenColumns() != null)\r
- {\r
- hasHiddenColumns = true;\r
- }\r
- }\r
-\r
- public ColumnSelection getColumnSelection()\r
- {\r
- return colSel;\r
- }\r
-\r
- public void resetSeqLimits(int height)\r
- {\r
- setEndSeq(height / getCharHeight());\r
- }\r
-\r
- public void setCurrentTree(NJTree tree)\r
- {\r
- currentTree = tree;\r
- }\r
-\r
- public NJTree getCurrentTree()\r
- {\r
- return currentTree;\r
- }\r
-\r
- public void setColourAppliesToAllGroups(boolean b)\r
- {\r
- colourAppliesToAllGroups = b;\r
- }\r
-\r
- public boolean getColourAppliesToAllGroups()\r
- {\r
- return colourAppliesToAllGroups;\r
- }\r
-\r
- public boolean getShowJVSuffix()\r
- {\r
- return showJVSuffix;\r
- }\r
-\r
- public void setShowJVSuffix(boolean b)\r
- {\r
- showJVSuffix = b;\r
- }\r
-\r
- public boolean getShowAnnotation()\r
- {\r
- return showAnnotation;\r
- }\r
-\r
- public void setShowAnnotation(boolean b)\r
- {\r
- showAnnotation = b;\r
- }\r
-\r
- public boolean getScaleAboveWrapped()\r
- {\r
- return scaleAboveWrapped;\r
- }\r
-\r
- public boolean getScaleLeftWrapped()\r
- {\r
- return scaleLeftWrapped;\r
- }\r
-\r
- public boolean getScaleRightWrapped()\r
- {\r
- return scaleRightWrapped;\r
- }\r
-\r
- public void setScaleAboveWrapped(boolean b)\r
- {\r
- scaleAboveWrapped = b;\r
- }\r
-\r
- public void setScaleLeftWrapped(boolean b)\r
- {\r
- scaleLeftWrapped = b;\r
- }\r
-\r
- public void setScaleRightWrapped(boolean b)\r
- {\r
- scaleRightWrapped = b;\r
- }\r
-\r
- public void setIgnoreGapsConsensus(boolean b)\r
- {\r
- ignoreGapsInConsensusCalculation = b;\r
- updateConsensus(null);\r
- if (globalColourScheme != null)\r
- {\r
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),\r
- ignoreGapsInConsensusCalculation);\r
-\r
- }\r
- }\r
-\r
- /**\r
- * Property change listener for changes in alignment\r
- *\r
- * @param listener DOCUMENT ME!\r
- */\r
- public void addPropertyChangeListener(\r
- java.beans.PropertyChangeListener listener)\r
- {\r
- changeSupport.addPropertyChangeListener(listener);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param listener DOCUMENT ME!\r
- */\r
- public void removePropertyChangeListener(\r
- java.beans.PropertyChangeListener listener)\r
- {\r
- changeSupport.removePropertyChangeListener(listener);\r
- }\r
-\r
- /**\r
- * Property change listener for changes in alignment\r
- *\r
- * @param prop DOCUMENT ME!\r
- * @param oldvalue DOCUMENT ME!\r
- * @param newvalue DOCUMENT ME!\r
- */\r
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
- {\r
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
- }\r
-\r
- public boolean getIgnoreGapsConsensus()\r
- {\r
- return ignoreGapsInConsensusCalculation;\r
- }\r
-\r
- public void hideSelectedColumns()\r
- {\r
- if (colSel.size() < 1)\r
- {\r
- return;\r
- }\r
-\r
- colSel.hideSelectedColumns();\r
- setSelectionGroup(null);\r
-\r
- hasHiddenColumns = true;\r
- }\r
-\r
- public void invertColumnSelection()\r
- {\r
- for (int i = 0; i < alignment.getWidth(); i++)\r
- {\r
- if (colSel.contains(i))\r
- {\r
- colSel.removeElement(i);\r
- }\r
- else\r
- {\r
- if (!hasHiddenColumns || colSel.isVisible(i))\r
- {\r
- colSel.addElement(i);\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void hideColumns(int start, int end)\r
- {\r
- if (start == end)\r
- {\r
- colSel.hideColumns(start);\r
- }\r
- else\r
- {\r
- colSel.hideColumns(start, end);\r
- }\r
-\r
- hasHiddenColumns = true;\r
- }\r
-\r
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)\r
- {\r
- int sSize = sg.getSize();\r
- if (sSize < 2)\r
- {\r
- return;\r
- }\r
-\r
- if (hiddenRepSequences == null)\r
- {\r
- hiddenRepSequences = new Hashtable();\r
- }\r
-\r
- hiddenRepSequences.put(repSequence, sg);\r
-\r
- //Hide all sequences except the repSequence\r
- SequenceI[] seqs = new SequenceI[sSize - 1];\r
- int index = 0;\r
- for (int i = 0; i < sSize; i++)\r
- {\r
- if (sg.getSequenceAt(i) != repSequence)\r
- {\r
- if (index == sSize - 1)\r
- {\r
- return;\r
- }\r
-\r
- seqs[index++] = sg.getSequenceAt(i);\r
- }\r
- }\r
-\r
- hideSequence(seqs);\r
-\r
- }\r
-\r
- public void hideAllSelectedSeqs()\r
- {\r
- if (selectionGroup == null || selectionGroup.getSize()<1)\r
- {\r
- return;\r
- }\r
-\r
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);\r
-\r
- hideSequence(seqs);\r
-\r
- setSelectionGroup(null);\r
- }\r
-\r
- public void hideSequence(SequenceI[] seq)\r
- {\r
- if (seq != null)\r
- {\r
- for (int i = 0; i < seq.length; i++)\r
- {\r
- alignment.getHiddenSequences().hideSequence(seq[i]);\r
- }\r
-\r
- hasHiddenRows = true;\r
- firePropertyChange("alignment", null, alignment.getSequences());\r
- }\r
- }\r
-\r
- public void showColumn(int col)\r
- {\r
- colSel.revealHiddenColumns(col);\r
- if (colSel.getHiddenColumns() == null)\r
- {\r
- hasHiddenColumns = false;\r
- }\r
- }\r
-\r
- public void showAllHiddenColumns()\r
- {\r
- colSel.revealAllHiddenColumns();\r
- hasHiddenColumns = false;\r
- }\r
-\r
- public void showAllHiddenSeqs()\r
- {\r
- if (alignment.getHiddenSequences().getSize() > 0)\r
- {\r
- if (selectionGroup == null)\r
- {\r
- selectionGroup = new SequenceGroup();\r
- selectionGroup.setEndRes(alignment.getWidth() - 1);\r
- }\r
- Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);\r
- for (int t = 0; t < tmp.size(); t++)\r
- {\r
- selectionGroup.addSequence(\r
- (SequenceI) tmp.elementAt(t), false\r
- );\r
- }\r
- firePropertyChange("alignment", null, alignment.getSequences());\r
- hasHiddenRows = false;\r
- hiddenRepSequences = null;\r
- }\r
- }\r
-\r
- public int adjustForHiddenSeqs(int alignmentIndex)\r
- {\r
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
- }\r
-\r
- /**\r
- * This method returns the a new SequenceI [] with\r
- * the selection sequence and start and end points adjusted\r
- * @return String[]\r
- */\r
- public SequenceI[] getSelectionAsNewSequence()\r
- {\r
- SequenceI[] sequences;\r
-\r
- if (selectionGroup == null)\r
- {\r
- sequences = alignment.getSequencesArray();\r
- }\r
- else\r
- {\r
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);\r
- }\r
-\r
- return sequences;\r
- }\r
-\r
- /**\r
- * This method returns the visible alignment as text, as\r
- * seen on the GUI, ie if columns are hidden they will not\r
- * be returned in the result.\r
- * Use this for calculating trees, PCA, redundancy etc on views\r
- * which contain hidden columns.\r
- * @return String[]\r
- */\r
- public jalview.datamodel.CigarArray getViewAsCigars(boolean\r
- selectedRegionOnly)\r
- {\r
- CigarArray selection = null;\r
- SequenceI[] seqs = null;\r
- int i, iSize;\r
- int start = 0, end = 0;\r
- if (selectedRegionOnly && selectionGroup != null)\r
- {\r
- iSize = selectionGroup.getSize();\r
- seqs = selectionGroup.getSequencesInOrder(alignment);\r
- start = selectionGroup.getStartRes();\r
- end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor\r
- }\r
- else\r
- {\r
- iSize = alignment.getHeight();\r
- seqs = alignment.getSequencesArray();\r
- end = alignment.getWidth() - 1;\r
- }\r
- SeqCigar[] selseqs = new SeqCigar[iSize];\r
- for (i = 0; i < iSize; i++)\r
- {\r
- selseqs[i] = new SeqCigar(seqs[i], start, end);\r
- }\r
- selection = new CigarArray(selseqs);\r
- // now construct the CigarArray operations\r
- if (hasHiddenColumns)\r
- {\r
- Vector regions = colSel.getHiddenColumns();\r
- int[] region;\r
- int hideStart, hideEnd;\r
- int last = start;\r
- for (int j = 0; last < end & j < regions.size(); j++)\r
- {\r
- region = (int[]) regions.elementAt(j);\r
- hideStart = region[0];\r
- hideEnd = region[1];\r
- // edit hidden regions to selection range\r
- if (hideStart < last)\r
- {\r
- if (hideEnd > last)\r
- {\r
- hideStart = last;\r
- }\r
- else\r
- {\r
- continue;\r
- }\r
- }\r
-\r
- if (hideStart > end)\r
- {\r
- break;\r
- }\r
-\r
- if (hideEnd > end)\r
- {\r
- hideEnd = end;\r
- }\r
-\r
- if (hideStart > hideEnd)\r
- {\r
- break;\r
- }\r
- /**\r
- * form operations...\r
- */\r
- if (last < hideStart)\r
- {\r
- selection.addOperation(CigarArray.M, hideStart - last);\r
- }\r
- selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);\r
- last = hideEnd + 1;\r
- }\r
- // Final match if necessary.\r
- if (last < end)\r
- {\r
- selection.addOperation(CigarArray.M, end - last + 1);\r
- }\r
- }\r
- else\r
- {\r
- selection.addOperation(CigarArray.M, end - start + 1);\r
- }\r
- return selection;\r
- }\r
-\r
- /**\r
- * return a compact representation of the current alignment selection to\r
- * pass to an analysis function\r
- * @param selectedOnly boolean true to just return the selected view\r
- * @return AlignmentView\r
- */\r
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)\r
- {\r
- // JBPNote:\r
- // this is here because the AlignmentView constructor modifies the CigarArray\r
- // object. Refactoring of Cigar and alignment view representation should\r
- // be done to remove redundancy.\r
- CigarArray aligview = getViewAsCigars(selectedOnly);\r
- if (aligview != null)\r
- {\r
- return new AlignmentView(aligview,\r
- (selectedOnly && selectionGroup != null) ?\r
- selectionGroup.getStartRes() : 0);\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * This method returns the visible alignment as text, as\r
- * seen on the GUI, ie if columns are hidden they will not\r
- * be returned in the result.\r
- * Use this for calculating trees, PCA, redundancy etc on views\r
- * which contain hidden columns.\r
- * @return String[]\r
- */\r
- public String[] getViewAsString(boolean selectedRegionOnly)\r
- {\r
- String[] selection = null;\r
- SequenceI[] seqs = null;\r
- int i, iSize;\r
- int start = 0, end = 0;\r
- if (selectedRegionOnly && selectionGroup != null)\r
- {\r
- iSize = selectionGroup.getSize();\r
- seqs = selectionGroup.getSequencesInOrder(alignment);\r
- start = selectionGroup.getStartRes();\r
- end = selectionGroup.getEndRes() + 1;\r
- }\r
- else\r
- {\r
- iSize = alignment.getHeight();\r
- seqs = alignment.getSequencesArray();\r
- end = alignment.getWidth();\r
- }\r
-\r
- selection = new String[iSize];\r
-\r
- for (i = 0; i < iSize; i++)\r
- {\r
- if (hasHiddenColumns)\r
- {\r
- StringBuffer visibleSeq = new StringBuffer();\r
- Vector regions = colSel.getHiddenColumns();\r
-\r
- int blockStart = start, blockEnd = end;\r
- int[] region;\r
- int hideStart, hideEnd;\r
-\r
- for (int j = 0; j < regions.size(); j++)\r
- {\r
- region = (int[]) regions.elementAt(j);\r
- hideStart = region[0];\r
- hideEnd = region[1];\r
-\r
- if (hideStart < start)\r
- {\r
- continue;\r
- }\r
-\r
- blockStart = Math.min(blockStart, hideEnd + 1);\r
- blockEnd = Math.min(blockEnd, hideStart);\r
-\r
- if (blockStart > blockEnd)\r
- {\r
- break;\r
- }\r
-\r
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
-\r
- blockStart = hideEnd + 1;\r
- blockEnd = end;\r
- }\r
-\r
- if (end > blockStart)\r
- {\r
- visibleSeq.append(seqs[i].getSequence(blockStart, end));\r
- }\r
-\r
- selection[i] = visibleSeq.toString();\r
- }\r
- else\r
- {\r
- selection[i] = seqs[i].getSequenceAsString(start, end);\r
- }\r
- }\r
-\r
- return selection;\r
- }\r
-\r
- public boolean getShowHiddenMarkers()\r
- {\r
- return showHiddenMarkers;\r
- }\r
-\r
- public void setShowHiddenMarkers(boolean show)\r
- {\r
- showHiddenMarkers = show;\r
- }\r
-\r
- public Color getSequenceColour(SequenceI seq)\r
- {\r
- if (sequenceColours == null || !sequenceColours.containsKey(seq))\r
- {\r
- return Color.white;\r
- }\r
- else\r
- {\r
- return (Color) sequenceColours.get(seq);\r
- }\r
- }\r
-\r
- public void setSequenceColour(SequenceI seq, Color col)\r
- {\r
- if (sequenceColours == null)\r
- {\r
- sequenceColours = new Hashtable();\r
- }\r
-\r
- if (col == null)\r
- {\r
- sequenceColours.remove(seq);\r
- }\r
- else\r
- {\r
- sequenceColours.put(seq, col);\r
- }\r
- }\r
-\r
- public String getSequenceSetId()\r
- {\r
- if (sequenceSetID == null)\r
- {\r
- sequenceSetID = alignment.hashCode() + "";\r
- }\r
-\r
- return sequenceSetID;\r
- }\r
-\r
- public void alignmentChanged(AlignmentPanel ap)\r
- {\r
- alignment.padGaps();\r
-\r
- if (hconsensus != null && autocalculateConsensus)\r
- {\r
- updateConsensus(ap);\r
- updateConservation(ap);\r
- }\r
-\r
- //Reset endRes of groups if beyond alignment width\r
- int alWidth = alignment.getWidth();\r
- Vector groups = alignment.getGroups();\r
- if (groups != null)\r
- {\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (sg.getEndRes() > alWidth)\r
- {\r
- sg.setEndRes(alWidth - 1);\r
- }\r
- }\r
- }\r
-\r
- if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)\r
- {\r
- selectionGroup.setEndRes(alWidth - 1);\r
- }\r
-\r
- resetAllColourSchemes();\r
-\r
- //AW alignment.adjustSequenceAnnotations();\r
- }\r
-\r
- void resetAllColourSchemes()\r
- {\r
- ColourSchemeI cs = globalColourScheme;\r
- if (cs != null)\r
- {\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) cs).\r
- resetClustalX(alignment.getSequences(),\r
- alignment.getWidth());\r
- }\r
-\r
- cs.setConsensus(hconsensus);\r
- if (cs.conservationApplied())\r
- {\r
- Alignment al = (Alignment) alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, ConsPercGaps);\r
-\r
- cs.setConservation(c);\r
- }\r
- }\r
-\r
- int s, sSize = alignment.getGroups().size();\r
- for (s = 0; s < sSize; s++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);\r
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) sg.cs).resetClustalX(\r
- sg.getSequences(hiddenRepSequences), sg.getWidth());\r
- }\r
- sg.recalcConservation();\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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.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;
+
+ 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;
+ setFont(font);
+
+ if (System.getProperty("os.name").startsWith("Mac"))
+ {
+ MAC = true;
+ }
+
+ 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("upperCase");
+ if (param != null)
+ {
+ if (param.equalsIgnoreCase("bold"))
+ {
+ upperCasebold = true;
+ }
+ }
+
+ }
+
+ 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(true);
+ }
+ Thread.sleep(200);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ UPDATING_CONSERVATION = true;
+
+ int alWidth = alignment.getWidth();
+ if (alWidth < 0)
+ {
+ return;
+ }
+
+ Conservation cons = new jalview.analysis.Conservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1);
+
+ cons.calculate();
+ cons.verdict(false, ConsPercGaps);
+
+ if (quality != null)
+ {
+ cons.findQuality();
+ }
+
+ char[] sequence = cons.getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ conservation.annotations = new Annotation[alWidth];
+
+ if (quality != null)
+ {
+ quality.graphMax = cons.qualityRange[1].floatValue();
+ quality.annotations = new Annotation[alWidth];
+ qmin = cons.qualityRange[0].floatValue();
+ qmax = cons.qualityRange[1].floatValue();
+ }
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
+
+ if (Character.isDigit(c))
+ {
+ value = (int) (c - '0');
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ float vprop = value - min;
+ vprop /= max;
+ conservation.annotations[i] =
+ new Annotation(String.valueOf(c),
+ String.valueOf(value), ' ', value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+
+ // Quality calc
+ if (quality != null)
+ {
+ value = ( (Double) cons.quality.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(true);
+ }
+
+ 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;
+ 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
+ */
+ /**
+ * 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;
+ 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(fm.getHeight());
+ 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()
+ {
+ 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;
+ }
+
+ /**
+ * 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();
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff