+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
-import jalview.bin.*;\r
+\r
import jalview.analysis.*;\r
+import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.util.*;\r
\r
public class AlignViewport\r
{\r
int startSeq;\r
int endSeq;\r
\r
- boolean showFullId = true;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\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 = new SequenceGroup();\r
+ SequenceGroup selectionGroup;\r
\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
+ int charHeight;\r
+ int charWidth;\r
+ int wrappedWidth;\r
\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ boolean validCharWidth = true;\r
+ AlignmentI alignment;\r
\r
ColumnSelection colSel = new ColumnSelection();\r
\r
NJTree currentTree = null;\r
\r
boolean scaleAboveWrapped = true;\r
- boolean scaleLeftWrapped = 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
+\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.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
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.endRes = al.getWidth() - 1;\r
this.startSeq = 0;\r
- this.endSeq = al.getHeight()-1;\r
+ this.endSeq = al.getHeight() - 1;\r
setFont(font);\r
\r
+ if(System.getProperty("os.name").startsWith("Mac"))\r
+ MAC = true;\r
\r
- if(applet!=null)\r
+ if (applet != null)\r
{\r
String param = applet.getParameter("showFullId");\r
if (param != null)\r
- showFullId = Boolean.valueOf(param).booleanValue();\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
+ upperCasebold = true;\r
+ }\r
+\r
}\r
- // We must set conservation and consensus before setting colour,\r
- // as Blosum and Clustal require this to be done\r
- updateConservation();\r
- updateConsensus();\r
\r
- if(applet!=null && applet.getParameter("defaultColour")!=null)\r
+ if (applet != null)\r
{\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
- applet.getParameter("defaultColour"));\r
- if(globalColourScheme!=null)\r
- globalColourScheme.setConsensus( vconsensus );\r
- }\r
- }\r
+ String colour = applet.getParameter("defaultColour");\r
+\r
+ if(colour == null)\r
+ {\r
+ colour = applet.getParameter("userDefinedColour");\r
+ if(colour !=null)\r
+ colour = "User Defined";\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
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
+ if(applet.getParameter("userDefinedColour")!=null)\r
+ {\r
+ ((UserColourScheme)globalColourScheme).parseAppletParameter(\r
+ applet.getParameter("userDefinedColour"));\r
+ }\r
\r
- public Vector vconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\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
+\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
+\r
+ alignment.addAnnotation(quality);\r
+ }\r
+ }\r
\r
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ new Annotation[1], 0f, 100f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ consensus.hasText = true;\r
+\r
+ if (showConsensus)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- public void updateConservation()\r
+ public void showSequenceFeatures(boolean b)\r
{\r
- Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth()-1);\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
- cons.findQuality();\r
- int alWidth = alignment.getWidth();\r
- Annotation [] annotations = new Annotation[alWidth];\r
- Annotation [] qannotations = new Annotation[alWidth];\r
- String sequence = cons.getConsSequence().getSequence();\r
- float minR,minG,minB, maxR,maxG,maxB;\r
- minR = 0.3f;\r
- minG = 0.0f;\r
- minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality\r
- float min = 0f;\r
- float max = 11f;\r
- float qmin = cons.qualityRange[0].floatValue();\r
- float qmax = cons.qualityRange[1].floatValue();\r
-\r
- for (int i = 0; i < alWidth; i++)\r
+ showSequenceFeatures = b;\r
+ }\r
+\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return showSequenceFeatures;\r
+ }\r
+\r
+\r
+ class ConservationThread extends Thread\r
+ {\r
+ AlignmentPanel ap;\r
+ public ConservationThread(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ }\r
+\r
+ public void run()\r
{\r
- float value = 0;\r
try\r
+ {\r
+ updatingConservation = true;\r
+\r
+ while (UPDATING_CONSERVATION)\r
{\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
- catch (Exception ex)\r
+\r
+ UPDATING_CONSERVATION = true;\r
+\r
+\r
+ int alWidth = alignment.getWidth();\r
+ if(alWidth<0)\r
+ return;\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
- if (sequence.charAt(i) == '*') value = 11;\r
- if (sequence.charAt(i) == '+') value = 10;\r
+ cons.findQuality();\r
}\r
- float vprop = value-min;\r
- vprop/=max;\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
- // Quality calc\r
- value = ((Double) cons.quality.elementAt(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop/=qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
- }\r
\r
- if(conservation==null)\r
- {\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- 1);\r
- if(showConservation)\r
- alignment.addAnnotation(conservation);\r
- quality = new AlignmentAnnotation("Quality",\r
- "Alignment Quality based on Blosum62 scores",\r
- qannotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(),\r
- 1);\r
- if(showQuality)\r
- alignment.addAnnotation(quality);\r
- }\r
- else {\r
- conservation.annotations = annotations;\r
- quality.annotations = qannotations;\r
- quality.graphMax = cons.qualityRange[1].floatValue();\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
+ value = (int) (c - '0');\r
+ else if (c == '*')\r
+ value = 11;\r
+ else if (c == '+')\r
+ value = 10;\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
+ 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.repaint();\r
+ }\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
+ return;\r
+\r
+ conservationThread = new ConservationThread(ap);\r
+ conservationThread.start();\r
}\r
\r
- public void updateConsensus()\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConsensus(final AlignmentPanel ap)\r
{\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+ consensusThread = new ConsensusThread(ap);\r
+ consensusThread.start();\r
+ }\r
\r
- // this routine prevents vconsensus becoming a new object each time\r
- // consenus is calculated. Important for speed of Blosum62\r
- // and PID colouring of alignment\r
- if(vconsensus == null)\r
- vconsensus = alignment.getAAFrequency();\r
- else\r
+\r
+ class ConsensusThread extends Thread\r
+ {\r
+ AlignmentPanel ap;\r
+ public ConsensusThread(AlignmentPanel ap)\r
{\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.removeAllElements();\r
- Enumeration e = temp.elements();\r
- while(e.hasMoreElements())\r
- {\r
- vconsensus.addElement(e.nextElement());\r
- }\r
+ this.ap = ap;\r
}\r
- Hashtable hash = null;\r
- for (int i = 0; i<alignment.getWidth(); i++)\r
+ public void run()\r
{\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
- float value = new Float(hash.get("maxCount").toString()).floatValue();\r
- value /= new Float(hash.get("size").toString()).floatValue();\r
-\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue")+" ";\r
- String mouseOver = hash.get("maxResidue")+" ";\r
- if(maxRes.length()>2)\r
+ updatingConsensus = true;\r
+ while (UPDATING_CONSENSUS)\r
+ {\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
{\r
- mouseOver = "["+maxRes+"] ";\r
- maxRes = "+ ";\r
+ ex.printStackTrace();\r
}\r
+ }\r
\r
- mouseOver += (int)value+"%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
\r
- }\r
+ UPDATING_CONSENSUS = true;\r
+\r
+ try\r
+ {\r
+ int aWidth = alignment.getWidth();\r
+ if(aWidth<0)\r
+ return;\r
\r
- if(consensus==null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, 1);\r
- if(showConsensus)\r
- alignment.addAnnotation(consensus);\r
- }\r
- else\r
- consensus.annotations = annotations;\r
+ consensus.annotations = null;\r
+ consensus.annotations = new Annotation[aWidth];\r
\r
- }\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
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).\r
+ floatValue();\r
+ else\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).\r
+ floatValue();\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, ' ', value);\r
+ }\r
+\r
+\r
+ if (globalColourScheme != null)\r
+ globalColourScheme.setConsensus(hconsensus);\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.repaint();\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
+ return null;\r
+ StringBuffer seqs=new StringBuffer();\r
+ for (int i=0; i<consensus.annotations.length; i++) {\r
+ if (consensus.annotations[i]!=null) {\r
+ if (consensus.annotations[i].description.charAt(0) == '[')\r
+ seqs.append(consensus.annotations[i].description.charAt(1));\r
+ else\r
+ seqs.append(consensus.annotations[i].displayCharacter);\r
+ }\r
+ }\r
+ SequenceI sq = new Sequence("Consensus", seqs.toString());\r
+ sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));\r
+ return sq;\r
+ }\r
public SequenceGroup getSelectionGroup()\r
{\r
return selectionGroup;\r
selectionGroup = sg;\r
}\r
\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
\r
- public int getStartRes() {\r
+ public int getStartRes()\r
+ {\r
return startRes;\r
}\r
\r
- public int getEndRes() {\r
+ public int getEndRes()\r
+ {\r
return endRes;\r
}\r
\r
- public int getStartSeq() {\r
+ public int getStartSeq()\r
+ {\r
return startSeq;\r
}\r
\r
public void setGlobalColourScheme(ColourSchemeI cs)\r
{\r
- globalColourScheme = cs;\r
+ globalColourScheme = cs;\r
}\r
\r
public ColourSchemeI getGlobalColourScheme()\r
return globalColourScheme;\r
}\r
\r
-\r
- public void setStartRes(int res) {\r
+ public void setStartRes(int res)\r
+ {\r
this.startRes = res;\r
}\r
- public void setStartSeq(int seq) {\r
+\r
+ public void setStartSeq(int seq)\r
+ {\r
this.startSeq = seq;\r
}\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\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
+ res = alignment.getWidth() - 1;\r
}\r
- if (res < 0) {\r
+ if (res < 0)\r
+ {\r
res = 0;\r
}\r
this.endRes = res;\r
}\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
+\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
seq = alignment.getHeight();\r
}\r
- if (seq < 0) {\r
+ if (seq < 0)\r
+ {\r
seq = 0;\r
}\r
this.endSeq = seq;\r
}\r
- public int getEndSeq() {\r
+\r
+ public int getEndSeq()\r
+ {\r
return endSeq;\r
}\r
\r
- public void setFont(Font f) {\r
+ java.awt.Frame nullFrame;\r
+ public void setFont(Font f)\r
+ {\r
font = f;\r
- java.awt.Frame temp = new java.awt.Frame();\r
- temp.addNotify();\r
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\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
- setCharWidth(fm.charWidth('M'));\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
+ public Font getFont()\r
+ {\r
return font;\r
}\r
- public void setCharWidth(int w) {\r
- this.charWidth = w;\r
- }\r
- public int getCharWidth() {\r
+\r
+ public int getCharWidth()\r
+ {\r
return charWidth;\r
}\r
- public void setCharHeight(int h) {\r
+\r
+ public void setCharHeight(int h)\r
+ {\r
this.charHeight = h;\r
}\r
- public int getCharHeight() {\r
+\r
+ public int getCharHeight()\r
+ {\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 void setWrappedWidth(int w)\r
+ {\r
+ this.wrappedWidth = w;\r
}\r
- public int getChunkHeight() {\r
- return chunkHeight;\r
+\r
+ public int getwrappedWidth()\r
+ {\r
+ return wrappedWidth;\r
}\r
- public AlignmentI getAlignment() {\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
return alignment;\r
}\r
- public void setAlignment(AlignmentI align) {\r
+\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
this.alignment = align;\r
}\r
\r
- public void setWrapAlignment(boolean state) {\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
wrapAlignment = state;\r
}\r
- public void setShowText(boolean state) {\r
+\r
+ public void setShowText(boolean state)\r
+ {\r
showText = state;\r
}\r
\r
- public void setRenderGaps(boolean state){\r
+ public void setRenderGaps(boolean state)\r
+ {\r
renderGaps = state;\r
}\r
\r
-\r
public boolean getColourText()\r
{\r
return showColourText;\r
showColourText = state;\r
}\r
\r
- public void setShowBoxes(boolean state) {\r
+ public void setShowBoxes(boolean state)\r
+ {\r
showBoxes = state;\r
}\r
\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
}\r
- public boolean getShowText() {\r
+\r
+ public boolean getShowText()\r
+ {\r
return showText;\r
}\r
- public boolean getShowBoxes() {\r
+\r
+ public boolean getShowBoxes()\r
+ {\r
return showBoxes;\r
}\r
\r
- public char getGapCharacter() {\r
+ public char getGapCharacter()\r
+ {\r
return getAlignment().getGapCharacter();\r
}\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
+\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
getAlignment().setGapCharacter(gap);\r
}\r
}\r
- public void setThreshold(int thresh) {\r
+\r
+ public void setThreshold(int thresh)\r
+ {\r
threshold = thresh;\r
}\r
- public int getThreshold() {\r
+\r
+ public int getThreshold()\r
+ {\r
return threshold;\r
}\r
- public void setIncrement(int inc) {\r
+\r
+ public void setIncrement(int inc)\r
+ {\r
increment = inc;\r
}\r
- public int getIncrement() {\r
+\r
+ public int getIncrement()\r
+ {\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
+ public void setHiddenColumns(ColumnSelection colsel)\r
+ {\r
+ this.colSel = colsel;\r
+ if(colSel.getHiddenColumns()!=null)\r
+ hasHiddenColumns = true;\r
}\r
\r
- public ColumnSelection getColumnSelection() {\r
+ public ColumnSelection getColumnSelection()\r
+ {\r
return colSel;\r
}\r
\r
- public void resetSeqLimits(int height) {\r
- setEndSeq(height/getCharHeight());\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
}\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
}\r
- public NJTree getCurrentTree() {\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
return currentTree;\r
}\r
\r
-\r
public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
+ {\r
+ colourAppliesToAllGroups = b;\r
+ }\r
\r
public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\r
+ {\r
+ return colourAppliesToAllGroups;\r
+ }\r
\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
}\r
\r
public boolean getShowAnnotation()\r
}\r
\r
public boolean getScaleAboveWrapped()\r
- { return scaleAboveWrapped;}\r
+ {\r
+ return scaleAboveWrapped;\r
+ }\r
\r
public boolean getScaleLeftWrapped()\r
- { return scaleLeftWrapped; }\r
+ {\r
+ return scaleLeftWrapped;\r
+ }\r
\r
public boolean getScaleRightWrapped()\r
- { return scaleRightWrapped; }\r
+ {\r
+ return scaleRightWrapped;\r
+ }\r
\r
public void setScaleAboveWrapped(boolean b)\r
- { scaleAboveWrapped = b; }\r
+ {\r
+ scaleAboveWrapped = b;\r
+ }\r
\r
public void setScaleLeftWrapped(boolean b)\r
- { scaleLeftWrapped = b; }\r
+ {\r
+ scaleLeftWrapped = b;\r
+ }\r
\r
public void setScaleRightWrapped(boolean b)\r
- { scaleRightWrapped = 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
+\r
+\r
+ public boolean getIgnoreGapsConsensus()\r
+ {\r
+ return ignoreGapsInConsensusCalculation;\r
+ }\r
+ public void hideSelectedColumns()\r
+ {\r
+ if (colSel.size() < 1)\r
+ return;\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
+ colSel.removeElement(i);\r
+ else\r
+ {\r
+ if (!hasHiddenColumns || colSel.isVisible(i))\r
+ {\r
+ colSel.addElement(i);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ public void hideColumns(int start, int end)\r
+ {\r
+ if(start==end)\r
+ colSel.hideColumns(start);\r
+ else\r
+ colSel.hideColumns(start, end);\r
+\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
+ public void hideAllSelectedSeqs()\r
+ {\r
+ if (selectionGroup == null)\r
+ return;\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
+ alignment.getHiddenSequences().hideSequence(seq[i]);\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
+ hasHiddenColumns = false;\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();\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
+ }\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
+ sequences = alignment.getSequencesArray();\r
+ else\r
+ sequences = selectionGroup.getSelectionAsNewSequences(alignment);\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 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(false);\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
+ 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
+ if (hideEnd > last)\r
+ {\r
+ hideStart = last;\r
+ } else\r
+ continue;\r
+ }\r
+\r
+ if (hideStart>end)\r
+ break;\r
+\r
+ if (hideEnd>end)\r
+ hideEnd=end;\r
+\r
+ if (hideStart>hideEnd)\r
+ break;\r
+ /**\r
+ * form operations...\r
+ */\r
+ if (last<hideStart)\r
+ selection.addOperation(CigarArray.M, hideStart-last);\r
+ selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);\r
+ last = hideEnd+1;\r
+ }\r
+ // Final match if necessary.\r
+ if (last<end)\r
+ selection.addOperation(CigarArray.M, end-last+1);\r
+ } else {\r
+ selection.addOperation(CigarArray.M, end-start+1);\r
+ }\r
+ return selection;\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
+ // 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
+ return new AlignmentView(aligview,\r
+ (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);\r
+ }\r
+ return null;\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(false);\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
+\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
+\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
+\r
+ blockStart = hideEnd+1;\r
+ blockEnd = end;\r
+ }\r
+\r
+ if(end>blockStart)\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));\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
+ return Color.white;\r
+ else\r
+ return (Color) sequenceColours.get(seq);\r
+ }\r
+\r
+ public void setSequenceColour(SequenceI seq, Color col)\r
+ {\r
+ if (sequenceColours == null)\r
+ sequenceColours = new Hashtable();\r
+\r
+ if (col == null)\r
+ sequenceColours.remove(seq);\r
+ else\r
+ sequenceColours.put(seq, col);\r
+ }\r
+\r
+ public String getSequenceSetId()\r
+ {\r
+ if (sequenceSetID == null)\r
+ sequenceSetID = alignment.hashCode() + "";\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
+ sg.setEndRes(alWidth-1);\r
+ }\r
+ }\r
+\r
+ if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)\r
+ selectionGroup.setEndRes(alWidth-1);\r
+\r
+ resetAllColourSchemes();\r
+\r
+ 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(true), sg.getWidth());\r
+ }\r
+ sg.recalcConservation();\r
+ }\r
+ }\r
\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff