import jalview.datamodel.*;\r
import jalview.schemes.*;\r
import java.util.*;\r
+import jalview.bin.Cache;\r
\r
public class AlignViewport\r
{\r
boolean renderGaps = true;\r
boolean showSequenceFeatures = false;\r
boolean showAnnotation = true;\r
+ boolean showConservation = true;\r
+ boolean showQuality = true;\r
+ boolean showIdentity = true;\r
\r
boolean colourAppliesToAllGroups = true;\r
ColourSchemeI globalColourScheme = null;\r
\r
NJTree currentTree = null;\r
\r
+ boolean scaleAboveWrapped = false;\r
+ boolean scaleLeftWrapped = true;\r
+ boolean scaleRightWrapped = true;\r
\r
- public AlignViewport(AlignmentI al,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
\r
+ public AlignViewport(AlignmentI al)\r
+ {\r
+ setAlignment(al);\r
this.startRes = 0;\r
this.endRes = al.getWidth()-1;\r
this.startSeq = 0;\r
this.endSeq = al.getHeight()-1;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
- this.wrapAlignment = wrapAlignment;\r
\r
- setAlignment(al);\r
- setFont( font );\r
+ updateFromPreferences();\r
+\r
+ }\r
+\r
+ public void updateFromPreferences()\r
+ {\r
+ String string = Cache.getProperty("SHOW_FULL_ID");\r
+ if(string!=null)\r
+ showFullId = Boolean.valueOf(string).booleanValue();\r
+\r
+ string = Cache.getProperty("SHOW_ANNOTATIONS");\r
+ if(string!=null)\r
+ showAnnotation = Boolean.valueOf(string).booleanValue();\r
+\r
+ string = Cache.getProperty("SHOW_CONSERVATION");\r
+ if(string!=null)\r
+ showConservation = Boolean.valueOf(string).booleanValue();\r
+ string = Cache.getProperty("SHOW_QUALITY");\r
+ if(string!=null)\r
+ showQuality = Boolean.valueOf(string).booleanValue();\r
+ string = Cache.getProperty("SHOW_IDENTITY");\r
+ if(string!=null)\r
+ showIdentity = Boolean.valueOf(string).booleanValue();\r
+\r
+ string = Cache.getProperty("SHOW_FULL_ID");\r
+ if(string!=null)\r
+ showFullId = Boolean.valueOf(string).booleanValue();\r
+\r
+ String fontName = Cache.getProperty("FONT_NAME");\r
+ String fontStyle= Cache.getProperty("FONT_STYLE");\r
+ String fontSize = Cache.getProperty("FONT_SIZE");\r
+ if(fontName!=null && fontStyle!=null && fontSize!=null)\r
+ setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
+ else\r
+ setFont( font );\r
+\r
+ string = Cache.getProperty("GAP_SYMBOL");\r
+ if(string!=null)\r
+ alignment.setGapCharacter( string.charAt(0) );\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
+ string = Cache.getProperty("DEFAULT_COLOUR");\r
+ if(string!=null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, string);\r
+ if(globalColourScheme!=null)\r
+ globalColourScheme.setConsensus( vconsensus );\r
+ }\r
+\r
}\r
\r
public void showSequenceFeatures(boolean b)\r
showSequenceFeatures = b;\r
}\r
\r
+ public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\r
+\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+\r
public void updateConservation()\r
{\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
-\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
alignment.getSequences(), 0,\r
- alignment.getWidth());\r
+ alignment.getWidth()-1);\r
cons.calculate();\r
- cons.verdict(false, 100);\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 = 0f;\r
+ minG = 0.0f;\r
minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring\r
- float min = cons.qualityRange[0].floatValue();\r
- float max = cons.qualityRange[1].floatValue();\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 < alignment.getWidth(); i++)\r
+ for (int i = 0; i < alWidth; i++)\r
{\r
float value = 0;\r
try\r
- {\r
- //value = Integer.parseInt(sequence.charAt(i) + "");\r
- value = ((Double) cons.quality.get(i)).floatValue();\r
- }\r
+ {\r
+ value = Integer.parseInt(sequence.charAt(i) + "");\r
+ }\r
catch (Exception ex)\r
- {\r
- if (sequence.charAt(i) == '*') value = 10;\r
- }\r
+ {\r
+ if (sequence.charAt(i) == '*') value = 11;\r
+ if (sequence.charAt(i) == '+') value = 10;\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, minB+maxB*vprop, minB+maxB*vprop));\r
+ "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ // Quality calc\r
+ value = ((Double) cons.quality.get(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",\r
+ "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
annotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(), 1);\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
+ else {\r
conservation.annotations = annotations;\r
+ quality.annotations = qannotations;\r
+ quality.graphMax = cons.qualityRange[1].floatValue();\r
+ }\r
+\r
\r
}\r
\r
{\r
Annotation [] annotations = new Annotation[alignment.getWidth()];\r
\r
- Vector cons = alignment.getAAFrequency();\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
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.clear();\r
+ Enumeration e = temp.elements();\r
+ while(e.hasMoreElements())\r
+ {\r
+ vconsensus.add(e.nextElement());\r
+ }\r
+ }\r
Hashtable hash = null;\r
- for (int i = 0; i < alignment.getWidth(); i++)\r
+ for (int i = 0; i<alignment.getWidth(); i++)\r
{\r
- hash = (Hashtable) cons.elementAt(i);\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
float value = Float.parseFloat(hash.get("maxCount").toString());\r
value /= Float.parseFloat(hash.get("size").toString());\r
\r
{\r
consensus = new AlignmentAnnotation("% Identity",\r
"PID", annotations, 0f, 100f, 1);\r
- alignment.addAnnotation(consensus);\r
+ if(showIdentity)\r
+ alignment.addAnnotation(consensus);\r
}\r
else\r
consensus.annotations = annotations;\r
\r
}\r
\r
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\r
- }\r
-\r
- String visibleConsensus;\r
- Vector consensusV = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
- {\r
- if(recalculate || consensusV.size()<1)\r
- {\r
- consensusV = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensusV.size(); i++)\r
- {\r
- hash = (Hashtable) consensusV.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
- }\r
- visibleConsensus = sb.toString();\r
- }\r
-\r
-\r
- return consensusV;\r
- }\r
-\r
\r
public SequenceGroup getSelectionGroup()\r
{\r
public void setEndRes(int res) {\r
if (res > alignment.getWidth()-1) {\r
System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() -1;\r
+ res = alignment.getWidth()-1;\r
}\r
if (res < 0) {\r
res = 0;\r
showAnnotation = b;\r
}\r
\r
+ public boolean getScaleAboveWrapped()\r
+ { return scaleAboveWrapped;}\r
+\r
+ public boolean getScaleLeftWrapped()\r
+ { return scaleLeftWrapped; }\r
+\r
+ public boolean getScaleRightWrapped()\r
+ { return scaleRightWrapped; }\r
+\r
+ public void setScaleAboveWrapped(boolean b)\r
+ { scaleAboveWrapped = b; }\r
+\r
+ public void setScaleLeftWrapped(boolean b)\r
+ { scaleLeftWrapped = b; }\r
+\r
+ public void setScaleRightWrapped(boolean b)\r
+ { scaleRightWrapped = b; }\r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff