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
SequenceGroup selectionGroup = new SequenceGroup();\r
\r
- RendererI renderer = new SequenceRenderer(this);\r
\r
int charHeight;\r
int charWidth;\r
boolean scaleRightWrapped = true;\r
\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
+ showFullId = Preferences.showFullId;\r
+ showAnnotation = Preferences.showAnnotation;\r
+ showConservation = Preferences.showConservation;\r
+ showQuality = Preferences.showQuality;\r
+ showIdentity = Preferences.showIdentity;\r
+ showFullId = Preferences.showFullId;\r
+ String fontName = Preferences.fontName;\r
+ String fontStyle = Preferences.fontStyle;\r
+ String fontSize = Cache.getProperty("FONT_SIZE");\r
+ if (fontName != null && fontStyle != null && fontSize != null)\r
+ {\r
+ int style = 0;\r
+ if(fontStyle.equals("bold"))\r
+ style = 1;\r
+ else if(fontStyle.equals("italic"))\r
+ style = 2;\r
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));\r
+ }\r
+ else\r
+ setFont(font);\r
+\r
+ alignment.setGapCharacter(Preferences.gapSymbol);\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
+ if(Preferences.defaultColour!=null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);\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
- int percGaps = 100; // JBPNote : This should be a scalable property!\r
Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 1,\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
alignment.getSequences(), 0,\r
- alignment.getWidth());\r
+ alignment.getWidth()-1);\r
cons.calculate();\r
- cons.verdict(false, percGaps);\r
+ cons.verdict(false, ConsPercGaps);\r
cons.findQuality();\r
int alWidth = alignment.getWidth();\r
Annotation [] annotations = new Annotation[alWidth];\r
value = ((Double) cons.quality.get(i)).floatValue();\r
vprop = value - qmin;\r
vprop/=qmax;\r
- qannotations[i] = new Annotation(sequence.charAt(i) + "",\r
- new String().valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\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 "+percGaps+"% gaps",\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
cons.qualityRange[0].floatValue(),\r
cons.qualityRange[1].floatValue(),\r
1);\r
- alignment.addAnnotation(quality);\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
}\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, alWidth=alignment.getWidth(); i<alWidth; 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
if(consensus==null)\r
{\r
- consensus = new AlignmentAnnotation("% Identity",\r
+ consensus = new AlignmentAnnotation("Consensus",\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, sz=consensusV.size(); i < sz; 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
\r
public void setRenderGaps(boolean state){\r
renderGaps = state;\r
- if(renderer instanceof SequenceRenderer)\r
- {\r
- SequenceRenderer sr = (SequenceRenderer)renderer;\r
- sr.renderGaps(state);\r
- }\r
}\r
\r
\r
return currentTree;\r
}\r
\r
- public void setRenderer(RendererI rend) {\r
- this.renderer = rend;\r
- }\r
-\r
- public RendererI getRenderer() {\r
- return renderer;\r
- }\r
-\r
public void setColourAppliesToAllGroups(boolean b)\r
{ colourAppliesToAllGroups = b; }\r
\r
git://source.jalview.org / jalview.git / blobdiff