From af563e083b2a94e50f23d317f260fb734c52c266 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 29 Aug 2012 16:25:12 +0100 Subject: [PATCH] JAL-1153 new runtime property set to first non-null annotation element colour --- src/jalview/datamodel/AlignmentAnnotation.java | 130 +++++++++++++++--------- src/jalview/gui/Jalview2XML.java | 18 +++- src/jalview/ws/jws2/AADisorderClient.java | 1 + 3 files changed, 94 insertions(+), 55 deletions(-) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index f5d34a6..6212d4d 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -38,7 +38,7 @@ public class AlignmentAnnotation public boolean autoCalculated = false; public String annotationId; - + public SequenceI sequenceRef; /** DOCUMENT ME!! */ @@ -54,10 +54,12 @@ public class AlignmentAnnotation * RNA secondary structure contact positions */ public SequenceFeature[] _rnasecstr = null; + /** * position of annotation resulting in invalid WUSS parsing or -1 */ - private long invalidrnastruc=-1; + private long invalidrnastruc = -1; + /** * Updates the _rnasecstr field Determines the positions that base pair and * the positions of helices based on secondary structure from a Stockholm file @@ -66,30 +68,31 @@ public class AlignmentAnnotation */ private void _updateRnaSecStr(CharSequence RNAannot) { - try { - _rnasecstr = Rna.GetBasePairs(RNAannot); - invalidrnastruc=-1; - } - catch (WUSSParseException px) + try + { + _rnasecstr = Rna.GetBasePairs(RNAannot); + invalidrnastruc = -1; + } catch (WUSSParseException px) { - invalidrnastruc=px.getProblemPos(); + invalidrnastruc = px.getProblemPos(); } - if (invalidrnastruc>-1) + if (invalidrnastruc > -1) { return; } Rna.HelixMap(_rnasecstr); // setRNAStruc(RNAannot); - + if (_rnasecstr != null && _rnasecstr.length > 0) { // show all the RNA secondary structure annotation symbols. - isrna=true; + isrna = true; showAllColLabels = true; scaleColLabel = true; } // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); } + public java.util.Hashtable sequenceMapping; /** DOCUMENT ME!! */ @@ -321,65 +324,79 @@ public class AlignmentAnnotation annotationId = this.hashCode() + ""; } + /** - * flyweight access to positions in the alignment annotation row for RNA processing + * flyweight access to positions in the alignment annotation row for RNA + * processing + * * @author jimp - * + * */ - private class AnnotCharSequence implements CharSequence + private class AnnotCharSequence implements CharSequence { - int offset=0; - int max=0; - - public AnnotCharSequence() { - this(0,annotations.length); + int offset = 0; + + int max = 0; + + public AnnotCharSequence() + { + this(0, annotations.length); } - public AnnotCharSequence(int start, int end) { - offset=start; - max=end; + + public AnnotCharSequence(int start, int end) + { + offset = start; + max = end; } + @Override public CharSequence subSequence(int start, int end) { - return new AnnotCharSequence(offset+start, offset+end); + return new AnnotCharSequence(offset + start, offset + end); } - + @Override public int length() { - return max-offset; + return max - offset; } - + @Override public char charAt(int index) { String dc; - return ((index+offset<0) || (index+offset)>=max || annotations[index+offset]==null || (dc=annotations[index+offset].displayCharacter.trim()).length()<1) - ? '.' : dc.charAt(0); + return ((index + offset < 0) || (index + offset) >= max + || annotations[index + offset] == null || (dc = annotations[index + + offset].displayCharacter.trim()).length() < 1) ? '.' : dc + .charAt(0); } + public String toString() { - char[] string=new char[max-offset]; - int mx=annotations.length; - - for (int i=offset;i 0) @@ -518,9 +539,9 @@ public class AlignmentAnnotation this.label = annotation.label; this.padGaps = annotation.padGaps; this.visible = annotation.visible; - this.centreColLabels=annotation.centreColLabels; - this.scaleColLabel=annotation.scaleColLabel; - this.showAllColLabels=annotation.showAllColLabels; + this.centreColLabels = annotation.centreColLabels; + this.scaleColLabel = annotation.scaleColLabel; + this.showAllColLabels = annotation.showAllColLabels; this.calcId = annotation.calcId; if (this.hasScore = annotation.hasScore) { @@ -572,7 +593,7 @@ public class AlignmentAnnotation } } // TODO: check if we need to do this: JAL-952 - //if (this.isrna=annotation.isrna) + // if (this.isrna=annotation.isrna) { // _rnasecstr=new SequenceFeature[annotation._rnasecstr]; } @@ -964,11 +985,12 @@ public class AlignmentAnnotation { if (seqname && this.sequenceRef != null) { - int i=description.toLowerCase().indexOf(""); - if (i>-1) + int i = description.toLowerCase().indexOf(""); + if (i > -1) { // move the html tag to before the sequence reference. - return ""+sequenceRef.getName()+" : "+description.substring(i+6); + return "" + sequenceRef.getName() + " : " + + description.substring(i + 6); } return sequenceRef.getName() + " : " + description; } @@ -977,8 +999,9 @@ public class AlignmentAnnotation public boolean isValidStruc() { - return invalidrnastruc==-1; + return invalidrnastruc == -1; } + public long getInvalidStrucPos() { return invalidrnastruc; @@ -987,7 +1010,14 @@ public class AlignmentAnnotation /** * machine readable ID string indicating what generated this annotation */ - protected String calcId=""; + protected String calcId = ""; + + /** + * base colour for line graphs. If null, will be set automatically by + * searching the alignment annotation + */ + public java.awt.Color _linecolour; + public String getCalcId() { return calcId; @@ -997,5 +1027,5 @@ public class AlignmentAnnotation { this.calcId = calcId; } - + } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 8872be0..bde3035 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -2267,16 +2267,19 @@ public class Jalview2XML // Construct new annotation from model. AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; - + java.awt.Color firstColour=null; + int anpos; if (!an[i].getScoreOnly()) { anot = new jalview.datamodel.Annotation[al.getWidth()]; for (int aa = 0; aa < ae.length && aa < anot.length; aa++) { - if (ae[aa].getPosition() >= anot.length) + anpos = ae[aa].getPosition(); + + if (anpos >= anot.length) continue; - anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( + anot[anpos] = new jalview.datamodel.Annotation( ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa].getSecondaryStructure() == null || ae[aa] @@ -2292,8 +2295,12 @@ public class Jalview2XML // { // anot[ae[aa].getPosition()].displayCharacter = ""; // } - anot[ae[aa].getPosition()].colour = new java.awt.Color( + anot[anpos].colour = new java.awt.Color( ae[aa].getColour()); + if (firstColour==null) + { + firstColour=anot[anpos].colour; + } } } jalview.datamodel.AlignmentAnnotation jaa = null; @@ -2309,7 +2316,7 @@ public class Jalview2XML an[i].getGraphType()); jaa.graphGroup = an[i].getGraphGroup(); - + jaa._linecolour=firstColour; if (an[i].getThresholdLine() != null) { jaa.setThreshold(new jalview.datamodel.GraphLine(an[i] @@ -2329,6 +2336,7 @@ public class Jalview2XML { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); + jaa._linecolour=firstColour; } // register new annotation if (an[i].getId() != null) diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index 7bf2045a..ef6752f 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -210,6 +210,7 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements annot.annotations[p].colour = col; } } + annot._linecolour=col; } } if (lastAnnot + 1 == ourAnnot.size()) -- 1.7.10.2