JAL-1153 new runtime property set to first non-null annotation element colour

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f5d34a6..6212d4d 100755 (executable)
--- 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<mx;i++)
+      char[] string = new char[max - offset];
+      int mx = annotations.length;
+
+      for (int i = offset; i < mx; i++)
       {
         String dc;
-        string[i]=(annotations[i]==null || (dc=annotations[i].displayCharacter.trim()).length()<1 )? '.' : dc.charAt(0);
+        string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
+                .trim()).length() < 1) ? '.' : dc.charAt(0);
       }
       return new String(string);
     }
   };
-  
-  private long _lastrnaannot=-1;
-  public String getRNAStruc(){
+
+  private long _lastrnaannot = -1;
+
+  public String getRNAStruc()
+  {
     if (isrna)
     {
       String rnastruc = new AnnotCharSequence().toString();
-      if (_lastrnaannot!=rnastruc.hashCode())
+      if (_lastrnaannot != rnastruc.hashCode())
       {
         // ensure rna structure contacts are up to date
-        _lastrnaannot=rnastruc.hashCode();
+        _lastrnaannot = rnastruc.hashCode();
         _updateRnaSecStr(rnastruc);
       }
       return rnastruc;
@@ -387,7 +404,7 @@ public class AlignmentAnnotation
     return null;
   }
 
-/**
+  /**
    * Creates a new AlignmentAnnotation object.
    * 
    * @param label
@@ -435,7 +452,7 @@ public class AlignmentAnnotation
     float min = graphMin;
     float max = graphMax;
     boolean drawValues = true;
-
+    _linecolour=null;
     if (min == max)
     {
       min = 999999999;
@@ -461,6 +478,10 @@ public class AlignmentAnnotation
         {
           min = annotations[i].value;
         }
+        if (_linecolour == null && annotations[i].colour != null)
+        {
+          _linecolour = annotations[i].colour;
+        }
       }
       // ensure zero is origin for min/max ranges on only one side of zero
       if (min > 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("<html>");
-      if (i>-1)
+      int i = description.toLowerCase().indexOf("<html>");
+      if (i > -1)
       {
         // move the html tag to before the sequence reference.
-        return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+        return "<html>" + 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 (file)
--- 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 7bf2045..ef6752f 100644 (file)
--- 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())