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

[jalview.git] / src / jalview / gui / Jalview2XML.java

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)