X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=76ad093130eb3b2f39cf0f4239f95003e707b754;hb=refs%2Fheads%2Ffeatures%2FJAL-2465_No-mapping_Jmol-structures-loaded-via-url;hp=c77569e21ce16c7ad78c8e8339f5eb70859c882a;hpb=b0832234b2a89510d715951d94ae213e449ca6b2;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c77569e..76ad093 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,8 +22,8 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
@@ -71,7 +71,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Colourscheme applied to group if any
    */
-  public CollectionColourSchemeI cs;
+  public ResidueShaderI cs;
 
   // start column (base 0)
   int startRes = 0;
@@ -118,7 +118,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public SequenceGroup()
   {
     groupName = "JGroup:" + this.hashCode();
-    cs = new CollectionColourScheme();
+    cs = new ResidueShader();
   }
 
   /**
@@ -145,7 +145,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.cs = new CollectionColourScheme(scheme);
+    this.cs = new ResidueShader(scheme);
     startRes = start;
     endRes = end;
     recalcConservation();
@@ -1289,12 +1289,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     return aa;
   }
 
-  /**
-   * Returns a list of annotations that match the specified sequenceRef, calcId
-   * and label, ignoring null values.
-   * 
-   * @return list of AlignmentAnnotation objects
-   */
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
@@ -1302,9 +1296,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
-      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
-              && ann.sequenceRef != null && ann.sequenceRef == seq
-              && ann.label != null && ann.label.equals(label))
+      if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
+              .equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
+              && (label == null || (ann.label != null && ann.label
+                      .equals(label))))
       {
         aa.add(ann);
       }
@@ -1347,13 +1343,25 @@ public class SequenceGroup implements AnnotatedCollectionI
   private AnnotatedCollectionI context;
 
   /**
-   * set the alignment or group context for this group
+   * Sets the alignment or group context for this group
    * 
-   * @param context
+   * @param ctx
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
    */
-  public void setContext(AnnotatedCollectionI context)
+  public void setContext(AnnotatedCollectionI ctx)
   {
-    this.context = context;
+    AnnotatedCollectionI ref = ctx;
+    while (ref != null)
+    {
+      if (ref == this || ref.getContext() == ctx)
+      {
+        throw new IllegalArgumentException(
+                "Circular reference in SequenceGroup.context");
+      }
+      ref = ref.getContext();
+    }
+    this.context = ctx;
   }
 
   /*
@@ -1371,12 +1379,12 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     if (cs == null)
     {
-      cs = new CollectionColourScheme();
+      cs = new ResidueShader();
     }
     cs.setColourScheme(scheme);
   }
 
-  public void setGroupColourScheme(CollectionColourSchemeI scheme)
+  public void setGroupColourScheme(ResidueShaderI scheme)
   {
     cs = scheme;
   }
@@ -1386,7 +1394,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     return cs == null ? null : cs.getColourScheme();
   }
 
-  public CollectionColourSchemeI getGroupColourScheme()
+  public ResidueShaderI getGroupColourScheme()
   {
     return cs;
   }
@@ -1399,4 +1407,24 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     return false;
   }
+
+  /**
+   * @param seq
+   * @return true if seq is a member of the group
+   */
+
+  public boolean contains(SequenceI seq1)
+  {
+    return sequences.contains(seq1);
+  }
+
+  /**
+   * @param seq
+   * @param apos
+   * @return true if startRes<=apos and endRes>=apos and seq is in the group
+   */
+  public boolean contains(SequenceI seq, int apos)
+  {
+    return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+  }
 }