X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=6ab49b27575086a59ec507741236224830cdadcc;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=fdc74e2fed6f1f8cf4ba65a040c99374255163c0;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index fdc74e2..6ab49b2 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,8 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.Locale;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -31,6 +29,7 @@ import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.NoSuchElementException;
@@ -46,6 +45,7 @@ import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.IncompleteCodonException;
@@ -1471,7 +1471,19 @@ public class AlignmentUtils
          */
         final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
                 .findAnnotations(seq, dsann.getCalcId(), dsann.label);
-        if (!matchedAlignmentAnnotations.iterator().hasNext())
+        boolean found = false;
+        if (matchedAlignmentAnnotations != null)
+        {
+          for (AlignmentAnnotation matched : matchedAlignmentAnnotations)
+          {
+            if (dsann.description.equals(matched.description))
+            {
+              found = true;
+              break;
+            }
+          }
+        }
+        if (!found)
         {
           result.add(dsann);
           if (labelForCalcId != null)
@@ -1492,14 +1504,15 @@ public class AlignmentUtils
 
   /**
    * Adds annotations to the top of the alignment annotations, in the same order
-   * as their related sequences.
+   * as their related sequences. If you already have an annotation and want to
+   * add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
    * 
    * @param annotations
    *          the annotations to add
    * @param alignment
    *          the alignment to add them to
    * @param selectionGroup
-   *          current selection group (or null if none)
+   *          current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
    */
   public static void addReferenceAnnotations(
           Map<SequenceI, List<AlignmentAnnotation>> annotations,
@@ -1509,31 +1522,60 @@ public class AlignmentUtils
     {
       for (AlignmentAnnotation ann : annotations.get(seq))
       {
-        AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
-        int startRes = 0;
-        int endRes = ann.annotations.length;
-        if (selectionGroup != null)
-        {
-          startRes = selectionGroup.getStartRes();
-          endRes = selectionGroup.getEndRes();
-        }
-        copyAnn.restrict(startRes, endRes);
+        addReferenceAnnotationTo(alignment, seq, ann, selectionGroup);
+      }
+    }
+  }
 
-        /*
-         * Add to the sequence (sets copyAnn.datasetSequence), unless the
-         * original annotation is already on the sequence.
-         */
-        if (!seq.hasAnnotation(ann))
-        {
-          seq.addAlignmentAnnotation(copyAnn);
-        }
-        // adjust for gaps
-        copyAnn.adjustForAlignment();
-        // add to the alignment and set visible
-        alignment.addAnnotation(copyAnn);
-        copyAnn.visible = true;
+  /**
+   * Make a copy of a reference annotation {@code ann} and add it to an
+   * alignment sequence {@code seq} in {@code alignment}, optionally limited to
+   * the extent of {@code selectionGroup}
+   * 
+   * @param alignment
+   * @param seq
+   * @param ann
+   * @param selectionGroup
+   *          current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
+   * @return annotation added to {@code seq and {@code alignment}
+   */
+  public static AlignmentAnnotation addReferenceAnnotationTo(
+          final AlignmentI alignment, final SequenceI seq,
+          final AlignmentAnnotation ann, final SequenceGroup selectionGroup)
+  {
+    AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+    int startRes = 0;
+    int endRes = ann.annotations.length;
+    if (selectionGroup != null)
+    {
+      startRes = -1 + Math.min(seq.getEnd(), Math.max(seq.getStart(),
+              seq.findPosition(selectionGroup.getStartRes())));
+      endRes = -1 + Math.min(seq.getEnd(),
+              seq.findPosition(selectionGroup.getEndRes()));
+
+    }
+    copyAnn.restrict(startRes, endRes + 0);
+
+    /*
+     * Add to the sequence (sets copyAnn.datasetSequence), unless the
+     * original annotation is already on the sequence.
+     */
+    if (!seq.hasAnnotation(ann))
+    {
+      ContactMatrixI cm = seq.getDatasetSequence().getContactMatrixFor(ann);
+      if (cm != null)
+      {
+        seq.addContactListFor(copyAnn, cm);
       }
+      seq.addAlignmentAnnotation(copyAnn);
     }
+    // adjust for gaps
+    copyAnn.adjustForAlignment();
+    // add to the alignment and set visible
+    alignment.addAnnotation(copyAnn);
+    copyAnn.visible = true;
+
+    return copyAnn;
   }
 
   /**
@@ -1573,6 +1615,21 @@ public class AlignmentUtils
     }
   }
 
+  public static AlignmentAnnotation getFirstSequenceAnnotationOfType(
+          AlignmentI al, int graphType)
+  {
+    AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
+    if (anns != null)
+    {
+      for (AlignmentAnnotation aa : anns)
+      {
+        if (aa.sequenceRef != null && aa.graph == graphType)
+          return aa;
+      }
+    }
+    return null;
+  }
+
   /**
    * Returns true if either sequence has a cross-reference to the other
    *