From e0a4b92352ee3e31a8dea075a51ec080ae3945f2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:40:26 +0000
Subject: [PATCH] Add annotation with sequence ref updated

---
 src/jalview/datamodel/Alignment.java           |  126 ++++++++++++++++++++----
 src/jalview/datamodel/AlignmentAnnotation.java |   29 +++++-
 src/jalview/datamodel/AlignmentI.java          |    6 +-
 3 files changed, 140 insertions(+), 21 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2545ec1..78aa015 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -59,6 +59,16 @@ public class Alignment implements AlignmentI
         for (i = 0; i < seqs.length; i++)
         {
             sequences.addElement(seqs[i]);
+
+            if(seqs[i].getDatasetSequence()!=null
+            && seqs[i].getDatasetSequence().getAnnotation()!=null)
+            {
+
+              for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
+              {
+                       this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
+              }
+            }
         }
 
         getWidth();
@@ -642,25 +652,83 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
-
-    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)
+    /**
+     *
+     * @param aa AlignmentAnnotation
+     * @param seqRef The sequence to associate this annotation with
+     * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added
+     */
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)
     {
-      aa.refSequence = seqRef;
-      if(seqRef!=null && index!=0)
+      if(seqRef!=null)
       {
-        int aSize = aa.annotations.length;
-        int newIndex;
-        Annotation [] temp = new Annotation[seqRef.getLength()];
-        for(int a=0; a<aSize; a++)
+          //We can only add Annotations to the dataset sequences
+           if(seqRef.getDatasetSequence()==null)
+           {
+                  setDataset(null);
+            }
+
+        AlignmentAnnotation []  old = seqRef.getDatasetSequence().getAnnotation();
+
+        //First check if this is a new annotation or not. If it is new,
+        //we must add the annotation to the dataset
+        boolean newAnnotation = true;
+        if(seqRef.getDatasetSequence().getAnnotation()!=null)
         {
-          newIndex = seqRef.findIndex(a + index)-1;
-          temp[newIndex] = aa.annotations[a];
+          for(int a=0; a<old.length; a++)
+          {
+            if(old[a] == aa)
+            {
+
+              newAnnotation = false;
+              break;
+            }
+          }
         }
 
-        aa.annotations = temp;
+        if(newAnnotation)
+         {
+           seqRef.getDatasetSequence().addAlignmentAnnotation(aa);
+         }
+
+          AlignmentAnnotation copy = null;
+          if (aa.graph > 0)
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations, aa.graphMin,
+                aa.graphMax, aa.graph
+                );
+          else
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations
+                );
+
+         copy.datasetAnnotation = aa;
+
+         addAnnotation(copy);
+
+         copy.sequenceRef = seqRef;
+
+         return copy;
+      }
+      else
+      {
+        addAnnotation(aa);
+        return aa;
       }
+    }
 
-      addAnnotation(aa);
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
     }
 
     /**
@@ -671,30 +739,52 @@ public class Alignment implements AlignmentI
     public void addAnnotation(AlignmentAnnotation aa)
     {
         int aSize = 1;
-
         if (annotations != null)
         {
             aSize = annotations.length + 1;
         }
 
-
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
 
-        temp[0] = aa;
+        temp[aSize-1] = aa;
 
-        int i = 1;
+        int i = 0;
 
         if (aSize > 1)
         {
-            for (i = 1; i < (aSize); i++)
+            for (i = 0; i < (aSize-1); i++)
             {
-                temp[i] = annotations[i-1];
+                temp[i] = annotations[i];
             }
         }
 
         annotations = temp;
     }
 
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+    {
+      if(aa==null || annotations==null || annotations.length-1<index)
+        return;
+
+      int aSize = annotations.length;
+      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+      temp[index] = aa;
+
+      for (int i = 0; i < aSize; i++)
+      {
+        if(i==index)
+          continue;
+
+        if(i<index)
+          temp[i] = annotations[i];
+        else
+          temp[i] = annotations[i-1];
+      }
+
+        annotations = temp;
+    }
+
     /**
      * DOCUMENT ME!
      *
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index fcf9844..b93f178 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,7 +27,12 @@ package jalview.datamodel;
  */
 public class AlignmentAnnotation
 {
-    public SequenceI refSequence;
+    public SequenceI sequenceRef;
+
+    /** This annotation is the original loaded annotation
+     *  without any gaps. It is necessary to adjust the annotation
+     *  if sequences are updated */
+    public AlignmentAnnotation datasetAnnotation;
 
     /** DOCUMENT ME!! */
     public String label;
@@ -233,7 +238,7 @@ public class AlignmentAnnotation
         if(graphLines==null)
           graphLines = new java.util.Vector();
 
-        graphLines.add(line);
+        graphLines.addElement(line);
       }
 
       public GraphLine getGraphLine(int index)
@@ -244,6 +249,26 @@ public class AlignmentAnnotation
         else
           return null;
       }
+
+      public void adjustForAlignment()
+      {
+          int a=0, aSize = sequenceRef.getLength();
+
+          int index = 0;
+          Annotation[] temp = new Annotation[aSize];
+
+          for (a = 0; a < aSize; a++)
+          {
+            if (!jalview.util.Comparison.isGap(sequenceRef.getCharAt(a)))
+            {
+              index = sequenceRef.findPosition(a);
+              if(datasetAnnotation.annotations.length>index)
+                temp[a] = datasetAnnotation.annotations[index];
+            }
+          }
+
+          annotations = temp;
+      }
 }
 
 
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 69a5ac6..ebd95d9 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -251,7 +251,9 @@ public interface AlignmentI
      * Adds a new AlignmentAnnotation to this alignment,
      *  associated to Sequence starting at sequence index
      */
-    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index);
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);
+
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
     /**
      * Deletes a specific AlignmentAnnotation from the alignment.
@@ -312,5 +314,7 @@ public interface AlignmentI
      */
     public boolean padGaps();
 
+     public void adjustSequenceAnnotations();
+
 
 }
-- 
1.7.10.2