From 7e4c4ad887a30dc26496087b0150f4ac2fe355ec Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 30 Jan 2006 14:48:47 +0000
Subject: [PATCH] AddAnnotation with start index

---
 src/jalview/datamodel/Alignment.java           |   32 ++++++++++++++---
 src/jalview/datamodel/AlignmentAnnotation.java |   45 +++++++++++++++++++++---
 src/jalview/datamodel/AlignmentI.java          |    6 ++++
 3 files changed, 74 insertions(+), 9 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e9af7f4..2545ec1 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -642,6 +642,27 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
+
+    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)
+    {
+      aa.refSequence = seqRef;
+      if(seqRef!=null && index!=0)
+      {
+        int aSize = aa.annotations.length;
+        int newIndex;
+        Annotation [] temp = new Annotation[seqRef.getLength()];
+        for(int a=0; a<aSize; a++)
+        {
+          newIndex = seqRef.findIndex(a + index)-1;
+          temp[newIndex] = aa.annotations[a];
+        }
+
+        aa.annotations = temp;
+      }
+
+      addAnnotation(aa);
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -658,18 +679,19 @@ public class Alignment implements AlignmentI
 
 
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-        int i = 0;
+
+        temp[0] = aa;
+
+        int i = 1;
 
         if (aSize > 1)
         {
-            for (i = 0; i < (aSize - 1); i++)
+            for (i = 1; i < (aSize); i++)
             {
-                temp[i] = annotations[i];
+                temp[i] = annotations[i-1];
             }
         }
 
-        temp[i] = aa;
-
         annotations = temp;
     }
 
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e4d64fa..fcf9844 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,6 +27,8 @@ package jalview.datamodel;
  */
 public class AlignmentAnnotation
 {
+    public SequenceI refSequence;
+
     /** DOCUMENT ME!! */
     public String label;
 
@@ -43,6 +45,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public float graphMax;
 
+    public java.util.Vector graphLines;
 
     // Graphical hints and tips
 
@@ -58,16 +61,30 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public boolean visible = true;
 
+    public int graphGroup = -1;
+
     /** DOCUMENT ME!! */
     public int height = 0;
 
     public int graph = 0;
 
-    public static int NO_GRAPH = 0;
+    public int graphHeight = 40;
 
-    public static int BAR_GRAPH = 1;
+    public static final int NO_GRAPH = 0;
 
-    public static int LINE_GRAPH = 2;
+    public static final int BAR_GRAPH = 1;
+
+    public static final int LINE_GRAPH = 2;
+
+    public static int getGraphValueFromString(String string)
+    {
+      if(string.equalsIgnoreCase("BAR_GRAPH"))
+        return BAR_GRAPH;
+      else if(string.equalsIgnoreCase("LINE_GRAPH"))
+        return LINE_GRAPH;
+      else
+        return NO_GRAPH;
+    }
 
     /**
      * Creates a new AlignmentAnnotation object.
@@ -123,6 +140,7 @@ public class AlignmentAnnotation
 
         if (min == max)
         {
+            min = 999999999;
             for (int i = 0; i < annotations.length; i++)
             {
                 if (annotations[i] == null)
@@ -208,5 +226,24 @@ public class AlignmentAnnotation
         }
 
         return buffer.toString();
-    }
+      }
+
+      public void addGraphLine(GraphLine line)
+      {
+        if(graphLines==null)
+          graphLines = new java.util.Vector();
+
+        graphLines.add(line);
+      }
+
+      public GraphLine getGraphLine(int index)
+      {
+        if(graphLines!=null && index<graphLines.size())
+          return (GraphLine)graphLines.elementAt(index);
+
+        else
+          return null;
+      }
 }
+
+
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 59610b3..69a5ac6 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -248,6 +248,12 @@ public interface AlignmentI
     public void addAnnotation(AlignmentAnnotation aa);
 
     /**
+     * Adds a new AlignmentAnnotation to this alignment,
+     *  associated to Sequence starting at sequence index
+     */
+    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index);
+
+    /**
      * Deletes a specific AlignmentAnnotation from the alignment.
      *
      * @param aa DOCUMENT ME!
-- 
1.7.10.2