X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=c3ccb0ba99b0eba2867bdc5ec17bf02a2e84eb07;hb=476d13d644d3bf2886519b13bc7f02d1ae9729f9;hp=e4d64fad3f16ab044886da976aa0432515584116;hpb=848bef9fdc243cfab564acb0b82fc7ee3bcffe9f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e4d64fa..c3ccb0b 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,6 +27,13 @@ package jalview.datamodel;
  */
 public class AlignmentAnnotation
 {
+    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;
 
@@ -43,6 +50,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public float graphMax;
 
+    public GraphLine threshold;
 
     // Graphical hints and tips
 
@@ -58,16 +66,30 @@ 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 +145,7 @@ public class AlignmentAnnotation
 
         if (min == max)
         {
+            min = 999999999;
             for (int i = 0; i < annotations.length; i++)
             {
                 if (annotations[i] == null)
@@ -208,5 +231,37 @@ public class AlignmentAnnotation
         }
 
         return buffer.toString();
-    }
+      }
+
+      public void setThreshold(GraphLine line)
+      {
+        threshold = line;
+      }
+
+      public GraphLine getThreshold()
+      {
+          return threshold;
+      }
+
+      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;
+      }
 }
+
+