X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=5a2c46e0b3e2be52032af8a67f02cfbefdde6cfc;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=9cfdff6dbadd957baeb30925cdecc56a29523dfc;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 9cfdff6..5a2c46e 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 sequenceRef;
+
     /** DOCUMENT ME!! */
     public String label;
 
@@ -36,8 +38,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public Annotation[] annotations;
 
-    /** DOCUMENT ME!! */
-    public boolean isGraph = false;
+    public java.util.Hashtable sequenceMapping;
 
     /** DOCUMENT ME!! */
     public float graphMin;
@@ -45,8 +46,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public float graphMax;
 
-    /** DOCUMENT ME!! */
-    public int windowLength;
+    public GraphLine threshold;
 
     // Graphical hints and tips
 
@@ -62,9 +62,31 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */
     public boolean visible = true;
 
+    public int graphGroup = -1;
+
     /** DOCUMENT ME!! */
     public int height = 0;
 
+    public int graph = 0;
+
+    public int graphHeight = 40;
+
+    public static final int NO_GRAPH = 0;
+
+    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.
      *
@@ -109,16 +131,19 @@ public class AlignmentAnnotation
      * @param winLength DOCUMENT ME!
      */
     public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations, float min, float max, int winLength)
+        Annotation[] annotations, float min, float max, int graphType)
     {
         // graphs are not editable
         this.label = label;
         this.description = description;
         this.annotations = annotations;
-        isGraph = true;
+        graph = graphType;
+
+        boolean drawValues = true;
 
         if (min == max)
         {
+            min = 999999999;
             for (int i = 0; i < annotations.length; i++)
             {
                 if (annotations[i] == null)
@@ -126,6 +151,11 @@ public class AlignmentAnnotation
                     continue;
                 }
 
+                if(drawValues && annotations[i].displayCharacter.length() > 1 )
+                {
+                  drawValues = false;
+                }
+
                 if (annotations[i].value > max)
                 {
                     max = annotations[i].value;
@@ -140,23 +170,33 @@ public class AlignmentAnnotation
 
         graphMin = min;
         graphMax = max;
-        windowLength = winLength;
 
         for (int i = 0; i < annotations.length; i++)
         {
-            if ((annotations[i] != null) &&
-                    ((annotations[i].secondaryStructure == 'H') ||
+            if (!hasIcons
+                && annotations[i] != null
+                && ((annotations[i].secondaryStructure == 'H') ||
                     (annotations[i].secondaryStructure == 'E')))
             {
                 hasIcons = true;
             }
 
-            if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0))
+            if (!hasText
+                && annotations[i]!=null
+                && annotations[i].displayCharacter.length() > 0)
             {
                 hasText = true;
             }
         }
+
+        if(!drawValues && graphType!=NO_GRAPH)
+        {
+          for (int i = 0; i < annotations.length; i++)
+          {
+            if (annotations[i] != null)
+              annotations[i].displayCharacter = "";
+          }
+        }
     }
 
     /**
@@ -172,7 +212,7 @@ public class AlignmentAnnotation
         {
             if (annotations[i] != null)
             {
-                if (isGraph)
+                if (graph!=0)
                 {
                     buffer.append(annotations[i].value);
                 }
@@ -205,5 +245,85 @@ public class AlignmentAnnotation
         }
 
         return buffer.toString();
-    }
+      }
+
+      public void setThreshold(GraphLine line)
+      {
+        threshold = line;
+      }
+
+      public GraphLine getThreshold()
+      {
+          return threshold;
+      }
+
+      /**
+       * This
+       */
+      public void createSequenceMapping(SequenceI seqRef, int startRes)
+      {
+        if(seqRef == null)
+          return;
+
+        sequenceMapping = new java.util.Hashtable();
+
+        sequenceRef = seqRef;
+
+        if(startRes < sequenceRef.getStart())
+          startRes = sequenceRef.getStart();
+
+        int seqPos;
+
+        int fileOffset = 0;
+        if(startRes > sequenceRef.getStart())
+        {
+          fileOffset = startRes - sequenceRef.getStart();
+        }
+
+        for(int i = 0; i < annotations.length; i++)
+        {
+            seqPos = sequenceRef.findPosition(i + fileOffset);
+            if(seqPos<annotations.length)
+            {
+              if (annotations[i] != null)
+              {
+                  sequenceMapping.put(new Integer(seqPos),
+                                      annotations[i]);
+              }
+            }
+         }
+
+        adjustForAlignment();
+
+      }
+
+      public void adjustForAlignment()
+      {
+          int a=0, aSize = sequenceRef.getLength();
+
+          if(aSize == 0)
+          {
+            //Its been deleted
+            return;
+          }
+
+          int position;
+          Annotation[] temp = new Annotation[aSize];
+          Integer index;
+
+          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+          {
+              index = new Integer(a);
+              if(sequenceMapping.containsKey(index))
+              {
+                position = sequenceRef.findIndex(a)-1;
+
+                temp[position] = (Annotation)sequenceMapping.get(index);
+              }
+          }
+
+          annotations = temp;
+      }
 }
+
+