AddAnnotation with start index

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e9af7f4..2545ec1 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -642,6 +642,27 @@ public class Alignment implements AlignmentI
         annotations = temp;\r
     }\r
 \r
+\r
+    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)\r
+    {\r
+      aa.refSequence = seqRef;\r
+      if(seqRef!=null && index!=0)\r
+      {\r
+        int aSize = aa.annotations.length;\r
+        int newIndex;\r
+        Annotation [] temp = new Annotation[seqRef.getLength()];\r
+        for(int a=0; a<aSize; a++)\r
+        {\r
+          newIndex = seqRef.findIndex(a + index)-1;\r
+          temp[newIndex] = aa.annotations[a];\r
+        }\r
+\r
+        aa.annotations = temp;\r
+      }\r
+\r
+      addAnnotation(aa);\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -658,18 +679,19 @@ public class Alignment implements AlignmentI
 \r
 \r
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
-        int i = 0;\r
+\r
+        temp[0] = aa;\r
+\r
+        int i = 1;\r
 \r
         if (aSize > 1)\r
         {\r
-            for (i = 0; i < (aSize - 1); i++)\r
+            for (i = 1; i < (aSize); i++)\r
             {\r
-                temp[i] = annotations[i];\r
+                temp[i] = annotations[i-1];\r
             }\r
         }\r
 \r
-        temp[i] = aa;\r
-\r
         annotations = temp;\r
     }\r
 \r

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e4d64fa..fcf9844 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,6 +27,8 @@ package jalview.datamodel;
  */\r
 public class AlignmentAnnotation\r
 {\r
+    public SequenceI refSequence;\r
+\r
     /** DOCUMENT ME!! */\r
     public String label;\r
 \r
@@ -43,6 +45,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public float graphMax;\r
 \r
+    public java.util.Vector graphLines;\r
 \r
     // Graphical hints and tips\r
 \r
@@ -58,16 +61,30 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public boolean visible = true;\r
 \r
+    public int graphGroup = -1;\r
+\r
     /** DOCUMENT ME!! */\r
     public int height = 0;\r
 \r
     public int graph = 0;\r
 \r
-    public static int NO_GRAPH = 0;\r
+    public int graphHeight = 40;\r
 \r
-    public static int BAR_GRAPH = 1;\r
+    public static final int NO_GRAPH = 0;\r
 \r
-    public static int LINE_GRAPH = 2;\r
+    public static final int BAR_GRAPH = 1;\r
+\r
+    public static final int LINE_GRAPH = 2;\r
+\r
+    public static int getGraphValueFromString(String string)\r
+    {\r
+      if(string.equalsIgnoreCase("BAR_GRAPH"))\r
+        return BAR_GRAPH;\r
+      else if(string.equalsIgnoreCase("LINE_GRAPH"))\r
+        return LINE_GRAPH;\r
+      else\r
+        return NO_GRAPH;\r
+    }\r
 \r
     /**\r
      * Creates a new AlignmentAnnotation object.\r
@@ -123,6 +140,7 @@ public class AlignmentAnnotation
 \r
         if (min == max)\r
         {\r
+            min = 999999999;\r
             for (int i = 0; i < annotations.length; i++)\r
             {\r
                 if (annotations[i] == null)\r
@@ -208,5 +226,24 @@ public class AlignmentAnnotation
         }\r
 \r
         return buffer.toString();\r
-    }\r
+      }\r
+\r
+      public void addGraphLine(GraphLine line)\r
+      {\r
+        if(graphLines==null)\r
+          graphLines = new java.util.Vector();\r
+\r
+        graphLines.add(line);\r
+      }\r
+\r
+      public GraphLine getGraphLine(int index)\r
+      {\r
+        if(graphLines!=null && index<graphLines.size())\r
+          return (GraphLine)graphLines.elementAt(index);\r
+\r
+        else\r
+          return null;\r
+      }\r
 }\r
+\r
+\r

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 59610b3..69a5ac6 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -248,6 +248,12 @@ public interface AlignmentI
     public void addAnnotation(AlignmentAnnotation aa);\r
 \r
     /**\r
+     * Adds a new AlignmentAnnotation to this alignment,\r
+     *  associated to Sequence starting at sequence index\r
+     */\r
+    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index);\r
+\r
+    /**\r
      * Deletes a specific AlignmentAnnotation from the alignment.\r
      *\r
      * @param aa DOCUMENT ME!\r