AddAnnotation with start index

[jalview.git] / src / jalview / datamodel / Alignment.java

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