+\r
+ public void adjustForAlignment()\r
+ {\r
+ int a=0, aSize = sequenceRef.getLength();\r
+\r
+ int index = 0;\r
+ Annotation[] temp = new Annotation[aSize];\r
+\r
+ for (a = 0; a < aSize; a++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(sequenceRef.getCharAt(a)))\r
+ {\r
+ index = sequenceRef.findPosition(a);\r
+ if(datasetAnnotation.annotations.length>index)\r
+ temp[a] = datasetAnnotation.annotations[index];\r
+ }\r
+ }\r
+\r
+ annotations = temp;\r
+ }\r