+ *\r
+ * @param aa AlignmentAnnotation\r
+ * @param seqRef The sequence to associate this annotation with\r
+ * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added\r
+ */\r
+ public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)\r
+ {\r
+ if(seqRef!=null)\r
+ {\r
+ //We can only add Annotations to the dataset sequences\r
+ if(seqRef.getDatasetSequence()==null)\r
+ {\r
+ setDataset(null);\r
+ }\r
+\r
+ AlignmentAnnotation [] old = seqRef.getDatasetSequence().getAnnotation();\r
+\r
+ //First check if this is a new annotation or not. If it is new,\r
+ //we must add the annotation to the dataset\r
+ boolean newAnnotation = true;\r
+ if(seqRef.getDatasetSequence().getAnnotation()!=null)\r
+ {\r
+ for(int a=0; a<old.length; a++)\r
+ {\r
+ if(old[a] == aa)\r
+ {\r
+\r
+ newAnnotation = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ if(newAnnotation)\r
+ {\r
+ seqRef.getDatasetSequence().addAlignmentAnnotation(aa);\r
+ }\r
+\r
+ AlignmentAnnotation copy = null;\r
+ if (aa.graph > 0)\r
+ copy = new AlignmentAnnotation(\r
+ aa.label, aa.description, aa.annotations, aa.graphMin,\r
+ aa.graphMax, aa.graph\r
+ );\r
+ else\r
+ copy = new AlignmentAnnotation(\r
+ aa.label, aa.description, aa.annotations\r
+ );\r
+\r
+ copy.datasetAnnotation = aa;\r
+\r
+ addAnnotation(copy);\r
+\r
+ copy.sequenceRef = seqRef;\r
+\r
+ return copy;\r
+ }\r
+ else\r
+ {\r
+ addAnnotation(aa);\r
+ return aa;\r
+ }\r
+ }\r
+\r
+ public void adjustSequenceAnnotations()\r
+ {\r
+ if(annotations!=null)\r
+ {\r
+ for (int a = 0; a < annotations.length; a++)\r
+ {\r
+ if (annotations[a].sequenceRef != null)\r
+ {\r
+ annotations[a].adjustForAlignment();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r