*/package jalview.io;\r
\r
import jalview.datamodel.*;\r
-import java.net.URL;\r
-import java.io.BufferedReader;\r
-import java.io.InputStreamReader;\r
-import java.io.FileReader;\r
-\r
\r
public class JnetAnnotationMaker\r
{\r
AlignmentAnnotation annot;\r
Annotation[] annotations = null;\r
\r
+ int existingAnnotations = 0;\r
+ if(al.getAlignmentAnnotation()!=null)\r
+ existingAnnotations = al.getAlignmentAnnotation().length;\r
+\r
+\r
while (i < preds.length)\r
{\r
String id = preds[i].getName().toUpperCase();\r
\r
if (seqRef != null)\r
{\r
- annot.createSequenceMapping(seqRef, 0);\r
+ annot.createSequenceMapping(seqRef, 1, false);\r
seqRef.addAlignmentAnnotation(annot);\r
}\r
\r
al.addAnnotation(annot);\r
+ al.setAnnotationIndex(annot,\r
+ al.getAlignmentAnnotation().\r
+ length - existingAnnotations - 1);\r
\r
if (noMsa)\r
{\r