else\r
newal = new Alignment(viewport.alignment.getSequencesArray());\r
\r
+ if(viewport.alignment.getAlignmentAnnotation()!=null)\r
+ {\r
+ for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+ }\r
+ }\r
+ }\r
+\r
AlignFrame newaf = new AlignFrame(newal,\r
viewport.applet,\r
"",\r