+ int aSize = 0;\r
+ AlignmentAnnotation [] tmp;\r
+ for(int s=0; s<command.seqs.length; s++)\r
+ {\r
+ if(command.seqs[s].getAnnotation()==null)\r
+ continue;\r
+\r
+ if (aSize == 0)\r
+ annotations = command.seqs[s].getAnnotation();\r
+ else\r
+ {\r
+ tmp = new AlignmentAnnotation\r
+ [aSize + command.seqs[s].getAnnotation().length];\r
+\r
+ System.arraycopy(annotations,0,tmp,0,aSize);\r
+\r
+ System.arraycopy(command.seqs[s].getAnnotation(),\r
+ 0,tmp,aSize,command.seqs[s].getAnnotation().length);\r
+\r
+ annotations = tmp;\r
+ }\r
+\r
+\r
+ aSize = annotations.length;\r
+ }\r
+ }\r
+\r
+ if(annotations==null)\r
+ return;\r
+\r
+\r