+ SequenceI [] getVisibleAndRepresentedSeqs()\r
+ {\r
+ if(hiddenSequences==null || hiddenSequences.getSize()<1)\r
+ return getSequencesArray();\r
+\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ SequenceGroup hidden;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq = (SequenceI) sequences.elementAt(i);\r
+ seqs.addElement(seq);\r
+ hidden = seq.getHiddenSequences();\r
+ if(hidden!=null)\r
+ {\r
+ for(int j=0; j<hidden.getSize(false); j++)\r
+ {\r
+ seqs.addElement(hidden.getSequenceAt(j));\r
+ }\r
+ }\r
+ }\r
+ SequenceI [] result = new SequenceI[seqs.size()];\r
+ for(int i=0; i<seqs.size(); i++)\r
+ result[i] = (SequenceI)seqs.elementAt(i);\r
+\r
+ return result;\r
+\r
+ }\r
+\r