+ public SequenceI [] getSelectionAsNewSequences(AlignmentI align)\r
+ {\r
+ int iSize = sequences.size();\r
+ SequenceI [] seqs = new SequenceI[iSize];\r
+ SequenceI [] inorder = getSequencesInOrder(align);\r
+\r
+\r
+ for (int i = 0; i < iSize; i++)\r
+ {\r
+ SequenceI seq = inorder[i];\r
+\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(startRes, endRes + 1),\r
+ seq.findPosition(startRes),\r
+ findEndRes(seq));\r
+\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ if (seq.getDatasetSequence() != null)\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+ if(seq.getAnnotation()!=null)\r
+ {\r
+ for(int a=0; a<seq.getAnnotation().length; a++)\r
+ seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ }\r
+ }\r
+\r
+ return seqs;\r
+\r
+ }\r
+\r
+ /**\r
+ * If sequence ends in gaps, the end residue can\r
+ * be correctly calculated here\r
+ * @param seq SequenceI\r
+ * @return int\r
+ */\r
+ public int findEndRes(SequenceI seq)\r
+ {\r
+ int eres = 0;\r
+ char ch;\r
+\r
+ for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ eres++;\r
+ }\r
+ }\r
+\r
+ if (eres > 0)\r
+ {\r
+ eres += seq.getStart() - 1;\r
+ }\r
+\r
+ return eres;\r
+ }\r
+\r
+ public Vector getSequences(boolean includeHidden)\r
+ {\r
+ if(!includeHidden)\r
+ return sequences;\r
+ else\r
+ {\r
+ Vector allSequences = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq = (SequenceI) sequences.elementAt(i);\r
+ allSequences.addElement(seq);\r
+ if (seq.getHiddenSequences() != null)\r
+ {\r
+ for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)\r
+ {\r
+ allSequences.addElement(\r
+ seq.getHiddenSequences().getSequenceAt(h)\r
+ );\r
+ }\r
+ }\r
+ }\r
+\r
+ return allSequences;\r
+ }\r
+ }\r
+\r
+ public SequenceI[] getSequencesAsArray(boolean includeHidden)\r
+ {\r
+ Vector tmp = getSequences(includeHidden);\r
+ if(tmp==null)\r
+ return null;\r
+ SequenceI [] result = new SequenceI[tmp.size()];\r
+ for(int i=0; i<result.length; i++)\r
+ result[i] = (SequenceI)tmp.elementAt(i);\r
+\r
+ return result;\r
+ }\r
+\r