+ startRes = start;\r
+ endRes = end;\r
+ recalcConservation();\r
+ }\r
+\r
+ public SequenceI[] getSelectionAsNewSequences(AlignmentI align)\r
+ {\r
+ int iSize = sequences.size();\r
+ SequenceI[] seqs = new SequenceI[iSize];\r
+ SequenceI[] inorder = getSequencesInOrder(align);\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
+ {\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+ }\r
+\r
+ if (seq.getAnnotation() != null)\r
+ {\r
+ for (int a = 0; a < seq.getAnnotation().length; a++)\r
+ {\r
+ seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ }\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(Hashtable hiddenReps)\r
+ {\r
+ if (hiddenReps == null)\r
+ {\r
+ return sequences;\r
+ }\r
+ else\r
+ {\r
+ Vector allSequences = new Vector();\r
+ SequenceI seq, seq2;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq = (SequenceI) sequences.elementAt(i);\r
+ allSequences.addElement(seq);\r
+ if (hiddenReps.containsKey(seq))\r
+ {\r
+ SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);\r
+ for (int h = 0; h < hsg.getSize(); h++)\r
+ {\r
+ seq2 = hsg.getSequenceAt(h);\r
+ if (seq2 != seq\r
+ && !allSequences.contains(seq2))\r
+ {\r
+ allSequences.addElement(seq2);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ return allSequences;\r
+ }\r
+ }\r
+\r
+ public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)\r
+ {\r
+ Vector tmp = getSequences(hiddenReps);\r
+ if (tmp == null)\r
+ {\r
+ return null;\r
+ }\r
+ SequenceI[] result = new SequenceI[tmp.size()];\r
+ for (int i = 0; i < result.length; i++)\r
+ {\r
+ result[i] = (SequenceI) tmp.elementAt(i);\r
+ }\r
+\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param col DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean adjustForRemoveLeft(int col)\r
+ {\r
+ // return value is true if the group still exists\r
+ if (startRes >= col)\r
+ {\r
+ startRes = startRes - col;\r
+ }\r
+\r
+ if (endRes >= col)\r
+ {\r
+ endRes = endRes - col;\r
+\r
+ if (startRes > endRes)\r
+ {\r
+ startRes = 0;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // must delete this group!!\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param col DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean adjustForRemoveRight(int col)\r
+ {\r
+ if (startRes > col)\r
+ {\r
+ // delete this group\r
+ return false;\r
+ }\r
+\r
+ if (endRes >= col)\r
+ {\r
+ endRes = col;\r
+ }\r
+\r
+ return true;\r