+\r
+ /**\r
+ * Creates a new SequenceGroup object.\r
+ *\r
+ * @param sequences DOCUMENT ME!\r
+ * @param groupName DOCUMENT ME!\r
+ * @param scheme DOCUMENT ME!\r
+ * @param displayBoxes DOCUMENT ME!\r
+ * @param displayText DOCUMENT ME!\r
+ * @param colourText DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public SequenceGroup(Vector sequences, String groupName,\r
+ ColourSchemeI scheme, boolean displayBoxes, boolean displayText,\r
+ boolean colourText, int start, int end)\r
+ {\r
+ this.sequences = sequences;\r
+ this.groupName = groupName;\r
+ this.displayBoxes = displayBoxes;\r
+ this.displayText = displayText;\r
+ this.colourText = colourText;\r
+ this.cs = scheme;\r
+ startRes = start;\r
+ endRes = end;\r
+ recalcConservation();\r
+ }\r
+\r
+ /**\r
+ * Creates a new SequenceGroup object.\r
+ *\r
+ * @param groupName DOCUMENT ME!\r
+ * @param scheme DOCUMENT ME!\r
+ * @param displayBoxes DOCUMENT ME!\r
+ * @param displayText DOCUMENT ME!\r
+ * @param colourText DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public SequenceGroup(String groupName, ColourSchemeI scheme,\r
+ boolean displayBoxes, boolean displayText, boolean colourText,\r
+ int start, int end)\r
+ {\r
+ this.groupName = groupName;\r
+ this.displayBoxes = displayBoxes;\r
+ this.displayText = displayText;\r
+ this.colourText = colourText;\r
+ this.cs = scheme;\r
+ startRes = start;\r
+ endRes = end;\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
+ char ch;\r
+ int sres, eres;\r
+\r
+ for (int i = 0; i < iSize; i++)\r
+ {\r
+ SequenceI seq = inorder[i];\r
+\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ sres = seq.findPosition(startRes);\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ eres = 0;\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
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(startRes, endRes + 1),\r
+ sres,\r
+ eres);\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
+ 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
+ /**\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
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return groupName;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public void setName(String name)\r
+ {\r
+ groupName = name;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Conservation getConservation()\r
+ {\r
+ return conserve;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setConservation(Conservation c)\r
+ {\r
+ conserve = c;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param recalc DOCUMENT ME!\r
+ */\r
+ public void addSequence(SequenceI s, boolean recalc)\r
+ {\r
+ if (!sequences.contains(s))\r
+ {\r
+ sequences.addElement(s);\r
+ }\r
+\r
+ if (recalc)\r
+ {\r
+ recalcConservation();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void recalcConservation()\r
+ {\r
+ if(cs == null)\r
+ return;\r
+\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r