- static boolean sortIdAscending = true;\r
- static int lastGroupHash = 0;\r
- static boolean sortGroupAscending = true;\r
- static AlignmentOrder lastOrder = null;\r
- static boolean sortOrderAscending = true;\r
- static NJTree lastTree = null;\r
- static boolean sortTreeAscending = true;\r
-\r
- /**\r
- * Sort by Percentage Identity\r
- *\r
- * @param align AlignmentI\r
- * @param s SequenceI\r
- */\r
- public static void sortByPID(AlignmentI align, SequenceI s)\r
- {\r
- int nSeq = align.getHeight();\r
-\r
- float[] scores = new float[nSeq];\r
- SequenceI[] seqs = new SequenceI[nSeq];\r
-\r
- for (int i = 0; i < nSeq; i++)\r
- {\r
- scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),\r
- s.getSequenceAsString());\r
- seqs[i] = align.getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(scores, 0, scores.length - 1, seqs);\r
-\r
- setReverseOrder(align, seqs);\r
+ static boolean sortIdAscending = true;\r
+ static int lastGroupHash = 0;\r
+ static boolean sortGroupAscending = true;\r
+ static AlignmentOrder lastOrder = null;\r
+ static boolean sortOrderAscending = true;\r
+ static NJTree lastTree = null;\r
+ static boolean sortTreeAscending = true;\r
+\r
+ /**\r
+ * Sort by Percentage Identity\r
+ *\r
+ * @param align AlignmentI\r
+ * @param s SequenceI\r
+ */\r
+ public static void sortByPID(AlignmentI align, SequenceI s)\r
+ {\r
+ int nSeq = align.getHeight();\r
+\r
+ float[] scores = new float[nSeq];\r
+ SequenceI[] seqs = new SequenceI[nSeq];\r
+\r
+ for (int i = 0; i < nSeq; i++)\r
+ {\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),\r
+ s.getSequenceAsString());\r
+ seqs[i] = align.getSequenceAt(i);\r