- String groupName;\r
- Conservation conserve;\r
- Vector aaFrequency;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
-\r
- /** DOCUMENT ME!! */\r
- public Vector sequences = new Vector();\r
- int width = -1;\r
-\r
- /** DOCUMENT ME!! */\r
- public ColourSchemeI cs;\r
- int startRes = 0;\r
- int endRes = 0;\r
- Color outlineColour = Color.black;\r
-\r
- /**\r
- * Creates a new SequenceGroup object.\r
- */\r
- public SequenceGroup()\r
- {\r
- groupName = "Group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\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
+ String groupName;\r
+ String description;\r
+ Conservation conserve;\r
+ Vector aaFrequency;\r
+ boolean displayBoxes = true;\r
+ boolean displayText = true;\r
+ boolean colourText = true;\r
+ private Vector sequences = new Vector();\r
+ int width = -1;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public ColourSchemeI cs;\r
+ int startRes = 0;\r
+ int endRes = 0;\r
+ Color outlineColour = Color.black;\r
+ public int thresholdTextColour = 0;\r
+ public Color textColour = Color.black;\r
+ public Color textColour2 = Color.white;\r
+\r
+ /**\r
+ * Creates a new SequenceGroup object.\r
+ */\r
+ public SequenceGroup()\r
+ {\r
+ groupName = "JGroup:" + this.hashCode();\r
+ }\r
+\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,\r
+ 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
+ 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