- String groupName;\r
- Conservation conserve;\r
- Vector aaFrequency;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public Vector sequences = new Vector();\r
- int width = -1;\r
- public ColourSchemeI cs;\r
- int startRes = 0;\r
- int endRes = 0;\r
- Color outlineColour = Color.black;\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
- public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- 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 SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- 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 boolean adjustForRemoveLeft(int col)\r
- {\r
- // return value is true if the group still exists\r
- if (startRes >= col)\r
+ 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