- String groupName;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public ColourSchemeI cs;\r
- ArrayList sequenceGroups = new ArrayList();\r
-\r
- public SuperGroup()\r
- {\r
- groupName = "Super group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\r
-\r
- public SuperGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText)\r
- {\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- }\r
-\r
- public String getName()\r
- {\r
- return groupName;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- groupName = name;\r
- }\r
-\r
-\r
- public void addGroup(SequenceGroup sg)\r
- {\r
- if(!sequenceGroups.contains(sg))\r
- sequenceGroups.add(sg);\r
- }\r
-\r
- public void addOrRemove(SequenceGroup sg)\r
- {\r
- if(sequenceGroups.contains(sg))\r
- deleteGroup(sg);\r
- else\r
- addGroup(sg);\r
- }\r
-\r
- public void deleteGroup(SequenceGroup sg)\r
- {\r
- sequenceGroups.remove(sg);\r
- }\r
-\r
- public void setSuperGroupProperties(SequenceGroup sg)\r
- {\r
- cs = sg.cs;\r
- colourText = sg.colourText;\r
- displayText = sg.displayText;\r
- displayBoxes = sg.displayBoxes;\r
-\r
- for(int i=0; i<sequenceGroups.size(); i++)\r
+ String groupName;\r
+ boolean displayBoxes;\r
+ boolean displayText;\r
+ boolean colourText;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public ColourSchemeI cs;\r
+ Vector sequenceGroups = new Vector();\r
+\r
+ /**\r
+ * Creates a new SuperGroup object.\r
+ */\r
+ public SuperGroup()\r
+ {\r
+ groupName = "Super group";\r
+ this.displayBoxes = true;\r
+ this.displayText = true;\r
+ this.colourText = false;\r
+ cs = null;\r
+ }\r
+\r
+ /**\r
+ * Creates a new SuperGroup 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
+ */\r
+ public SuperGroup(String groupName, ColourSchemeI scheme,\r
+ boolean displayBoxes, boolean displayText, boolean colourText)\r
+ {\r
+ this.groupName = groupName;\r
+ this.displayBoxes = displayBoxes;\r
+ this.displayText = displayText;\r
+ this.colourText = colourText;\r
+ this.cs = scheme;\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
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void addGroup(SequenceGroup sg)\r