Formatting changes

[jalview.git] / src / jalview / datamodel / SuperGroup.java

diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java
index ad6f703..b2993b5 100755 (executable)
--- a/src/jalview/datamodel/SuperGroup.java
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -18,8 +18,6 @@
 */\r
 package jalview.datamodel;\r
 \r
-import jalview.analysis.*;\r
-\r
 import jalview.datamodel.*;\r
 \r
 import jalview.schemes.*;\r
@@ -27,15 +25,28 @@ import jalview.schemes.*;
 import java.util.*;\r
 \r
 \r
-public class SuperGroup {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SuperGroup\r
+{\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
-    public SuperGroup() {\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
@@ -43,8 +54,18 @@ public class SuperGroup {
         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
+        boolean displayBoxes, boolean displayText, boolean colourText)\r
+    {\r
         this.groupName = groupName;\r
         this.displayBoxes = displayBoxes;\r
         this.displayText = displayText;\r
@@ -52,39 +73,80 @@ public class SuperGroup {
         this.cs = scheme;\r
     }\r
 \r
-    public String getName() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public String getName()\r
+    {\r
         return groupName;\r
     }\r
 \r
-    public void setName(String name) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param name DOCUMENT ME!\r
+     */\r
+    public void setName(String name)\r
+    {\r
         groupName = name;\r
     }\r
 \r
-    public void addGroup(SequenceGroup sg) {\r
-        if (!sequenceGroups.contains(sg)) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param sg DOCUMENT ME!\r
+     */\r
+    public void addGroup(SequenceGroup sg)\r
+    {\r
+        if (!sequenceGroups.contains(sg))\r
+        {\r
             sequenceGroups.addElement(sg);\r
         }\r
     }\r
 \r
-    public void addOrRemove(SequenceGroup sg) {\r
-        if (sequenceGroups.contains(sg)) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param sg DOCUMENT ME!\r
+     */\r
+    public void addOrRemove(SequenceGroup sg)\r
+    {\r
+        if (sequenceGroups.contains(sg))\r
+        {\r
             deleteGroup(sg);\r
-        } else {\r
+        }\r
+        else\r
+        {\r
             addGroup(sg);\r
         }\r
     }\r
 \r
-    public void deleteGroup(SequenceGroup sg) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param sg DOCUMENT ME!\r
+     */\r
+    public void deleteGroup(SequenceGroup sg)\r
+    {\r
         sequenceGroups.removeElement(sg);\r
     }\r
 \r
-    public void setSuperGroupProperties(SequenceGroup sg) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param sg DOCUMENT ME!\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
+        for (int i = 0; i < sequenceGroups.size(); i++)\r
+        {\r
             SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);\r
             temp.cs = sg.cs;\r
             temp.colourText = sg.colourText;\r
@@ -93,11 +155,25 @@ public class SuperGroup {
         }\r
     }\r
 \r
-    public int getSize() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public int getSize()\r
+    {\r
         return sequenceGroups.size();\r
     }\r
 \r
-    public SequenceGroup getGroupeAt(int i) {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param i DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public SequenceGroup getGroupeAt(int i)\r
+    {\r
         return (SequenceGroup) sequenceGroups.elementAt(i);\r
     }\r
 }\r