X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSuperGroup.java;h=b2993b5a1871a8af53aef67364875edf8325e8ce;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=ad6f703ad002ee72d9852ae48a3f1a78b238f192;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

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