X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSuperGroup.java;h=b2993b5a1871a8af53aef67364875edf8325e8ce;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=4e2ac1cad48b822a3dd2a9e6b5a74fae5a509cd3;hpb=00b702186f1676036db687a8df5d335a4d5da54d;p=jalview.git

diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java
index 4e2ac1c..b2993b5 100755
--- a/src/jalview/datamodel/SuperGroup.java
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -1,95 +1,179 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 package jalview.datamodel;
 
-import jalview.schemes.*;
-import jalview.analysis.*;
 import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
 import java.util.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SuperGroup
 {
-  String groupName;
-  boolean displayBoxes;
-  boolean displayText;
-  boolean colourText;
-  public ColourSchemeI cs;
-  Vector sequenceGroups = new Vector();
-
-  public SuperGroup()
-  {
-    groupName = "Super group";
-    this.displayBoxes = true;
-    this.displayText = true;
-    this.colourText = false;
-    cs = null;
-  }
-
-
-  public SuperGroup(String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText)
-     {
-       this.groupName = groupName;
-       this.displayBoxes = displayBoxes;
-       this.displayText = displayText;
-       this.colourText = colourText;
-       this.cs = scheme;
-     }
-
-  public String getName()
-  {
-    return groupName;
-  }
-
-  public void setName(String name)
-  {
-    groupName = name;
-  }
-
-
-  public void addGroup(SequenceGroup sg)
-  {
-    if(!sequenceGroups.contains(sg))
-      sequenceGroups.addElement(sg);
-  }
-
-  public void addOrRemove(SequenceGroup sg)
-  {
-    if(sequenceGroups.contains(sg))
-      deleteGroup(sg);
-    else
-      addGroup(sg);
-  }
-
-  public void deleteGroup(SequenceGroup sg)
-  {
-    sequenceGroups.removeElement(sg);
-  }
-
-  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++)
+    String groupName;
+    boolean displayBoxes;
+    boolean displayText;
+    boolean colourText;
+
+    /** DOCUMENT ME!! */
+    public ColourSchemeI cs;
+    Vector sequenceGroups = new Vector();
+
+    /**
+     * Creates a new SuperGroup object.
+     */
+    public SuperGroup()
     {
-      SequenceGroup temp = (SequenceGroup)sequenceGroups.elementAt(i);
-      temp.cs = sg.cs;
-      temp.colourText = sg.colourText;
-      temp.displayText = sg.displayText;
-      temp.displayBoxes = sg.displayBoxes;
+        groupName = "Super group";
+        this.displayBoxes = true;
+        this.displayText = true;
+        this.colourText = false;
+        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)
+    {
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+    }
 
-  public int getSize()
-  {
-    return sequenceGroups.size();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
+        return groupName;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
+        groupName = name;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void addGroup(SequenceGroup sg)
+    {
+        if (!sequenceGroups.contains(sg))
+        {
+            sequenceGroups.addElement(sg);
+        }
+    }
 
-  public SequenceGroup getGroupeAt(int i)
-  {
-    return (SequenceGroup) sequenceGroups.elementAt(i);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void addOrRemove(SequenceGroup sg)
+    {
+        if (sequenceGroups.contains(sg))
+        {
+            deleteGroup(sg);
+        }
+        else
+        {
+            addGroup(sg);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void deleteGroup(SequenceGroup sg)
+    {
+        sequenceGroups.removeElement(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++)
+        {
+            SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);
+            temp.cs = sg.cs;
+            temp.colourText = sg.colourText;
+            temp.displayText = sg.displayText;
+            temp.displayBoxes = sg.displayBoxes;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSize()
+    {
+        return sequenceGroups.size();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup getGroupeAt(int i)
+    {
+        return (SequenceGroup) sequenceGroups.elementAt(i);
+    }
 }