From ba5b5887237cad6e47d46232b0704ac874cd3e3c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:14:22 +0000
Subject: [PATCH] now has a name

---
 src/jalview/datamodel/SequenceGroup.java |   48 +++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 17 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index de746ba..c8b375a 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,14 +1,12 @@
 package jalview.datamodel;
 
-import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
-
 import java.util.Vector;
-import java.awt.*;
 
-public class SequenceGroup {
+public class SequenceGroup{
+    String groupName;
     boolean isSelected;
     boolean displayBoxes;
     boolean displayText;
@@ -17,33 +15,50 @@ public class SequenceGroup {
     Conservation conserve;
     Vector   aaFrequency;
     boolean     aaFrequencyValid = false;
-    Vector sequences = new Vector();
+    public Vector sequences = new Vector();
     int         width = -1;
+    public ColourSchemeI cs;
 
 
   public SequenceGroup() {
+    groupName = "Group";
     this.isSelected = false;
     this.displayBoxes = true;
     this.displayText = true;
     this.colourText = false;
     this.display = true;
+    cs = new ZappoColourScheme();
   }
 
-  public SequenceGroup( ColourSchemeI scheme, boolean isSelected,
+  public SequenceGroup( String groupName, ColourSchemeI scheme, boolean isSelected,
                         boolean displayBoxes, boolean displayText,
                         boolean colourText,
                         boolean display) {
 
+    this.groupName = groupName;
     this.isSelected = isSelected;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
     this.display = display;
+    this.cs = scheme;
+  }
+
+  public String getName()
+  {
+    return groupName;
   }
 
+  public void setName(String name)
+  {
+    groupName = name;
+  }
   public Conservation getConservation() {
      return conserve;
   }
+  public void setConservation(Conservation c)
+  { conserve = c; }
+
   public void addSequence(SequenceI s) {
     sequences.addElement(s);
   }
@@ -84,22 +99,21 @@ public class SequenceGroup {
 
     public Vector getAAFrequency() {
 	if (aaFrequency == null || aaFrequencyValid == false) {
-	    aaFrequency = AAFrequency.calculate(sequences,1,getWidth());
+	    aaFrequency = AAFrequency.calculate(sequences,0,getWidth());
 	    aaFrequencyValid = true;
 	}
 	return aaFrequency;
     }
-    public int getWidth() {
-	// MC This needs to get reset when characters are inserted and deleted
-	if (width == -1) {
-	    for (int i = 0; i < sequences.size(); i++) {
-		SequenceI seq = (SequenceI)sequences.elementAt(i);
-		if (seq.getLength() > width) {
-		    width = seq.getLength();
-		}
-	    }
-	}
 
+    public int getWidth()
+    {
+	// MC This needs to get reset when characters are inserted and deleted
+        for (int i = 0; i < sequences.size(); i++)
+        {
+          SequenceI seq = (SequenceI) sequences.elementAt(i);
+          if (seq.getLength() > width)
+            width = seq.getLength();
+        }
 	return width;
     }
 }
-- 
1.7.10.2