From 7387d1f2fa08709dd4b954ce9f7cfc3d41b3dc8a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Dec 2004 16:24:30 +0000
Subject: [PATCH] Now has res start, res end

---
 src/jalview/datamodel/SequenceGroup.java |  153 +++++++++++++++++++-----------
 1 file changed, 98 insertions(+), 55 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c8b375a..051db30 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -5,35 +5,40 @@ import jalview.analysis.*;
 import jalview.datamodel.*;
 import java.util.Vector;
 
-public class SequenceGroup{
-    String groupName;
-    boolean isSelected;
-    boolean displayBoxes;
-    boolean displayText;
-    boolean colourText;
-    boolean display;
-    Conservation conserve;
-    Vector   aaFrequency;
-    boolean     aaFrequencyValid = false;
-    public Vector sequences = new Vector();
-    int         width = -1;
-    public ColourSchemeI cs;
-
-
-  public SequenceGroup() {
+public class SequenceGroup
+{
+  String groupName;
+  boolean isSelected;
+  boolean displayBoxes;
+  boolean displayText;
+  boolean colourText;
+  boolean display;
+  Conservation conserve;
+  Vector aaFrequency;
+  boolean aaFrequencyValid = false;
+  public Vector sequences = new Vector();
+  int width = -1;
+  public ColourSchemeI cs;
+  int startRes = 20;
+  int endRes = 35;
+
+  public SequenceGroup()
+  {
     groupName = "Group";
     this.isSelected = false;
     this.displayBoxes = true;
     this.displayText = true;
     this.colourText = false;
     this.display = true;
-    cs = new ZappoColourScheme();
+    cs = null;
   }
 
-  public SequenceGroup( String groupName, ColourSchemeI scheme, boolean isSelected,
-                        boolean displayBoxes, boolean displayText,
-                        boolean colourText,
-                        boolean display) {
+  public SequenceGroup(String groupName, ColourSchemeI scheme,
+                       boolean isSelected,
+                       boolean displayBoxes, boolean displayText,
+                       boolean colourText,
+                       boolean display)
+  {
 
     this.groupName = groupName;
     this.isSelected = isSelected;
@@ -53,69 +58,107 @@ public class SequenceGroup{
   {
     groupName = name;
   }
-  public Conservation getConservation() {
-     return conserve;
+
+  public Conservation getConservation()
+  {
+    return conserve;
   }
+
   public void setConservation(Conservation c)
-  { conserve = c; }
+  {
+    conserve = c;
+  }
 
-  public void addSequence(SequenceI s) {
+  public void addSequence(SequenceI s)
+  {
     sequences.addElement(s);
   }
 
-  public void deleteSequence(SequenceI s) {
+  public void deleteSequence(SequenceI s)
+  {
     sequences.removeElement(s);
   }
 
-  public void setColourText(boolean state) {
+  public void setColourText(boolean state)
+  {
     colourText = state;
   }
-  public boolean getColourText() {
+
+  public boolean getColourText()
+  {
     return colourText;
   }
 
-  public void setDisplayText(boolean state) {
+  public void setDisplayText(boolean state)
+  {
     displayText = state;
   }
 
-  public boolean getDisplayText() {
+  public boolean getDisplayText()
+  {
     return displayText;
   }
 
-  public void setDisplayBoxes(boolean state) {
+  public void setDisplayBoxes(boolean state)
+  {
     displayBoxes = state;
   }
 
-  public boolean getDisplayBoxes() {
+  public boolean getDisplayBoxes()
+  {
     return displayBoxes;
   }
 
-    public int getSize() {
-	return sequences.size();
-    }
-    public SequenceI  getSequenceAt(int i) {
-	return (SequenceI)sequences.elementAt(i);
-    }
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  public void setStartRes(int i)
+  {
+    startRes = i;
+  }
+
+  public void setEndRes(int i)
+  {
+    endRes = i;
+  }
+
+  public int getSize()
+  {
+    return sequences.size();
+  }
 
-    public Vector getAAFrequency() {
-	if (aaFrequency == null || aaFrequencyValid == false) {
-	    aaFrequency = AAFrequency.calculate(sequences,0,getWidth());
-	    aaFrequencyValid = true;
-	}
-	return aaFrequency;
+  public SequenceI getSequenceAt(int i)
+  {
+    return (SequenceI) sequences.elementAt(i);
+  }
+
+  public Vector getAAFrequency()
+  {
+    if (aaFrequency == null || aaFrequencyValid == false)
+    {
+      aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
+      aaFrequencyValid = true;
     }
+    return aaFrequency;
+  }
 
-    public int getWidth()
+  public int getWidth()
+  {
+    System.out.println("it is called");
+    // MC This needs to get reset when characters are inserted and deleted
+    for (int i = 0; i < sequences.size(); i++)
     {
-	// 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;
+      SequenceI seq = (SequenceI) sequences.elementAt(i);
+      if (seq.getLength() > width)
+        width = seq.getLength();
     }
+    return width;
+  }
 }
-
-
-- 
1.7.10.2