X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=4d7509d1a647fb18458d850dc4790c6db92d2b01;hb=cd1ded4a9a6f3478f3b704c9c97fd323ac5dbdd7;hp=6bccec3c51d0a288e38a9785108b1201237d41bc;hpb=8c7f6c70f34bcb8dfe5e327288806ec6cb363042;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6bccec3..4d7509d 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -8,45 +8,41 @@ import java.util.Vector;
 public class SequenceGroup
 {
   String groupName;
-  boolean isSelected;
+  Conservation conserve;
+  Vector aaFrequency;
   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;
+  int startRes = 0;
+  int endRes = 0;
 
   public SequenceGroup()
   {
     groupName = "Group";
-    this.isSelected = false;
     this.displayBoxes = true;
     this.displayText = true;
     this.colourText = false;
-    this.display = true;
     cs = null;
   }
 
   public SequenceGroup(String groupName, ColourSchemeI scheme,
-                       boolean isSelected,
                        boolean displayBoxes, boolean displayText,
                        boolean colourText,
-                       boolean display)
+                       int start,
+                       int end)
   {
 
     this.groupName = groupName;
-    this.isSelected = isSelected;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.display = display;
     this.cs = scheme;
+    startRes = start;
+    endRes = end;
   }
 
   public String getName()
@@ -75,69 +71,78 @@ public class SequenceGroup
       sequences.addElement(s);
   }
 
+  public void addOrRemove(SequenceI s)
+  {
+    if(sequences.contains(s))
+      deleteSequence(s);
+    else
+      addSequence(s);
+  }
+
   public void deleteSequence(SequenceI s)
   {
     sequences.removeElement(s);
   }
 
-  public void setColourText(boolean state)
+
+  public int getStartRes()
   {
-    colourText = state;
+    return startRes;
   }
 
-  public boolean getColourText()
+  public int getEndRes()
   {
-    return colourText;
+    return endRes;
   }
 
-  public void setDisplayText(boolean state)
+  public void setStartRes(int i)
   {
-    displayText = state;
+    startRes = i;
   }
 
-  public boolean getDisplayText()
+  public void setEndRes(int i)
   {
-    return displayText;
+    endRes = i;
   }
 
-  public void setDisplayBoxes(boolean state)
+  public int getSize()
   {
-    displayBoxes = state;
+    return sequences.size();
   }
 
-  public boolean getDisplayBoxes()
+  public SequenceI getSequenceAt(int i)
   {
-    return displayBoxes;
+    return (SequenceI) sequences.elementAt(i);
   }
 
-  public int getStartRes()
+  public void setColourText(boolean state)
   {
-    return startRes;
+    colourText = state;
   }
 
-  public int getEndRes()
+  public boolean getColourText()
   {
-    return endRes;
+    return colourText;
   }
 
-  public void setStartRes(int i)
+  public void setDisplayText(boolean state)
   {
-    startRes = i;
+    displayText = state;
   }
 
-  public void setEndRes(int i)
+  public boolean getDisplayText()
   {
-    endRes = i;
+    return displayText;
   }
 
-  public int getSize()
+  public void setDisplayBoxes(boolean state)
   {
-    return sequences.size();
+    displayBoxes = state;
   }
 
-  public SequenceI getSequenceAt(int i)
+  public boolean getDisplayBoxes()
   {
-    return (SequenceI) sequences.elementAt(i);
+    return displayBoxes;
   }
 
   public Vector getAAFrequency()