From c19db28827bb0f5704354e4bfc049855fc3f220a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:13:05 +0000
Subject: [PATCH] SequenceGroup may have name

---
 src/jalview/datamodel/Alignment.java  |   35 ++++++++++++++++++++++-----------
 src/jalview/datamodel/AlignmentI.java |    2 ++
 2 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 69b66e0..9b6d729 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,7 +1,5 @@
 package jalview.datamodel;
 
-import jalview.jbgui.*;
-import jalview.schemes.*;
 import jalview.analysis.*;
 import jalview.util.*;
 import java.util.*;
@@ -23,16 +21,17 @@ public class Alignment implements AlignmentI
   public Alignment(SequenceI[] seqs) {
     sequences = new Vector();
 
-    for (int i=0; i < seqs.length; i++) {
+    for (int i=0; i < seqs.length; i++)
       sequences.addElement(seqs[i]);
-    }
 
-    groups.addElement(new SequenceGroup());
+    SequenceGroup all = new SequenceGroup();
+    all.setName("Group 1");
+    groups.addElement(all);
 
     int i = 0;
 
     while (i < seqs.length) {
-      addToGroup((SequenceGroup)groups.elementAt(0),seqs[i]);
+      addToGroup(all,seqs[i]);
       i++;
     }
 
@@ -324,11 +323,12 @@ public class Alignment implements AlignmentI
 
   /**    */
   public SequenceGroup findGroup(SequenceI s) {
-    for (int i = 0; i < this.groups.size();i++) {
+    for (int i = 0; i < this.groups.size();i++)
+    {
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-      if (sg.sequences.contains(s)) {
+      if (sg.sequences.contains(s))
         return sg;
-      }
+
     }
     return null;
 
@@ -375,9 +375,22 @@ public class Alignment implements AlignmentI
     int i = 0;
     while (i < sequences.size()) {
       SequenceI s = getSequenceAt(i);
-      if (s.getName().equals(name)) {
+      if (s.getName().equals(name))
         return s;
-      }
+
+      i++;
+    }
+    return null;
+  }
+
+  /**    */
+  public SequenceI findbyDisplayId(String name) {
+    int i = 0;
+    while (i < sequences.size()) {
+      SequenceI s = getSequenceAt(i);
+      if (s.getDisplayId().equals(name))
+        return s;
+
       i++;
     }
     return null;
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 6a1e026..5a21a04 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -29,6 +29,8 @@ public interface AlignmentI {
   public void        insertColumns(SequenceI[] seqs, int pos) ;
 
   public SequenceI   findName(String name) ;
+  public SequenceI findbyDisplayId(String name);
+
   public int         findIndex(SequenceI s) ;
 
   // Modifying
-- 
1.7.10.2