SequenceGroup may have name

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 6a1e026..5a21a04 100755 (executable)
--- 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) ;\r
 \r
   public SequenceI   findName(String name) ;\r
+  public SequenceI findbyDisplayId(String name);\r
+\r
   public int         findIndex(SequenceI s) ;\r
 \r
   // Modifying\r