X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=552a5f84a99600c4c6d4f0a3bb480a8d38fb2de1;hb=c1e70ea0a01d2c916675aa8020970c6696d0dba5;hp=b5f31bccc0ee0e5d3904f568d8b75c986d4eef47;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b5f31bc..552a5f8 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,8 +20,6 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 
-import jalview.util.*;
-
 import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
@@ -205,7 +203,7 @@ public class Alignment implements AlignmentI
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.getSequences(false).contains(s))
+            if (sg.getSequences(null).contains(s))
             {
                 return sg;
             }
@@ -229,14 +227,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.getSequences(false)==null)
+            if(sg==null || sg.getSequences(null)==null)
             {
               this.deleteGroup(sg);
               gSize--;
               continue;
             }
 
-            if (sg.getSequences(false).contains(s))
+            if (sg.getSequences(null).contains(s))
             {
                 temp.addElement(sg);
             }
@@ -261,9 +259,7 @@ public class Alignment implements AlignmentI
         {
           if(hiddenSequences.getSize()>0)
           {
-            //We're not going to make groups of
-            //Hidden sequences
-            int i, iSize = sg.getSize(false);
+            int i, iSize = sg.getSize();
             for (i = 0; i < iSize; i++)
             {
               if (!sequences.contains(sg.getSequenceAt(i)))
@@ -274,7 +270,7 @@ public class Alignment implements AlignmentI
               }
             }
 
-            if (sg.getSize(true) < 1)
+            if (sg.getSize() < 1)
               return;
           }
 
@@ -662,34 +658,6 @@ public class Alignment implements AlignmentI
     {
       return hiddenSequences;
     }
-    SequenceI [] getVisibleAndRepresentedSeqs()
-    {
-      if(hiddenSequences==null || hiddenSequences.getSize()<1)
-        return getSequencesArray();
-
-      Vector seqs = new Vector();
-      SequenceI seq;
-      SequenceGroup hidden;
-      for (int i = 0; i < sequences.size(); i++)
-      {
-        seq = (SequenceI) sequences.elementAt(i);
-        seqs.addElement(seq);
-        hidden = seq.getHiddenSequences();
-        if(hidden!=null)
-        {
-          for(int j=0; j<hidden.getSize(false); j++)
-          {
-            seqs.addElement(hidden.getSequenceAt(j));
-          }
-        }
-      }
-      SequenceI [] result = new SequenceI[seqs.size()];
-      for(int i=0; i<seqs.size(); i++)
-        result[i] = (SequenceI)seqs.elementAt(i);
-
-      return result;
-
-    }
 
   public CigarArray getCompactAlignment()
   {