X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=2479e763d2518da6ae9a67e95a85723ef665dbf2;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=4b21229f39dbb4483836245d773cd7bbe3935283;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 4b21229..2479e76 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,25 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.rest.params;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
 import jalview.ws.params.OptionI;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.Option;
@@ -27,14 +31,11 @@ import jalview.ws.rest.AlignmentProcessor;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Vector;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
@@ -91,7 +92,7 @@ public class SeqGroupIndexVector extends InputType implements
     // assume that alignment is properly ordered so groups form consecutive
     // blocks
     ArrayList<int[]> gl = new ArrayList<int[]>();
-    int p = 0;
+    int p = 0, lowest = al.getHeight(), highest = 0;
     List<SequenceGroup> sgs;
     synchronized (sgs = al.getGroups())
     {
@@ -99,8 +100,7 @@ public class SeqGroupIndexVector extends InputType implements
       {
         if (sg.getSize() < minsize)
         {
-          throw new NoValidInputDataException("Group contains less than "
-                  + minsize + " sequences.");
+          throw new NoValidInputDataException(MessageManager.formatMessage("exception.notvaliddata_group_contains_less_than_min_seqs", new String[]{Integer.valueOf(minsize).toString()}));
         }
         // TODO: refactor to sequenceGroup for efficiency -
         // getAlignmentRowInterval(AlignmentI al)
@@ -108,6 +108,14 @@ public class SeqGroupIndexVector extends InputType implements
         for (SequenceI sq : sg.getSequencesInOrder(al))
         {
           p = al.findIndex(sq);
+          if (lowest > p)
+          {
+            lowest = p;
+          }
+          if (highest < p)
+          {
+            highest = p;
+          }
           if (se == null)
           {
             se = new int[]
@@ -131,40 +139,15 @@ public class SeqGroupIndexVector extends InputType implements
     // remaining group ? - these might be at the start or the end
     if (gl.size() > 0)
     {
-      int[] tail = gl.get(0);
-      if (tail[0] > 0)
+      if (lowest - 1 > minsize)
       {
-        if (1 + tail[0] > minsize)
-        {
-          gl.add(0, new int[]
-          { 0, tail[0] - 1 });
-        }
-        else
-        {
-          // lets be intelligent here - if the remaining sequences aren't enough
-          // to make a final group, then don't make one.
-          // throw new
-          // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
-        }
+        gl.add(0, new int[]
+        { 0, lowest - 2 });
       }
-      else
+      if ((al.getHeight() - 1 - highest) > minsize)
       {
-        tail = gl.get(gl.size() - 1);
-        if (1 + tail[1] < al.getHeight())
-        {
-          if (al.getHeight() - (1 + tail[1]) > minsize)
-          {
-            gl.add(new int[]
-            { tail[1] + 1, al.getHeight() - 1 });
-          }
-          else
-          {
-            // lets be intelligent here - if the remaining sequences aren't
-            // enough to make a final group, then don't make one.
-            // throw new
-            // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
-          }
-        }
+        gl.add(new int[]
+        { highest + 1, al.getHeight() - 1 });
       }
     }
     else