X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=8306873e331f0f931d87e325f7322dd686735032;hb=6e5cc965552fadac700baa9b076777697f66386a;hp=1f568d6b46a4a54db5170b618d757c372367423b;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 1f568d6..8306873 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,6 +23,7 @@ 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;
@@ -52,8 +53,7 @@ public class SeqGroupIndexVector extends InputType implements
 {
   public SeqGroupIndexVector()
   {
-    super(new Class[]
-    { AlignmentI.class });
+    super(new Class[] { AlignmentI.class });
   }
 
   /**
@@ -91,7 +91,7 @@ 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,lowest=al.getHeight(), highest=0;
+    int p = 0, lowest = al.getHeight(), highest = 0;
     List<SequenceGroup> sgs;
     synchronized (sgs = al.getGroups())
     {
@@ -99,8 +99,12 @@ 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)
@@ -108,18 +112,17 @@ public class SeqGroupIndexVector extends InputType implements
         for (SequenceI sq : sg.getSequencesInOrder(al))
         {
           p = al.findIndex(sq);
-          if (lowest>p)
+          if (lowest > p)
           {
-            lowest=p;
+            lowest = p;
           }
-          if (highest<p)
+          if (highest < p)
           {
-            highest=p;
+            highest = p;
           }
           if (se == null)
           {
-            se = new int[]
-            { p, p };
+            se = new int[] { p, p };
           }
           else
           {
@@ -139,20 +142,18 @@ public class SeqGroupIndexVector extends InputType implements
     // remaining group ? - these might be at the start or the end
     if (gl.size() > 0)
     {
-      if (lowest-1>minsize)
+      if (lowest - 1 > minsize)
       {
-        gl.add(0, new int[]
-          { 0, lowest-2});
+        gl.add(0, new int[] { 0, lowest - 2 });
       }
-      if ((al.getHeight()-1-highest)>minsize)
+      if ((al.getHeight() - 1 - highest) > minsize)
       {
-        gl.add(new int[] { highest+1, al.getHeight()-1});
+        gl.add(new int[] { highest + 1, al.getHeight() - 1 });
       }
     }
     else
     {
-      gl.add(new int[]
-      { 0, al.getHeight() - 1 });
+      gl.add(new int[] { 0, al.getHeight() - 1 });
     }
     if (min >= 0 && gl.size() < min)
     {
@@ -278,8 +279,8 @@ public class SeqGroupIndexVector extends InputType implements
     List<OptionI> lst = getBaseOptions();
     lst.add(new Option("sep",
             "Separator character between elements of vector", true, ",",
-            sep, Arrays.asList(new String[]
-            { " ", ",", ";", "\t", "|" }), null));
+            sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+            null));
     lst.add(new IntegerParameter("minsize",
             "Minimum size of partition allowed by service", true, 1,
             minsize, 1, 0));