JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / rest / params / SeqGroupIndexVector.java

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 1f568d6..2479e76 100644 (file)
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 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;
@@ -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,lowest=al.getHeight(), highest=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)
@@ -108,13 +108,13 @@ 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)
           {
@@ -139,14 +139,15 @@ 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});
+        { 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