JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[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 0532035..6bc208b 100644 (file)
--- 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 2.9)
+ * Copyright (C) 2015 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;
@@ -49,8 +53,7 @@ public class SeqGroupIndexVector extends InputType implements
 {
   public SeqGroupIndexVector()
   {
-    super(new Class[]
-    { AlignmentI.class });
+    super(new Class[] { AlignmentI.class });
   }
 
   /**
@@ -88,7 +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())
     {
@@ -96,8 +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)
@@ -105,18 +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
           {
@@ -136,20 +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)
     {
@@ -275,8 +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));