X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=9210414bc55099d40b668cc465347f748dc2b13c;hb=0aa7f6fab658c9a203b410d4bead72217da5c9a0;hp=8306873e331f0f931d87e325f7322dd686735032;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 8306873..9210414 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -48,8 +48,8 @@ import org.apache.http.entity.mime.content.StringBody;
  * @author JimP
  * 
  */
-public class SeqGroupIndexVector extends InputType implements
-        AlignmentProcessor
+public class SeqGroupIndexVector extends InputType
+        implements AlignmentProcessor
 {
   public SeqGroupIndexVector()
   {
@@ -75,6 +75,7 @@ public class SeqGroupIndexVector extends InputType implements
    *          - alignment to be processed
    * @return al or a new alignment with appropriate attributes/order for input
    */
+  @Override
   public AlignmentI prepareAlignment(AlignmentI al)
   {
     jalview.analysis.AlignmentSorter.sortByGroup(al);
@@ -90,21 +91,19 @@ public class SeqGroupIndexVector extends InputType implements
     AlignmentI al = rj.getAlignmentForInput(token, type);
     // assume that alignment is properly ordered so groups form consecutive
     // blocks
-    ArrayList<int[]> gl = new ArrayList<int[]>();
+    ArrayList<int[]> gl = new ArrayList<>();
     int p = 0, lowest = al.getHeight(), highest = 0;
-    List<SequenceGroup> sgs;
-    synchronized (sgs = al.getGroups())
+    List<SequenceGroup> sgs = al.getGroups();
+    synchronized (sgs)
     {
       for (SequenceGroup sg : sgs)
       {
         if (sg.getSize() < minsize)
         {
-          throw new NoValidInputDataException(
-                  MessageManager
-                          .formatMessage(
-                                  "exception.notvaliddata_group_contains_less_than_min_seqs",
-                                  new String[] { Integer.valueOf(minsize)
-                                          .toString() }));
+          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)
@@ -127,9 +126,13 @@ public class SeqGroupIndexVector extends InputType implements
           else
           {
             if (p < se[0])
+            {
               se[0] = p;
+            }
             if (p > se[1])
+            {
               se[1] = p;
+            }
           }
         }
         if (se != null)
@@ -170,7 +173,9 @@ public class SeqGroupIndexVector extends InputType implements
     int[][] vals = gl.toArray(new int[gl.size()][]);
     int[] srt = new int[gl.size()];
     for (int i = 0; i < vals.length; i++)
+    {
       srt[i] = vals[i][0];
+    }
     jalview.util.QuickSort.sort(srt, vals);
     list = false;
     int last = vals[0][0] - 1;
@@ -212,7 +217,7 @@ public class SeqGroupIndexVector extends InputType implements
   @Override
   public List<String> getURLEncodedParameter()
   {
-    ArrayList<String> prms = new ArrayList<String>();
+    ArrayList<String> prms = new ArrayList<>();
     super.addBaseParams(prms);
     prms.add("minsize='" + minsize + "'");
     prms.add("sep='" + sep + "'");
@@ -245,7 +250,9 @@ public class SeqGroupIndexVector extends InputType implements
       {
         minsize = Integer.valueOf(val);
         if (minsize >= 0)
+        {
           return true;
+        }
       } catch (Exception x)
       {
 
@@ -261,8 +268,8 @@ public class SeqGroupIndexVector extends InputType implements
         return true;
       } catch (Exception x)
       {
-        warnings.append("Invalid molecule type '" + val
-                + "'. Must be one of (");
+        warnings.append(
+                "Invalid molecule type '" + val + "'. Must be one of (");
         for (molType v : molType.values())
         {
           warnings.append(" " + v);
@@ -279,8 +286,8 @@ 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));