Updated with latest from mchmmer branch

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index db6e03f..c4fc66b 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -75,7 +75,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     /**
      * input
      */
-    ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+    ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
 
     /**
      * output
@@ -139,7 +139,6 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       compbio.data.sequence.FastaSequence seq;
       for (int i = 0, n = 0; i < seqs.length; i++)
       {
-
         String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
         // for
         // any
@@ -379,7 +378,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
     public List<Argument> getJabaArguments()
     {
-      List<Argument> newargs = new ArrayList<Argument>();
+      List<Argument> newargs = new ArrayList<>();
       if (preset != null && preset instanceof JabaWsParamSet)
       {
         newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
@@ -931,7 +930,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   void displayResults(boolean newFrame)
   {
     // view input or result data for each block
-    List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
+    List<AlignmentOrder> alorders = new ArrayList<>();
     SequenceI[][] results = new SequenceI[jobs.length][];
     AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
     String lastProgram = null;
@@ -981,7 +980,6 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     if (newFrame)
     {
       displayInNewFrame(al, alorders, hidden);
-
     }
     else
     {
@@ -1077,7 +1075,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     else
     {
       // construct a non-redundant ordering set
-      List<String> names = new ArrayList<String>();
+      List<String> names = new ArrayList<>();
       for (int i = 0, l = alorders.size(); i < l; i++)
       {
         String orderName = " Region " + i;