JAL-2738 copy to spikes/mungo

[jalview.git] / src / jalview / io / JPredFile.java

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index fd971fd..026c879 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -219,8 +219,8 @@ public class JPredFile extends AlignFile
 
           for (int j = 0; j < i; j++)
           {
-            scores.setElementAt(
-                    ((Float) scores.elementAt(j)).toString(), j);
+            scores.setElementAt(((Float) scores.elementAt(j)).toString(),
+                    j);
           }
 
           scores.addElement(ascore);
@@ -299,20 +299,20 @@ public class JPredFile extends AlignFile
     {
       // Add all sequence like objects
       Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-              seq_entries.elementAt(i).toString(), 1, seq_entries
-                      .elementAt(i).toString().length());
+              seq_entries.elementAt(i).toString(), 1,
+              seq_entries.elementAt(i).toString().length());
 
       if (maxLength != seq_entries.elementAt(i).toString().length())
       {
-        throw new IOException(
-                MessageManager
-                        .formatMessage(
-                                "exception.jpredconcide_entry_has_unexpected_number_of_columns",
-                                new String[] { ids.elementAt(i).toString() }));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+                new String[]
+                { ids.elementAt(i).toString() }));
       }
 
-      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
-              .startsWith("align;")) && (QuerySeqPosition == -1))
+      if ((newSeq.getName().startsWith("QUERY")
+              || newSeq.getName().startsWith("align;"))
+              && (QuerySeqPosition == -1))
       {
         QuerySeqPosition = seqs.size();
       }
@@ -332,11 +332,10 @@ public class JPredFile extends AlignFile
       } catch (Exception e)
       {
         tal = null;
-        IOException ex = new IOException(
-                MessageManager
-                        .formatMessage(
-                                "exception.couldnt_parse_concise_annotation_for_prediction",
-                                new String[] { e.getMessage() }));
+        IOException ex = new IOException(MessageManager.formatMessage(
+                "exception.couldnt_parse_concise_annotation_for_prediction",
+                new String[]
+                { e.getMessage() }));
         e.printStackTrace(); // java 1.1 does not have :
                              // ex.setStackTrace(e.getStackTrace());
         throw ex;