X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=5bc615ec0af0d76c4966daee69633db919f79875;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=abd44c09da8f81e2a45dc1748e876ab7fe90f8a5;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index abd44c0..5bc615e 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,12 +25,17 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
 /**
  * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
  * line is either a sequence (QUERY), a sequence profile (align;), or jnet
@@ -294,7 +299,11 @@ public class JPredFile extends AlignFile
 
       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()
@@ -318,7 +327,11 @@ 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;