X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=ddb2ddcc57b38428880704b3afd1b9031a343bc4;hb=7ac2996be1e7428d1651793c4a1b7e4091f221b9;hp=f41c2c31caaa2b8c72505b215f1fd774fb49bcac;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index f41c2c3..ddb2ddc 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
* PredFile.java
@@ -22,10 +25,16 @@
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
+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
@@ -290,9 +299,11 @@ public class JPredFile extends AlignFile
if (maxLength != seq_entries.elementAt(i).toString().length())
{
- throw new IOException("JPredConcise: Entry ("
- + ids.elementAt(i).toString()
- + ") has an unexpected number of columns");
+ 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()
@@ -317,8 +328,10 @@ public class JPredFile extends AlignFile
{
tal = null;
IOException ex = new IOException(
- "Couldn't parse concise annotation for prediction profile.\n"
- + e);
+ 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;