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JAL-966 SearchResultsI now on viewmodels.AlignmentViewport rather than on SeqCanvas
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
c2bbe9e
..
ddb2ddc
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-25,10
+25,16
@@
*/
package jalview.io;
*/
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
/**
* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
@@
-293,9
+299,11
@@
public class JPredFile extends AlignFile
if (maxLength != seq_entries.elementAt(i).toString().length())
{
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()
}
if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
@@
-320,8
+328,10
@@
public class JPredFile extends AlignFile
{
tal = null;
IOException ex = new IOException(
{
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;
e.printStackTrace(); // java 1.1 does not have :
// ex.setStackTrace(e.getStackTrace());
throw ex;
@@
-351,7
+361,7
@@
public class JPredFile extends AlignFile
* @param args
* DOCUMENT ME!
*/
* @param args
* DOCUMENT ME!
*/
- public static void main(String[] args)
+ public static void main(String[] args)
{
try
{
{
try
{