X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=af8c949db48c581dd3eb0f59c75227b87de30e8f;hb=d131f05c68757d57e5e4a1f440196ae1b70f3b8a;hp=d9836c1ef3d4c106711ff6ef8400d0f5c573feeb;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index d9836c1..af8c949 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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
@@ -25,15 +28,8 @@ package jalview.io;
import java.io.*;
import java.util.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-
import jalview.datamodel.*;
+import jalview.util.MessageManager;
/**
* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
@@ -74,19 +70,13 @@ public class JPredFile extends AlignFile
*
* @throws IOException
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
*/
- public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public JPredFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public JPredFile(FileParse source) throws IOException
{
super(source);
}
@@ -304,9 +294,7 @@ 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()
@@ -330,9 +318,7 @@ public class JPredFile extends AlignFile
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(
- "Couldn't parse concise annotation for prediction profile.\n"
- + e);
+ 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;
@@ -361,14 +347,8 @@ public class JPredFile extends AlignFile
*
* @param args
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
*/
- public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public static void main(String[] args)
{
try
{