JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index d9836c1..5bc615e 100755 (executable)
--- 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 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 /**
  * PredFile.java
@@ -22,18 +25,16 @@
  */
 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.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
@@ -74,19 +75,13 @@ 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 +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()
@@ -331,8 +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;
@@ -361,14 +360,8 @@ 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
     {