X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=3908bc4c582a2edbb7613d2f9fd2d30d0c3f84d2;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=458fbba1f3af1960ba75e5c063a3739ad9ee7d5a;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 458fbba..3908bc4 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 2.9.0b2)
+ * 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 .
+ * 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
@@ -207,8 +216,8 @@ public class JPredFile extends AlignFile
for (int j = 0; j < i; j++)
{
- scores.setElementAt((Object) ((Float) scores.elementAt(j))
- .toString(), j);
+ scores.setElementAt(
+ (Object) ((Float) scores.elementAt(j)).toString(), j);
}
scores.addElement((Object) ascore);
@@ -290,14 +299,15 @@ 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()
- .startsWith("align;"))
- && (QuerySeqPosition == -1))
+ .startsWith("align;")) && (QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
}
@@ -318,8 +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;