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file format enum wip changes
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
c2bbe9e
..
451ece8
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
@@
-64,15
+70,16
@@
public class JPredFile extends AlignFile
*
* @param inFile
* DOCUMENT ME!
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public JPredFile(String inFile, String type) throws IOException
+ public JPredFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public JPredFile(FileParse source) throws IOException
}
public JPredFile(FileParse source) throws IOException
@@
-124,6
+131,7
@@
public class JPredFile extends AlignFile
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
public void initData()
{
super.initData();
@@
-135,6
+143,7
@@
public class JPredFile extends AlignFile
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
+ @Override
public void parse() throws IOException
{
// JBPNote log.System.out.println("all read in ");
public void parse() throws IOException
{
// JBPNote log.System.out.println("all read in ");
@@
-199,7
+208,7
@@
public class JPredFile extends AlignFile
ascore = symbols.nextToken();
Float score = new Float(ascore);
ascore = symbols.nextToken();
Float score = new Float(ascore);
- scores.addElement((Object) score);
+ scores.addElement(score);
}
Scores.put(id, scores);
}
Scores.put(id, scores);
@@
-211,15
+220,15
@@
public class JPredFile extends AlignFile
for (int j = 0; j < i; j++)
{
scores.setElementAt(
for (int j = 0; j < i; j++)
{
scores.setElementAt(
- (Object) ((Float) scores.elementAt(j)).toString(), j);
+ ((Float) scores.elementAt(j)).toString(), j);
}
}
- scores.addElement((Object) ascore);
+ scores.addElement(ascore);
while (symbols.hasMoreTokens())
{
ascore = symbols.nextToken();
while (symbols.hasMoreTokens())
{
ascore = symbols.nextToken();
- scores.addElement((Object) ascore);
+ scores.addElement(ascore);
}
Scores.put(id, scores);
}
Scores.put(id, scores);
@@
-259,7
+268,9
@@
public class JPredFile extends AlignFile
}
if (QuerySeqPosition == -1)
}
if (QuerySeqPosition == -1)
+ {
QuerySeqPosition = ids.size();
QuerySeqPosition = ids.size();
+ }
ids.addElement(name);
noSeqs++;
}
ids.addElement(name);
noSeqs++;
}
@@
-272,7
+283,7
@@
public class JPredFile extends AlignFile
seq_entries.addElement(newseq.toString());
ids.addElement(id);
seq_entries.addElement(newseq.toString());
ids.addElement(id);
- Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
+ Symscores.put(id, new Integer(ids.size() - 1));
}
}
}
}
}
}
@@
-293,9
+304,11
@@
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
+333,10
@@
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;
@@
-340,6
+355,7
@@
public class JPredFile extends AlignFile
*
* @return String
*/
*
* @return String
*/
+ @Override
public String print()
{
return "Not Supported";
public String print()
{
return "Not Supported";
@@
-351,17
+367,17
@@
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
{
- JPredFile blc = new JPredFile(args[0], "File");
+ JPredFile jpred = new JPredFile(args[0], DataSourceType.FILE);
- for (int i = 0; i < blc.seqs.size(); i++)
+ for (int i = 0; i < jpred.seqs.size(); i++)
{
{
- System.out.println(((Sequence) blc.seqs.elementAt(i)).getName()
+ System.out.println(((Sequence) jpred.seqs.elementAt(i)).getName()
+ "\n"
+ "\n"
- + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
+ + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
+ "\n");
}
} catch (java.io.IOException e)
+ "\n");
}
} catch (java.io.IOException e)
@@
-392,7
+408,7
@@
public class JPredFile extends AlignFile
}
// check that no stray annotations have been added at the end.
{
}
// check that no stray annotations have been added at the end.
{
- SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
+ SequenceI sq = seqs.elementAt(j - 1);
if (sq.getName().toUpperCase().startsWith("JPRED"))
{
annotSeqs.addElement(sq);
if (sq.getName().toUpperCase().startsWith("JPRED"))
{
annotSeqs.addElement(sq);