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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
0a1c408
..
a944f38
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-1,19
+1,21
@@
/*
/*
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* 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.
*
*
* 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.
*/
/**
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
@@
-23,10
+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
@@
-60,17
+68,20
@@
public class JPredFile extends AlignFile
/**
* Creates a new JPredFile object.
*
/**
* Creates a new JPredFile object.
*
+ * BH allows File or String
+ *
* @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(Object inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public JPredFile(FileParse source) throws IOException
}
public JPredFile(FileParse source) throws IOException
@@
-122,6
+133,7
@@
public class JPredFile extends AlignFile
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
public void initData()
{
super.initData();
@@
-133,6
+145,7
@@
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 ");
@@
-197,7
+210,7
@@
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);
@@
-208,16
+221,16
@@
public class JPredFile extends AlignFile
for (int j = 0; j < i; j++)
{
for (int j = 0; j < i; j++)
{
- scores.setElementAt(
- (Object) ((Float) scores.elementAt(j)).toString(), j);
+ scores.setElementAt(((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);
@@
-257,7
+270,9
@@
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++;
}
@@
-270,7
+285,7
@@
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));
}
}
}
}
}
}
@@
-286,18
+301,20
@@
public class JPredFile extends AlignFile
{
// Add all sequence like objects
Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
{
// Add all sequence like objects
Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
- seq_entries.elementAt(i).toString(), 1, seq_entries
- .elementAt(i).toString().length());
+ seq_entries.elementAt(i).toString(), 1,
+ seq_entries.elementAt(i).toString().length());
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()
- .startsWith("align;")) && (QuerySeqPosition == -1))
+ if ((newSeq.getName().startsWith("QUERY")
+ || newSeq.getName().startsWith("align;"))
+ && (QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
}
{
QuerySeqPosition = seqs.size();
}
@@
-317,9
+334,10
@@
public class JPredFile extends AlignFile
} catch (Exception e)
{
tal = null;
} 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;
e.printStackTrace(); // java 1.1 does not have :
// ex.setStackTrace(e.getStackTrace());
throw ex;
@@
-338,7
+356,8
@@
public class JPredFile extends AlignFile
*
* @return String
*/
*
* @return String
*/
- public String print()
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return "Not Supported";
}
{
return "Not Supported";
}
@@
-349,17
+368,17
@@
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)
@@
-390,7
+409,7
@@
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);