/*
- * 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 <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
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
-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 java.io.IOException;
+import java.util.Hashtable;
+import java.util.Locale;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @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, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
- public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public JPredFile(FileParse source) throws IOException
{
super(source);
}
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
/**
* 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 ");
{
ascore = symbols.nextToken();
- Float score = new Float(ascore);
- scores.addElement((Object) score);
+ Float score = Float.valueOf(ascore);
+ scores.addElement(score);
}
Scores.put(id, scores);
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();
- scores.addElement((Object) ascore);
+ scores.addElement(ascore);
}
Scores.put(id, scores);
}
if (QuerySeqPosition == -1)
+ {
QuerySeqPosition = ids.size();
+ }
ids.addElement(name);
noSeqs++;
}
seq_entries.addElement(newseq.toString());
ids.addElement(id);
- Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
+ Symscores.put(id, Integer.valueOf(ids.size() - 1));
}
}
}
{
// 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())
{
- 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();
}
} 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;
*
* @return String
*/
- public String print()
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return "Not Supported";
}
*
* @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
{
- 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"
- + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
+ + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
+ "\n");
}
} catch (java.io.IOException e)
}
// check that no stray annotations have been added at the end.
{
- SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
- if (sq.getName().toUpperCase().startsWith("JPRED"))
+ SequenceI sq = seqs.elementAt(j - 1);
+ if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
git://source.jalview.org / jalview.git / blobdiff