/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 java.util.Locale;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+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
Hashtable Scores; // Hash of names and score vectors
Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
- // vector
+
+ // vector
private int QuerySeqPosition;
/**
* Creates a new JPredFile object.
*
+ * BH allows File or String
+ *
* @param inFile
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
+ * @param sourceType
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * 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
* DOCUMENT ME!
*
* @param QuerySeqPosition
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setQuerySeqPosition(int QuerySeqPosition)
{
/**
* 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;"))
+ if ((newSeq.getName().startsWith("QUERY")
+ || newSeq.getName().startsWith("align;"))
&& (QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
seqs.addElement(newSeq);
}
- if (seqs.size() > 0 && QuerySeqPosition>-1)
+ if (seqs.size() > 0 && QuerySeqPosition > -1)
{
// try to make annotation for a prediction only input (default if no
- // alignment is given and prediction contains a QUERY or align;sequence_id line)
+ // alignment is given and prediction contains a QUERY or align;sequence_id
+ // line)
Alignment tal = new Alignment(this.getSeqsAsArray());
try
{
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(
- "Couldn't parse concise annotation for prediction profile.\n"
- + e);
- e.printStackTrace(); // java 1.1 does not have : ex.setStackTrace(e.getStackTrace());
+ 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;
}
this.annotations = new Vector();
*
* @return String
*/
- public String print()
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
return "Not Supported";
}
/**
- * DOCUMENT ME!
*
* @param args
- * DOCUMENT ME!
+ * @j2sIgnore
*/
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);
/*
* StringBuffer out = new StringBuffer();
*
- * out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++) {
- * out.append(s[0].sequence.substring(i, i + 1) + " ");
+ * out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++)
+ * { out.append(s[0].sequence.substring(i, i + 1) + " ");
* out.append(s[1].sequence.substring(i, i + 1) + " ");
* out.append(s[1].score[0].elementAt(i) + " ");
* out.append(s[1].score[1].elementAt(i) + " ");
*
* public static void main(String[] args) { try { BLCFile blc = new
* BLCFile(args[0], "File"); DrawableSequence[] s = new
- * DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++) {
- * s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String out =
- * BLCFile.print(s);
+ * DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++)
+ * { s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String
+ * out = BLCFile.print(s);
*
* AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
* System.out.println(out); } catch (java.io.IOException e) {
- * System.out.println("Exception " + e); } }
- * }
+ * System.out.println("Exception " + e); } } }
*/
git://source.jalview.org / jalview.git / blobdiff