/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
+ * 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
+ *
+ * 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.
+ *
+ * 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/>.
*/
-
/**
* PredFile.java
* JalviewX / Vamsas Project
import jalview.datamodel.*;
/**
- * Parser for the JPred/JNet concise format. This is a series of CSV lines,
- * each line is either a sequence (QUERY), a sequence profile (align;), or
- * jnet prediction annotation (anything else).
- * Automagic translation happens for annotation called 'JNETPRED' (translated to Secondary Structure Prediction), or 'JNETCONF' (translates to 'Prediction Confidence').
- * Numeric scores are differentiated from symbolic by being parseable into a float vector. They are put in Scores.
- * Symscores gets the others.
- * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment. It is automatically called
- * but can be used to transfer the annotation onto a sequence in another alignment (and insert gaps where necessary)
+ * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
+ * line is either a sequence (QUERY), a sequence profile (align;), or jnet
+ * prediction annotation (anything else). Automagic translation happens for
+ * annotation called 'JNETPRED' (translated to Secondary Structure Prediction),
+ * or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are
+ * differentiated from symbolic by being parseable into a float vector. They are
+ * put in Scores. Symscores gets the others. JNetAnnotationMaker translates the
+ * data parsed by this object into annotation on an alignment. It is
+ * automatically called but can be used to transfer the annotation onto a
+ * sequence in another alignment (and insert gaps where necessary)
+ *
* @author jprocter
* @version $Revision$
*/
-public class JPredFile
- extends AlignFile
+public class JPredFile extends AlignFile
{
Vector ids;
+
Vector conf;
+
Hashtable Scores; // Hash of names and score vectors
- Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
+
+ Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
+
+ // vector
+
private int QuerySeqPosition;
/**
* Creates a new JPredFile object.
- *
- * @param inFile DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public JPredFile(String inFile, String type)
- throws IOException
+ public JPredFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+ public JPredFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* DOCUMENT ME!
- *
- * @param QuerySeqPosition DOCUMENT ME!
+ *
+ * @param QuerySeqPosition
+ * DOCUMENT ME!
*/
public void setQuerySeqPosition(int QuerySeqPosition)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getQuerySeqPosition()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Hashtable getScores()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Hashtable getSymscores()
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
// JBPNote log.System.out.println("all read in ");
String line;
Vector ids = new Vector();
Hashtable Symscores = new Hashtable();
- while ( (line = nextLine()) != null)
+ while ((line = nextLine()) != null)
{
// Concise format allows no comments or non comma-formatted data
StringTokenizer str = new StringTokenizer(line, ":");
ascore = symbols.nextToken();
Float score = new Float(ascore);
- scores.addElement( (Object) score);
+ scores.addElement((Object) score);
}
Scores.put(id, scores);
- }
- catch (Exception e)
+ } catch (Exception e)
{
// or just keep them as strings
i = scores.size();
for (int j = 0; j < i; j++)
{
scores.setElementAt(
- (Object) ( (Float) scores.elementAt(j)).toString(), j);
+ (Object) ((Float) scores.elementAt(j)).toString(), j);
}
- scores.addElement( (Object) ascore);
+ scores.addElement((Object) ascore);
while (symbols.hasMoreTokens())
{
ascore = symbols.nextToken();
- scores.addElement( (Object) ascore);
+ scores.addElement((Object) ascore);
}
Scores.put(id, scores);
name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
}
- if (QuerySeqPosition==-1)
+ 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((Object) id, (Object) new Integer(ids.size() - 1));
}
}
}
- /* leave it to the parser user to actually check this.
- if (noSeqs < 1)
- {
- throw new IOException(
- "JpredFile Parser: No sequence in the prediction!");
- }*/
+ /*
+ * leave it to the parser user to actually check this. if (noSeqs < 1) {
+ * throw new IOException( "JpredFile Parser: No sequence in the
+ * prediction!"); }
+ */
maxLength = seq_entries.elementAt(0).toString().length();
{
// 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("JPredConcise: Entry ("
+ + ids.elementAt(i).toString()
+ + ") has an unexpected number of columns");
}
- 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();
}
seqs.addElement(newSeq);
}
- if (seqs.size()>0)
+ if (seqs.size() > 0 && QuerySeqPosition > -1)
{
- // try to make annotation for a prediction only input (default if no alignment is given)
+ // 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 tal = new Alignment(this.getSeqsAsArray());
- try {
- JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition, true);
+ try
+ {
+ JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition,
+ true);
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException("Couldn't parse concise annotation for prediction profile. ("+e.getMessage()+")");
- ex.setStackTrace(e.getStackTrace());
+ 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());
throw ex;
}
this.annotations = new Vector();
AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
- for (int aai = 0; aan!=null && aai<aan.length; aai++)
+ for (int aai = 0; aan != null && aai < aan.length; aai++)
{
annotations.addElement(aan[aai]);
}
- }
+ }
}
/**
* print
- *
+ *
* @return String
*/
public String print()
/**
* DOCUMENT ME!
- *
- * @param args DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
*/
public static void main(String[] args)
{
for (int i = 0; i < blc.seqs.size(); i++)
{
- System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName() +
- "\n" +
- ( (Sequence) blc.seqs.elementAt(i)).getSequenceAsString() +
- "\n");
+ System.out.println(((Sequence) blc.seqs.elementAt(i)).getName()
+ + "\n"
+ + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
+ + "\n");
}
- }
- catch (java.io.IOException e)
+ } catch (java.io.IOException e)
{
System.err.println("Exception " + e);
// e.printStackTrace(); not java 1.1 compatible!
}
Vector annotSeqs = null;
+
/**
* removeNonSequences
*/
}
/*
- 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(s[1].sequence.substring(i, i + 1) + " ");
- out.append(s[1].score[0].elementAt(i) + " ");
- out.append(s[1].score[1].elementAt(i) + " ");
- out.append(s[1].score[2].elementAt(i) + " ");
- out.append(s[1].score[3].elementAt(i) + " ");
-
- out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
- 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);
-
- 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);
- }
- }
-
- }
+ * 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(s[1].sequence.substring(i, i + 1) + " ");
+ * out.append(s[1].score[0].elementAt(i) + " ");
+ * out.append(s[1].score[1].elementAt(i) + " ");
+ * out.append(s[1].score[2].elementAt(i) + " ");
+ * out.append(s[1].score[3].elementAt(i) + " ");
+ *
+ * out.append("\n"); } out.append("END PRED\n"); return out.toString(); }
+ *
+ * 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);
+ *
+ * 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); } } }
*/
git://source.jalview.org / jalview.git / blobdiff