X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=a944f389dd5d18939cfeb27cf00658276312acc7;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=dfe1ecf920550e02e1c2dc65e89133f6b2195fe8;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index dfe1ecf..a944f38 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,22 +1,23 @@
/*
- * 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
+ * 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.
- *
- * 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 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
/**
* PredFile.java
* JalviewX / Vamsas Project
@@ -24,53 +25,75 @@
*/
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 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!
+ *
+ * BH allows File or String
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param sourceType
+ * 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
{
super(source);
}
+
/**
* DOCUMENT ME!
- *
- * @param QuerySeqPosition DOCUMENT ME!
+ *
+ * @param QuerySeqPosition
+ * DOCUMENT ME!
*/
public void setQuerySeqPosition(int QuerySeqPosition)
{
@@ -79,7 +102,7 @@ public class JPredFile
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getQuerySeqPosition()
@@ -89,7 +112,7 @@ public class JPredFile
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Hashtable getScores()
@@ -99,7 +122,7 @@ public class JPredFile
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Hashtable getSymscores()
@@ -110,6 +133,7 @@ public class JPredFile
/**
* DOCUMENT ME!
*/
+ @Override
public void initData()
{
super.initData();
@@ -121,8 +145,8 @@ public class JPredFile
/**
* parse a JPred concise file into a sequence-alignment like object.
*/
- public void parse()
- throws IOException
+ @Override
+ public void parse() throws IOException
{
// JBPNote log.System.out.println("all read in ");
String line;
@@ -133,7 +157,7 @@ public class JPredFile
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, ":");
@@ -186,28 +210,27 @@ public class JPredFile
ascore = symbols.nextToken();
Float score = new Float(ascore);
- scores.addElement( (Object) score);
+ scores.addElement(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);
+ 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);
@@ -246,8 +269,10 @@ public class JPredFile
name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
}
- if (QuerySeqPosition==-1)
+ if (QuerySeqPosition == -1)
+ {
QuerySeqPosition = ids.size();
+ }
ids.addElement(name);
noSeqs++;
}
@@ -260,17 +285,15 @@ public class JPredFile
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));
}
}
}
- /* 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();
@@ -278,75 +301,87 @@ public class JPredFile
{
// 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();
}
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.\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;
}
this.annotations = new Vector();
AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
- for (int aai = 0; aan!=null && aai