/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
+ * 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
+ */
/**
* PredFile.java
import jalview.datamodel.*;
-
/**
* DOCUMENT ME!
*
* @author $author$
* @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
- private int QuerySeqPosition;
-
-
- /**
- * Creates a new JPredFile object.
- *
- * @param inFile DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
- */
- public JPredFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
+ Vector ids;
+ Vector conf;
+ Hashtable Scores; // Hash of names and score vectors
+ Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
+ private int QuerySeqPosition;
- /**
- * DOCUMENT ME!
- *
- * @param QuerySeqPosition DOCUMENT ME!
- */
- public void setQuerySeqPosition(int QuerySeqPosition)
- {
- this.QuerySeqPosition = QuerySeqPosition;
- }
+ /**
+ * Creates a new JPredFile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public JPredFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getQuerySeqPosition()
- {
- return QuerySeqPosition;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param QuerySeqPosition DOCUMENT ME!
+ */
+ public void setQuerySeqPosition(int QuerySeqPosition)
+ {
+ this.QuerySeqPosition = QuerySeqPosition;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Hashtable getScores()
- {
- return Scores;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getQuerySeqPosition()
+ {
+ return QuerySeqPosition;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Hashtable getSymscores()
- {
- return Symscores;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getScores()
+ {
+ return Scores;
+ }
- /**
- * DOCUMENT ME!
- */
- public void initData()
- {
- super.initData();
- Scores = new Hashtable();
- ids = null;
- conf = null;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Hashtable getSymscores()
+ {
+ return Symscores;
+ }
- /**
- * parse a JPred concise file into a sequence-alignment like object.
- */
- public void parse() throws IOException
+ /**
+ * DOCUMENT ME!
+ */
+ public void initData()
+ {
+ super.initData();
+ Scores = new Hashtable();
+ ids = null;
+ conf = null;
+ }
+
+ /**
+ * parse a JPred concise file into a sequence-alignment like object.
+ */
+ public void parse()
+ throws IOException
+ {
+ // JBPNote log.System.out.println("all read in ");
+ String line;
+ QuerySeqPosition = -1;
+ noSeqs = 0;
+
+ Vector seq_entries = new Vector();
+ Vector ids = new Vector();
+ Hashtable Symscores = new Hashtable();
+
+ while ( (line = nextLine()) != null)
{
- // JBPNote log.System.out.println("all read in ");
- String line;
- QuerySeqPosition = -1;
- noSeqs = 0;
+ // Concise format allows no comments or non comma-formatted data
+ StringTokenizer str = new StringTokenizer(line, ":");
+ String id = "";
+
+ if (!str.hasMoreTokens())
+ {
+ continue;
+ }
+
+ id = str.nextToken();
+
+ String seqsym = str.nextToken();
+ StringTokenizer symbols = new StringTokenizer(seqsym, ",");
+
+ // decide if we have more than just alphanumeric symbols
+ int numSymbols = symbols.countTokens();
+
+ if (numSymbols == 0)
+ {
+ continue;
+ }
+
+ if (seqsym.length() != (2 * numSymbols))
+ {
+ // Set of scalars for some property
+ if (Scores.containsKey(id))
+ {
+ int i = 1;
+
+ while (Scores.containsKey(id + "_" + i))
+ {
+ i++;
+ }
+
+ id = id + "_" + i;
+ }
+
+ Vector scores = new Vector();
+
+ // Typecheck from first entry
+ int i = 0;
+ String ascore = "dead";
- Vector seq_entries = new Vector();
- Vector ids = new Vector();
- Hashtable Symscores = new Hashtable();
+ try
+ {
+ // store elements as floats...
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+
+ Float score = new Float(ascore);
+ scores.addElement( (Object) score);
+ }
- while ((line = nextLine()) != null)
+ Scores.put(id, scores);
+ }
+ catch (Exception e)
{
- // Concise format allows no comments or non comma-formatted data
- StringTokenizer str = new StringTokenizer(line, ":");
- String id = "";
-
- if (!str.hasMoreTokens())
- {
- continue;
- }
-
- id = str.nextToken();
-
- String seqsym = str.nextToken();
- StringTokenizer symbols = new StringTokenizer(seqsym, ",");
-
- // decide if we have more than just alphanumeric symbols
- int numSymbols = symbols.countTokens();
-
- if (numSymbols == 0)
- {
- continue;
- }
-
- if (seqsym.length() != (2 * numSymbols))
- {
- // Set of scalars for some property
- if (Scores.containsKey(id))
- {
- int i = 1;
-
- while (Scores.containsKey(id + "_" + i))
- {
- i++;
- }
-
- id = id + "_" + i;
- }
-
- Vector scores = new Vector();
-
- // Typecheck from first entry
- int i = 0;
- String ascore = "dead";
-
- try
- {
- // store elements as floats...
- while (symbols.hasMoreTokens())
- {
- ascore = symbols.nextToken();
-
- Float score = new Float(ascore);
- scores.addElement((Object) score);
- }
-
- Scores.put(id, scores);
- }
- 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.addElement((Object) ascore);
-
- while (symbols.hasMoreTokens())
- {
- ascore = symbols.nextToken();
- scores.addElement((Object) ascore);
- }
-
- Scores.put(id, scores);
- }
- }
- else if (id.equals("jnetconf"))
- {
- // log.debug System.out.println("here");
- id = "Prediction Confidence";
- this.conf = new Vector(numSymbols);
-
- for (int i = 0; i < numSymbols; i++)
- {
- conf.setElementAt( symbols.nextToken(), i);
- }
- }
- else
- {
- // Sequence or a prediction string (rendered as sequence)
- StringBuffer newseq = new StringBuffer();
-
- for (int i = 0; i < numSymbols; i++)
- {
- newseq.append(symbols.nextToken());
- }
-
- if (id.indexOf(";") > -1)
- {
- seq_entries.addElement(newseq);
-
- int i = 1;
- String name = id.substring(id.indexOf(";") + 1);
-
- while (ids.lastIndexOf(name) > -1)
- {
- name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
- }
-
- ids.addElement(name);
-
- noSeqs++;
- }
- else
- {
- if (id.equals("JNETPRED"))
- {
- id = "Predicted Secondary Structure";
- }
-
- seq_entries.addElement(newseq.toString());
- ids.addElement(id);
- Symscores.put((Object) id,
- (Object) new Integer(ids.size() - 1));
- }
- }
+ // 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.addElement( (Object) ascore);
+
+ while (symbols.hasMoreTokens())
+ {
+ ascore = symbols.nextToken();
+ scores.addElement( (Object) ascore);
+ }
+
+ Scores.put(id, scores);
}
- /* leave it to the parser user to actually check this.
- if (noSeqs < 1)
+ }
+ else if (id.equals("jnetconf"))
+ {
+ // log.debug System.out.println("here");
+ id = "Prediction Confidence";
+ this.conf = new Vector(numSymbols);
+
+ for (int i = 0; i < numSymbols; i++)
{
- throw new IOException(
- "JpredFile Parser: No sequence in the prediction!");
- }*/
+ conf.setElementAt(symbols.nextToken(), i);
+ }
+ }
+ else
+ {
+ // Sequence or a prediction string (rendered as sequence)
+ StringBuffer newseq = new StringBuffer();
- maxLength = seq_entries.elementAt(0).toString().length();
+ for (int i = 0; i < numSymbols; i++)
+ {
+ newseq.append(symbols.nextToken());
+ }
- for (int i = 0; i < ids.size(); i++)
+ if (id.indexOf(";") > -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());
-
-
- if (maxLength != seq_entries.elementAt(i).toString().length())
- {
- throw new IOException("JPredConcise: Entry (" +
- ids.elementAt(i).toString() +
- ") has an unexpected number of columns");
- }
-
- if (newSeq.getName().startsWith("QUERY") &&
- (QuerySeqPosition == -1))
- {
- QuerySeqPosition = seqs.size();
- }
-
- seqs.addElement(newSeq);
+ seq_entries.addElement(newseq);
+
+ int i = 1;
+ String name = id.substring(id.indexOf(";") + 1);
+
+ while (ids.lastIndexOf(name) > -1)
+ {
+ name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
+ }
+
+ ids.addElement(name);
+
+ noSeqs++;
+ }
+ else
+ {
+ if (id.equals("JNETPRED"))
+ {
+ id = "Predicted Secondary Structure";
+ }
+
+ seq_entries.addElement(newseq.toString());
+ ids.addElement(id);
+ 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!");
+ }*/
- /**
- * print
- *
- * @return String
- */
- public String print()
+ maxLength = seq_entries.elementAt(0).toString().length();
+
+ for (int i = 0; i < ids.size(); i++)
{
- return "Not Supported";
+ // 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());
+
+ if (maxLength != seq_entries.elementAt(i).toString().length())
+ {
+ throw new IOException("JPredConcise: Entry (" +
+ ids.elementAt(i).toString() +
+ ") has an unexpected number of columns");
+ }
+
+ if (newSeq.getName().startsWith("QUERY") &&
+ (QuerySeqPosition == -1))
+ {
+ QuerySeqPosition = seqs.size();
+ }
+
+ seqs.addElement(newSeq);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param args DOCUMENT ME!
- */
- public static void main(String[] args)
+ /**
+ * print
+ *
+ * @return String
+ */
+ public String print()
+ {
+ return "Not Supported";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args DOCUMENT ME!
+ */
+ public static void main(String[] args)
+ {
+ try
{
- try
- {
- JPredFile blc = new JPredFile(args[0], "File");
-
- 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");
- }
- }
- catch (java.io.IOException e)
- {
- System.err.println("Exception " + e);
- e.printStackTrace();
- }
+ JPredFile blc = new JPredFile(args[0], "File");
+
+ 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");
+ }
+ }
+ catch (java.io.IOException e)
+ {
+ System.err.println("Exception " + e);
+ e.printStackTrace();
}
- Vector annotSeqs=null;
+ }
+
+ Vector annotSeqs = null;
/**
* removeNonSequences
*/
public void removeNonSequences()
{
- if (annotSeqs!=null)
+ if (annotSeqs != null)
+ {
return;
+ }
annotSeqs = new Vector();
Vector newseqs = new Vector();
- int i=0;
- int j=seqs.size();
- for (; i<QuerySeqPosition; i++)
- annotSeqs.addElement(seqs.elementAt(i));
- // check that no stray annotations have been added at the end.
+ int i = 0;
+ int j = seqs.size();
+ for (; i < QuerySeqPosition; i++)
+ {
+ annotSeqs.addElement(seqs.elementAt(i));
+ }
+ // 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 = (SequenceI) seqs.elementAt(j-1);
- if (sq.getName().toUpperCase().startsWith("JPRED")) {
- annotSeqs.addElement(sq);
- seqs.removeElementAt(--j);
- }
+ annotSeqs.addElement(sq);
+ seqs.removeElementAt(--j);
}
- for (; i<j; i++)
- newseqs.addElement(seqs.elementAt(i));
+ }
+ for (; i < j; i++)
+ {
+ newseqs.addElement(seqs.elementAt(i));
+ }
seqs.removeAllElements();
seqs = newseqs;
}
}
-
/*
StringBuffer out = new StringBuffer();
git://source.jalview.org / jalview.git / blobdiff