Newer
Older
/* GFFStreamFeature.java
*
* created: Tue Sep 14 1999
*
* This file is part of Artemis
*
* Copyright (C) 1999,2000,2001 Genome Research Limited
*
* 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.3 2005-01-06 11:21:06 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
import uk.ac.sanger.artemis.util.*;
import java.io.*;
import java.util.Hashtable;
import java.util.StringTokenizer;
/**
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
* @version $Id: GFFStreamFeature.java,v 1.3 2005-01-06 11:21:06 tjc Exp $
public class GFFStreamFeature extends SimpleDocumentFeature
implements DocumentFeature, StreamFeature, ComparableFeature
{
/**
* Create a new GFFStreamFeature object. The feature should be added
* @param key The new feature key
* @param location The Location object for the new feature
* @param qualifiers The qualifiers for the new feature
**/
public GFFStreamFeature(final Key key, final Location location,
final QualifierVector qualifiers)
{
super(null);
try
{
setKey(key);
setLocation(location);
setQualifiers(qualifiers);
if(getQualifierByName("score") == null)
setQualifier(new Qualifier("score", "."));
if(getQualifierByName("gff_source") == null)
setQualifier(new Qualifier("gff_source", "artemis"));
if(getQualifierByName("gff_seqname") == null)
setQualifier(new Qualifier("gff_seqname", "."));
}
catch(EntryInformationException e)
{
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
}
catch(ReadOnlyException e)
{
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
}
catch(OutOfRangeException e)
{
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
}
}
/**
* Create a new GFFStreamFeature with the same key, location and
* qualifiers as the given feature. The feature should be added to an
public GFFStreamFeature(final Feature feature)
{
this(feature.getKey(), feature.getLocation(), feature.getQualifiers());
if(feature instanceof GFFStreamFeature)
gff_lines = new StringVector(((GFFStreamFeature)feature).gff_lines);
}
/**
* Create a new GFFStreamFeature from the given line. The String should be
* in gene finder format.
**/
private GFFStreamFeature(final String line)
throws ReadFormatException
{
super(null);
final StringVector line_bits = StringVector.getStrings(line, "\t", true);
if(line_bits.size() < 8)
throw new ReadFormatException("invalid GFF line: 8 fields needed " +
"(got " + line_bits.size () +
" fields) from: " + line);
final String start_base_string = line_bits.elementAt(3).trim();
final String end_base_string = line_bits.elementAt(4).trim();
try
{
start_base = Integer.parseInt(start_base_string);
}
catch(NumberFormatException e)
{
throw new ReadFormatException("Could not understand the start base " +
"of a GFF feature: " + start_base_string);
try
{
end_base = Integer.parseInt(end_base_string);
}
catch(NumberFormatException e)
{
throw new ReadFormatException("Could not understand the end base " +
"of a GFF feature: " + end_base_string);
else
{
if(line_bits.elementAt(6).equals("-"))
// must be unstranded
complement_flag = false;
// best we can do
final String note_string = "this feature is unstranded";
setQualifier(new Qualifier("note", note_string));
if(line_bits.size() == 9)
{
final String rest_of_line = decode(line_bits.elementAt(8));
final Hashtable attributes = parseAttributes(rest_of_line);
for(final java.util.Enumeration attribute_enum = attributes.keys();
attribute_enum.hasMoreElements();)
{
final String name = (String)attribute_enum.nextElement();
final StringVector values = (StringVector)attributes.get(name);
if(values.size() == 0)
setQualifier(new Qualifier(name));
else
setQualifier(new Qualifier(name, values));
new Qualifier("gff_seqname", decode(line_bits.elementAt(0)));
final Key key = new Key(line_bits.elementAt(2));
new Qualifier("gff_source", line_bits.elementAt(1));
new Qualifier("score", line_bits.elementAt(5));
if(!frame.equals("1") && !frame.equals("."))
{
if(start_base > end_base)
throw new ReadFormatException("start position is greater than end " +
"position: " + start_base + " > " +
end_base);
if(start_base < 0)
throw new ReadFormatException("start position must be positive: " +
start_base);
final Range location_range = new Range(start_base, end_base);
final RangeVector location_ranges = new RangeVector(location_range);
setLocation(new Location(location_ranges, complement_flag));
}
catch(ReadOnlyException e)
{
throw new Error("internal error - unexpected exception: " + e);
}
catch(EntryInformationException e)
{
throw new Error("internal error - unexpected exception: " + e);
}
catch(OutOfRangeException e)
{
throw new Error("internal error - unexpected exception: " + e);
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
this.gff_lines = new StringVector(line);
}
/**
*
* For gff-version 3:
* http://song.sourceforge.net/gff3-jan04.shtml
*
* Remove URL escaping rule (e.g. space="%20" or "+")
*
*/
private String decode(String s)
{
int ind;
// white space
while( (ind = s.indexOf("%20")) > -1)
s = s.substring(0,ind) + " " + s.substring(ind+3);
// comma
while( (ind = s.indexOf("%2C")) > -1)
s = s.substring(0,ind) + "," + s.substring(ind+3);
// white space
while( (ind = s.indexOf("+")) > -1)
s = s.substring(0,ind) + " " + s.substring(ind+1);
// semi-colon
while( (ind = s.indexOf("%3B")) > -1)
s = s.substring(0,ind) + ";" + s.substring(ind+3);
// equals
while( (ind = s.indexOf("%3D")) > -1)
s = s.substring(0,ind) + "=" + s.substring(ind+3);
// ind = -1;
// while( (ind = s.indexOf("=",ind+2)) > -1)
// s = s.substring(0,ind+1) + "\"" + s.substring(ind+1);
// ind = -1;
// while( (ind = s.indexOf(";",ind+2)) > -1)
// s = s.substring(0,ind+1) + "\"" + s.substring(ind+1);
return s;
}
/**
* Return the reference of a new copy of this Feature.
**/
public Feature copy()
{
final Feature return_value = new GFFStreamFeature(this);
return return_value;
}
/**
* Helper method for the constructor - returns a String that is the
* concatenation of the Strings in the given StringVector. The strings
* will be separated by four spaces
**/
private String joinStringVector(final StringVector string_vector)
{
final StringBuffer return_buffer = new StringBuffer();
for(int i = 0 ; i < string_vector.size() ; ++i)
{
if(i != 0)
return_buffer.append(" ");
return_buffer.append(string_vector.elementAt(i));
}
/**
* Read and return a GFFStreamFeature from a stream. A feature must be the
* next thing in the stream.
* @param stream the Feature is read from this stream
* @exception IOException thrown if there is a problem reading the Feature -
* most likely ReadFormatException.
* @exception InvalidRelationException Thrown if this Feature cannot contain
* the given Qualifier.
* @return null if in_stream is at the end of file when the method is
* called
*/
protected static GFFStreamFeature readFromStream(LinePushBackReader stream)
throws IOException, InvalidRelationException
{
try
{
final GFFStreamFeature new_feature = new GFFStreamFeature(line);
}
catch(ReadFormatException exception)
{
final String new_error_string = exception.getMessage();
throw new ReadFormatException(new_error_string,
stream.getLineNumber());
}
}
/**
* Read the details of a feature from an EMBL stream into the current
* object.
* @param entry_information The EntryInformation object of the Entry that
* will contain the Feature.
* @param in_stream the Feature is read from this stream
* @exception IOException thrown if there is a problem reading the Feature -
* most likely ReadFormatException if the stream does not contain GFF
* feature.
**/
public void setFromStream(final EntryInformation entry_information,
final LinePushBackReader in_stream)
throws IOException, InvalidRelationException, ReadOnlyException
{
throw new ReadOnlyException();
}
/**
* Write this Feature to the given stream.
* @param writer The stream to write to.
* @exception IOException thrown if there is an io problem while writing
* the Feature.
**/
public void writeToStream(final Writer writer)
throws IOException
{
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
if(gff_lines == null)
{
final RangeVector ranges = getLocation().getRanges();
for(int i = 0 ; i < ranges.size() ; ++i)
{
final Range this_range = ranges.elementAt(i);
Qualifier seqname = getQualifierByName("gff_seqname");
Qualifier source = getQualifierByName("gff_source");
Qualifier score = getQualifierByName("score");
Qualifier group = getQualifierByName("group");
if(seqname == null)
seqname = new Qualifier("gff_seqname", "");
if(source == null)
source = new Qualifier("source", "");
if(score == null)
score = new Qualifier("score", "");
if(group == null || group.getValues() == null ||
group.getValues().elementAt(0).equals(""))
{
final Qualifier gene = getQualifierByName("gene");
if(gene == null)
group = new Qualifier("group", "");
else
final Qualifier codon_start = getQualifierByName("codon_start");
if(codon_start != null && i == 0)
{
frame = codon_start.getValues().elementAt(0);
final String attribute_string = unParseAttributes();
writer.write(seqname.getValues().elementAt(0) + "\t" +
source.getValues().elementAt(0) + "\t" +
getKey() + "\t" +
this_range.getStart() + "\t" +
this_range.getEnd() + "\t" +
score.getValues() .elementAt(0)+ "\t" +
(getLocation().isComplement() ? "-\t" : "+\t") +
}
else
{
for(int i = 0 ; i < gff_lines.size() ; ++i)
writer.write(gff_lines.elementAt(i) + "\n");
}
}
/**
* Return a String containing the qualifiers of this feature in a form
* suitable for using as the last field of a GFF line. The codon_start
* attribute is not included since GFF has a frame field. gff_seqname,
* gff_source and score aren't included since they have corresponding
* fields.
**/
private String unParseAttributes()
{
final StringBuffer buffer = new StringBuffer();
final QualifierVector qualifiers = getQualifiers();
final QualifierVector qualifiers_to_write = new QualifierVector();
for(int i = 0 ; i < qualifiers.size() ; ++i)
{
final Qualifier this_qualifier = (Qualifier)qualifiers.elementAt(i);
final String name = this_qualifier.getName();
if(name.equals("codon_start") || name.equals("gff_source") ||
name.equals("gff_seqname") || name.equals("score"))
if(i != 0)
buffer.append(" ; ");
final StringVector values = this_qualifier.getValues();
buffer.append(name);
if(values != null)
{
for(int value_index = 0;
value_index < values.size();
++value_index)
{
final String this_value = values.elementAt(value_index);
buffer.append(' ');
try
{
buffer.append(Integer.valueOf(this_value));
}
catch(NumberFormatException _)
{
try
{
buffer.append(Double.valueOf(this_value));
}
catch (NumberFormatException __)
{
}
/**
* Parse the given String as ACeDB format attributes.
* Adapted from code by Matthew Pocock for the BioJava project.
* @return Return a Hashtable. Each key is an attribute name and each value
* of the Hashtable is a StringVector containing the attribute values.
* If the attribute has no value then the Hashtable value will be a zero
* length vector.
**/
private Hashtable parseAttributes(final String att_val_list)
{
Hashtable attributes = new Hashtable();
StringTokenizer tokeniser = new StringTokenizer(att_val_list, ";", false);
int index_of_first_space = this_token.indexOf(" ");
final StringVector att_values = new StringVector();
if(this_token.indexOf("=") > -1 &&
this_token.indexOf("=") < index_of_first_space)
{
index_of_first_space = this_token.indexOf("=");
att_name = this_token.substring(0, index_of_first_space);
att_values.add(this_token.substring(index_of_first_space+1).trim());
}
else if(index_of_first_space == -1)
else
{
att_name = this_token.substring(0, index_of_first_space);
this_token.substring(index_of_first_space+1).trim();
while(rest_of_token.length() > 0)
{
if(rest_of_token.startsWith("\""))
{
quote_index = rest_of_token.indexOf("\"", quote_index);
} while(quote_index > -1 &&
rest_of_token.charAt(quote_index - 1) == '\\');
final Hashtable panic_attributes = new Hashtable();
final StringVector notes = new StringVector();
notes.add(att_val_list);
panic_attributes.put("note", notes);
final String next_bit = rest_of_token.substring(1, quote_index);
att_values.add(next_bit);
rest_of_token = rest_of_token.substring(quote_index + 1).trim();
}
else
{
final int index_of_next_space = rest_of_token.indexOf(" ");
if(index_of_next_space == -1)
{
att_values.add(rest_of_token);
rest_of_token.substring(0, index_of_next_space);
rest_of_token.substring(index_of_next_space).trim();
if(!rest_of_token.equals(""))
att_values.add(rest_of_token);
if(attributes.get(att_name) != null)
((StringVector)attributes.get(att_name)).add(att_values);
else
attributes.put(att_name, att_values);
}
return attributes;
}
/**
* The DocumentEntry object that contains this Feature as passed to the
* constructor.
**/
private DocumentEntry entry;
/**
* This is the line of GFF input that was read to get this
* GFFStreamFeature. A GFFStreamFeature that was created from multiple GFF
* lines will have a gff_lines variable that contains multiple line.
**/
StringVector gff_lines = null;
}