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Commit 9cf82895 authored by tjc's avatar tjc
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gff optimise 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2444 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent bae65362
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uk/ac/sanger/artemis/io/GFFStreamFeature.java
+ 87
− 103
View file @ 9cf82895
......@@ -20,7 +20,7 @@
* 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 1.9 2005-05-03 13:25:57 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.10 2005-05-04 10:13:17 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
......@@ -35,7 +35,7 @@ import java.util.StringTokenizer;
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
* @version $Id: GFFStreamFeature.java,v 1.9 2005-05-03 13:25:57 tjc Exp $
* @version $Id: GFFStreamFeature.java,v 1.10 2005-05-04 10:13:17 tjc Exp $
**/
public class GFFStreamFeature extends SimpleDocumentFeature
......@@ -138,21 +138,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
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);
throw new ReadFormatException("Could not understand the start or end base " +
"of a GFF feature: " + start_base_string +
" " + end_base_string);
}
// start of qualifier parsing and setting
......@@ -170,8 +162,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
complement_flag = false;
// best we can do
final String note_string = "this feature is unstranded";
setQualifier(new Qualifier("note", note_string));
//final String note_string = "this feature is unstranded";
//setQualifier(new Qualifier("note", note_string));
}
if(line_bits.size() == 9)
......@@ -207,35 +199,26 @@ public class GFFStreamFeature extends SimpleDocumentFeature
setQualifier(gff_seqname);
final Key key = new Key(line_bits.elementAt(2));
setKey(key);
final Qualifier source_qualifier =
new Qualifier("gff_source", line_bits.elementAt(1));
setQualifier(source_qualifier);
final Qualifier score_qualifier =
new Qualifier("score", line_bits.elementAt(5));
setQualifier(score_qualifier);
String frame = line_bits.elementAt(7);
if(frame.equals ("0"))
frame = "1";
else
{
if(frame.equals("1"))
else if(frame.equals("1"))
frame = "2";
else
{
if(frame.equals("2"))
else if(frame.equals("2"))
frame = "3";
else
frame = ".";
}
}
if(!frame.equals("1") && !frame.equals("."))
{
......@@ -373,9 +356,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
protected static GFFStreamFeature readFromStream(LinePushBackReader stream)
throws IOException, InvalidRelationException
{
String line = stream.readLine();
if(line == null)
return null;
......@@ -420,14 +401,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
public void writeToStream(final Writer writer)
throws IOException
{
// for now GFF features are read-only so just write what we read
// if(gff_lines == null)
// {
final RangeVector ranges = getLocation().getRanges();
final int ranges_size = ranges.size();
for(int i = 0 ; i < ranges.size() ; ++i)
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");
......@@ -463,19 +443,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(frame.equals ("1"))
frame = "0";
else
{
if(frame.equals("2"))
else if(frame.equals("2"))
frame = "1";
else
{
if(frame.equals("3"))
else if(frame.equals("3"))
frame = "2";
else
frame = ".";
}
}
}
final String attribute_string = unParseAttributes();
......@@ -489,12 +463,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
frame + "\t" +
attribute_string + "\n");
}
// }
// else
// {
// for(int i = 0 ; i < gff_lines.size() ; ++i)
// writer.write(gff_lines.elementAt(i) + "\n");
// }
}
/**
......@@ -515,15 +486,16 @@ public class GFFStreamFeature extends SimpleDocumentFeature
"Dbxref", "Ontology_term" };
int count = 0;
Qualifier this_qualifier;
final int names_length = names.length;
for(int i=0; i<names.length; i++)
for(int i=0; i<names_length; i++)
{
this_qualifier = (Qualifier)qualifiers.getQualifierByName(names[i]);
if(this_qualifier == null)
continue;
String this_qualifier_str = getQualifierString(this_qualifier);
final String this_qualifier_str = getQualifierString(this_qualifier);
if(this_qualifier_str == null)
continue;
......@@ -534,7 +506,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
boolean lname;
for(int i = 0 ; i < qualifiers.size() ; ++i)
final int qualifiers_size = qualifiers.size();
for(int i = 0; i < qualifiers_size; ++i)
{
this_qualifier = (Qualifier)qualifiers.elementAt(i);
......@@ -543,7 +516,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
continue;
lname = false;
for(int j=0; j<names.length; j++)
for(int j=0; j<names_length; j++)
if(this_qualifier_str.startsWith(names[j]))
lname = true;
......@@ -615,11 +588,22 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
Hashtable attributes = new Hashtable();
StringTokenizer tokeniser = new StringTokenizer(att_val_list, ";", false);
// StringTokenizer tokeniser = new StringTokenizer(att_val_list, ";", false);
// while(tokeniser.hasMoreTokens())
// {
// final String this_token = tokeniser.nextToken().trim();
while(tokeniser.hasMoreTokens())
int ind_start = 0;
int ind_end;
while( (ind_end = att_val_list.indexOf(";",ind_start)) > -1 ||
ind_start < att_val_list.length() )
{
final String this_token = tokeniser.nextToken().trim();
if(ind_end < 0)
ind_end = att_val_list.length();
final String this_token = att_val_list.substring(ind_start, ind_end).trim();
ind_start = ind_end+1;
int index_of_first_space = this_token.indexOf(" ");
String att_name;
......
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