diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
index 12a62c45513fa451aea4183e2082715274a92742..f8f2c77f6622344fbc8b58fb74f49b846686b212 100644
--- a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
@@ -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/GFFDocumentEntry.java,v 1.9 2005-04-21 13:11:51 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.10 2005-04-22 15:04:25 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -36,7 +36,7 @@ import java.util.Vector;
* A DocumentEntry that can read an GFF entry from a Document.
*
* @author Kim Rutherford
- * @version $Id: GFFDocumentEntry.java,v 1.9 2005-04-21 13:11:51 tjc Exp $
+ * @version $Id: GFFDocumentEntry.java,v 1.10 2005-04-22 15:04:25 tjc Exp $
**/
public class GFFDocumentEntry extends SimpleDocumentEntry
@@ -176,7 +176,7 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
try
{
- if(this_feature.getQualifierByName("CDS") != null)
+ if(this_feature.getKey().getKeyString().equals("CDS"))
{
if(this_feature.getQualifierByName("Parent") != null)
{
@@ -185,8 +185,8 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
group_name = values.elementAt(0);
// check the parent is a gene
- if(!genes.contains(group_name))
- continue;
+// if(!genes.contains(group_name))
+// continue;
}
}
else
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 6c3bed741fcb222d97652890b942f0d29c46630c..989d99a69e2e79de2f9d8b8b333055d27ff2ea69 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -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 1.5 2005-04-19 14:49:47 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.6 2005-04-22 15:04:25 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -35,13 +35,27 @@ import java.util.StringTokenizer;
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
- * @version $Id: GFFStreamFeature.java,v 1.5 2005-04-19 14:49:47 tjc Exp $
+ * @version $Id: GFFStreamFeature.java,v 1.6 2005-04-22 15:04:25 tjc Exp $
**/
public class GFFStreamFeature extends SimpleDocumentFeature
implements DocumentFeature, StreamFeature, ComparableFeature
{
+
+ /**
+ * 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;
+
/**
* Create a new GFFStreamFeature object. The feature should be added
* to an Entry (with Entry.add()).
@@ -175,10 +189,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final StringVector values = (StringVector)attributes.get(name);
- if(name.equals("ID"))
- name = "systematic_id";
- else if(name.equals("Name"))
- name = type;
+// if(name.equals("ID"))
+// name = "systematic_id";
+// else if(name.equals("Name"))
+// name = type;
if(values.size() == 0)
setQualifier(new Qualifier(name));
@@ -303,6 +317,30 @@ public class GFFStreamFeature extends SimpleDocumentFeature
return s;
}
+
+ private String encode(String s)
+ {
+ int ind;
+
+ // white space
+ while( (ind = s.indexOf(" ")) > -1)
+ s = s.substring(0,ind) + "%20" + s.substring(ind+1);
+
+ // comma
+ while( (ind = s.indexOf(",")) > -1)
+ s = s.substring(0,ind) + "%2C" + s.substring(ind+1);
+
+ // semi-colon
+ while( (ind = s.indexOf(";")) > -1)
+ s = s.substring(0,ind) + "%3B" + s.substring(ind+1);
+
+ // equals
+ while( (ind = s.indexOf("=")) > -1)
+ s = s.substring(0,ind) + "%3D" + s.substring(ind+1);
+
+ return s;
+ }
+
/**
* Return the reference of a new copy of this Feature.
@@ -375,8 +413,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
throws IOException
{
// for now GFF features are read-only so just write what we read
- if(gff_lines == null)
- {
+ // if(gff_lines == null)
+ // {
final RangeVector ranges = getLocation().getRanges();
for(int i = 0 ; i < ranges.size() ; ++i)
@@ -443,12 +481,12 @@ 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");
- }
+ // }
+ // else
+ // {
+ // for(int i = 0 ; i < gff_lines.size() ; ++i)
+ // writer.write(gff_lines.elementAt(i) + "\n");
+ // }
}
/**
@@ -464,52 +502,85 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final QualifierVector qualifiers = getQualifiers();
final QualifierVector qualifiers_to_write = new QualifierVector();
- for(int i = 0 ; i < qualifiers.size() ; ++i)
+ final String names[] = { "ID", "Name", "Alias", "Parent",
+ "Target", "Gap", "Note",
+ "Dbxref", "Ontology_term" };
+ int count = 0;
+
+ for(int i=0; i<names.length; i++)
{
- final Qualifier this_qualifier = (Qualifier)qualifiers.elementAt(i);
+ Qualifier this_qualifier = (Qualifier)qualifiers.getQualifierByName(names[i]);
+
+ if(this_qualifier == null)
+ continue;
- final String name = this_qualifier.getName();
+ String this_qualifier_str = getQualifierString(this_qualifier);
+ if(this_qualifier_str == null)
+ continue;
+
+ if(count != 0)
+ buffer.append(";");
+ buffer.append(this_qualifier_str);
+ count++;
+ }
- if(name.equals("codon_start") || name.equals("gff_source") ||
- name.equals("gff_seqname") || name.equals("score"))
+/*
+ for(int i = 0 ; i < qualifiers.size() ; ++i)
+ {
+ this_qualifier = (Qualifier)qualifiers.elementAt(i);
+
+ String this_qualifier_str = getQualifierString(this_qualifier);
+ if(this_qualifier_str == null)
continue;
- if(i != 0)
- buffer.append(" ; ");
+ if(count != 0)
+ buffer.append("; ");
+ buffer.append(this_qualifier_str);
+ }
+*/
+
+ return buffer.toString();
+ }
+
- final StringVector values = this_qualifier.getValues();
+ private String getQualifierString(Qualifier q)
+ {
+ StringBuffer buffer = new StringBuffer();
+ final String name = q.getName();
+
+ if(name.equals("codon_start") || name.equals("gff_source") ||
+ name.equals("gff_seqname") || name.equals("score"))
+ return null;
- buffer.append(name);
+ final StringVector values = q.getValues();
+ buffer.append(encode(name));
- if(values != null)
+ if(values != null)
+ {
+ for(int value_index = 0; value_index < values.size();
+ ++value_index)
{
- 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 _)
{
- final String this_value = values.elementAt(value_index);
- buffer.append(' ');
- try
+ // not an integer
+ try
{
- buffer.append(Integer.valueOf(this_value));
- }
- catch(NumberFormatException _)
+ buffer.append(Double.valueOf(this_value));
+ }
+ catch (NumberFormatException __)
{
- // not an integer
- try
- {
- buffer.append(Double.valueOf(this_value));
- }
- catch (NumberFormatException __)
- {
- // not a double or integer so quote it
- buffer.append('"' + this_value + '"');
- }
+ // not a double or integer so quote it
+ buffer.append('"' + encode(this_value) + '"');
}
}
}
}
-
return buffer.toString();
}
@@ -616,16 +687,4 @@ public class GFFStreamFeature extends SimpleDocumentFeature
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;
}
diff --git a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
index 99490589b87b3f93a5651d5aebe58e132ba1efec..5b22424b5b590f2f478077a3c330427b09304b81 100644
--- a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
@@ -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/SimpleDocumentEntry.java,v 1.10 2005-04-20 14:54:28 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.11 2005-04-22 15:04:25 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -37,7 +37,7 @@ import java.util.Enumeration;
* This class contains the methods common to all DocumentEntry objects.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: SimpleDocumentEntry.java,v 1.10 2005-04-20 14:54:28 tjc Exp $
+ * @version $Id: SimpleDocumentEntry.java,v 1.11 2005-04-22 15:04:25 tjc Exp $
**/
abstract public class SimpleDocumentEntry
@@ -907,46 +907,43 @@ abstract public class SimpleDocumentEntry
}
}
}
- else
+ else if(new_line_group instanceof Feature)
{
- if(new_line_group instanceof Feature)
+ // Features before the Sequence and FeatureTable(if any)
+ for(int i = 0 ; i < line_groups.size() ; ++i)
{
- // Features before the Sequence and FeatureTable(if any)
- for(int i = 0 ; i < line_groups.size() ; ++i)
- {
- final LineGroup this_line_group = line_groups.elementAt(i);
+ final LineGroup this_line_group = line_groups.elementAt(i);
- if(this_line_group instanceof FeatureTable ||
- this_line_group instanceof Sequence)
- {
- line_groups.insertElementAt(new_line_group, i);
- return;
- }
+ if(this_line_group instanceof FeatureTable ||
+ this_line_group instanceof Sequence)
+ {
+ line_groups.insertElementAt(new_line_group, i);
+ return;
}
- }
- else
- {
- if(!(new_line_group instanceof Sequence) &&
+ }
+ }
+ else if(!(new_line_group instanceof Sequence) &&
!(new_line_group instanceof FeatureTable))
- {
- // insert before features and sequence
- for(int i = 0 ; i < line_groups.size() ; ++i)
- {
- final LineGroup this_line_group = line_groups.elementAt(i);
+ {
+ if(new_line_group instanceof GFFMisc)
+ {
+ String line = ((GFFMisc)new_line_group).toString();
+ if(line.indexOf("FASTA") > -1) // ignore
+ return;
+ }
- if(this_line_group instanceof Feature ||
- this_line_group instanceof FeatureTable ||
- this_line_group instanceof FeatureHeader ||
- this_line_group instanceof Sequence)
- {
- line_groups.insertElementAt(new_line_group, i);
- return;
- }
- }
- }
- else
+ // insert before features and sequence
+ for(int i = 0 ; i < line_groups.size() ; ++i)
+ {
+ final LineGroup this_line_group = line_groups.elementAt(i);
+
+ if(this_line_group instanceof Feature ||
+ this_line_group instanceof FeatureTable ||
+ this_line_group instanceof FeatureHeader ||
+ this_line_group instanceof Sequence)
{
- // fall throw
+ line_groups.insertElementAt(new_line_group, i);
+ return;
}
}
}