From 8e2163165565fa6f3d65ef2fe28a476a9d6a0da4 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 19 Apr 2005 14:49:47 +0000
Subject: [PATCH] gff features
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2400 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 44 ++-----------------
.../artemis/io/SimpleDocumentEntry.java | 9 ++--
2 files changed, 8 insertions(+), 45 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 4d304947d..6c3bed741 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 1.4 2005-04-19 09:22:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.5 2005-04-19 14:49:47 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -35,15 +35,13 @@ import java.util.StringTokenizer;
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
- * @version $Id: GFFStreamFeature.java,v 1.4 2005-04-19 09:22:18 tjc Exp $
+ * @version $Id: GFFStreamFeature.java,v 1.5 2005-04-19 14:49:47 tjc Exp $
**/
public class GFFStreamFeature extends SimpleDocumentFeature
implements DocumentFeature, StreamFeature, ComparableFeature
{
- private String region_name = null;
-
/**
* Create a new GFFStreamFeature object. The feature should be added
* to an Entry (with Entry.add()).
@@ -179,10 +177,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(name.equals("ID"))
name = "systematic_id";
-
- region_name = line_bits.elementAt(0).trim();
-
- if(name.equals("Name"))
+ else if(name.equals("Name"))
name = type;
if(values.size() == 0)
@@ -246,9 +241,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
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)
@@ -268,17 +261,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
- /**
- *
- * The ID of the landmark used to establish the coordinate
- * system for the current feature - GFF3.
- *
- */
- protected String getRegionName()
- {
- return region_name;
- }
-
/**
*
* For gff-version 3:
@@ -331,26 +313,6 @@ public class GFFStreamFeature extends SimpleDocumentFeature
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));
- }
-
- return return_buffer.toString();
- }
-
/**
* Read and return a GFFStreamFeature from a stream. A feature must be the
* next thing in the stream.
diff --git a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
index 7ffff76f6..77e3247de 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 1.8 2005-04-19 09:22:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.9 2005-04-19 14:49:47 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 1.8 2005-04-19 09:22:18 tjc Exp $
+ * @version $Id: SimpleDocumentEntry.java,v 1.9 2005-04-19 14:49:47 tjc Exp $
**/
abstract public class SimpleDocumentEntry
@@ -244,8 +244,9 @@ abstract public class SimpleDocumentEntry
while(gff_features.hasMoreElements())
{
GFFStreamFeature feature = (GFFStreamFeature)gff_features.nextElement();
- String id = feature.getRegionName();
- if(id != null && id.equals(header_strings[i]))
+ Qualifier qualifier = feature.getQualifierByName("gff_seqname");
+
+ if(qualifier.getValues().contains(header_strings[i]))
{
try
{
--
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