diff --git a/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java b/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java
index aaeed5af6f3df3cdbcf774700ec320f31e008107..3034e22c89fbb3227fea3c998e42815685f3d6cf 100644
--- a/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java
+++ b/uk/ac/sanger/artemis/io/ChadoCanonicalGene.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/ChadoCanonicalGene.java,v 1.3 2006-07-04 11:06:33 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java,v 1.4 2006-07-04 15:58:52 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -33,12 +33,12 @@ import java.util.Enumeration;
import java.util.List;
/**
- * Used by GFFStreamFaeture to represent the chado canonical gene.
+ * Used by GFFStreamFeature to represent the chado canonical gene.
+ * Contains gene, transcript, exons and proteins.
**/
public class ChadoCanonicalGene
{
private Object gene;
- private String gene_id;
// part_of gene
private List transcripts = new Vector();
@@ -52,20 +52,20 @@ public class ChadoCanonicalGene
// srcfeature length
private int seqlen;
- public void addObject(Object obj, String parent_id, String type)
- throws InvalidRelationException
- {
- if(type.equalsIgnoreCase("polypeptide"))
- addProtein(parent_id, obj);
- else if(type.equalsIgnoreCase("exon"))
- addExon(parent_id, obj);
- }
+ /**
+ * Get the gene feaure object.
+ * @return
+ */
public Object getGene()
{
return gene;
}
+ /**
+ * Set the gene feature object.
+ * @param gene
+ */
public void setGene(Object gene)
{
this.gene = gene;
@@ -76,33 +76,35 @@ public class ChadoCanonicalGene
transcripts.add(transcript);
}
- public void addExon(String transcript_id, Object exon, boolean reset)
+ public void addExon(String transcript_name,
+ Object exon, boolean reset)
throws InvalidRelationException
{
- exons = new Hashtable();
- addExon(transcript_id, exon);
+ if(reset)
+ exons = new Hashtable();
+ addExon(transcript_name, exon);
}
- public void addExon(String transcript_id, Object exon)
+ public void addExon(String transcript_name, Object exon)
throws InvalidRelationException
{
final List v_exons;
- if(exons.containsKey(transcript_id))
- v_exons = (Vector)exons.get(transcript_id);
+ if(exons.containsKey(transcript_name))
+ v_exons = (Vector)exons.get(transcript_name);
else
v_exons = new Vector();
v_exons.add(exon);
- exons.put(transcript_id, v_exons);
+ exons.put(transcript_name, v_exons);
}
- public void addProtein(String transcript_id, Object protein)
+ public void addProtein(String transcript_name, Object protein)
throws InvalidRelationException
{
- proteins.put(transcript_id, protein);
+ proteins.put(transcript_name, protein);
}
- public Object containsTranscript(final StringVector ids)
+ public Object containsTranscript(final StringVector names)
{
for(int i=0; i<transcripts.size(); i++)
{
@@ -110,7 +112,7 @@ public class ChadoCanonicalGene
{
Feature transcript = (Feature)transcripts.get(i);
- if( ids.contains((String)transcript.getQualifierByName("ID").getValues().get(0)) )
+ if( names.contains(getIDQualifier(transcript)) )
return transcript;
}
catch(InvalidRelationException e)
@@ -121,40 +123,51 @@ public class ChadoCanonicalGene
return null;
}
- public List getExonsOfTranscript(final String transcript_id)
+ public List getExonsOfTranscript(final String transcript_name)
{
- if(exons.containsKey(transcript_id))
- return (List)exons.get(transcript_id);;
+ if(exons.containsKey(transcript_name))
+ return (List)exons.get(transcript_name);
return null;
}
- public Object getProteinOfTranscript(final String transcript_id)
+ public Object getProteinOfTranscript(final String transcript_name)
{
- if(proteins.containsKey(transcript_id))
- return proteins.get(transcript_id);;
+ if(proteins.containsKey(transcript_name))
+ return proteins.get(transcript_name);;
return null;
}
-
- public Hashtable getExons()
- {
- return exons;
- }
+ /**
+ * Get a list of trancripts.
+ * @return
+ */
public List getTranscripts()
{
return transcripts;
}
- public Object getFeatureFromId(final String id)
+ /**
+ * Search for the feature with a particular uniquename
+ * @param name uniquename
+ * @return
+ */
+ public Object getFeatureFromId(final String name)
{
Object feature = null;
// check gene
try
{
- if(((String)(((Feature)gene).getQualifierByName("ID").getValues().get(0))).equals(id))
+ final String uniquename;
+
+ if(gene instanceof ChadoFeature)
+ uniquename = ((ChadoFeature)gene).getUniquename();
+ else
+ uniquename = getIDQualifier((Feature)gene);
+
+ if(uniquename.equals(name))
return gene;
}
catch(InvalidRelationException e)
@@ -164,7 +177,7 @@ public class ChadoCanonicalGene
// check transcript
StringVector sv = new StringVector();
- sv.add(id);
+ sv.add(name);
feature = containsTranscript(sv);
@@ -172,15 +185,21 @@ public class ChadoCanonicalGene
return feature;
// check exons
- feature = getExon(id);
+ feature = getExon(name);
if(feature != null)
return feature;
- return getProtein(id);
+ return getProtein(name);
}
- private Object getExon(final String id)
+ /**
+ * Routine to look for a exon with a particular
+ * uniquename
+ * @param name
+ * @return
+ */
+ private Object getExon(final String name)
{
Enumeration enum_exons = exons.elements();
try
@@ -196,9 +215,9 @@ public class ChadoCanonicalGene
if(exons.get(i) instanceof ChadoFeature)
uniquename = ((ChadoFeature)exons.get(i)).getUniquename();
else
- uniquename = (String)((Feature)exons.get(i)).getQualifierByName("ID").getValues().get(0);
+ uniquename = getIDQualifier((Feature)exons.get(i));
- if(uniquename.equals(id))
+ if(uniquename.equals(name))
return exons.get(i);
}
}
@@ -210,7 +229,7 @@ public class ChadoCanonicalGene
return null;
}
- private Feature getProtein(final String id)
+ private Object getProtein(final String id)
{
Enumeration enum_proteins = proteins.elements();
try
@@ -218,7 +237,7 @@ public class ChadoCanonicalGene
while(enum_proteins.hasMoreElements())
{
Feature protein = (Feature)enum_proteins.nextElement();
- if(((String)(protein.getQualifierByName("ID").getValues().get(0))).equals(id))
+ if(getIDQualifier(protein).equals(id))
return protein;
}
}
@@ -227,14 +246,28 @@ public class ChadoCanonicalGene
e.printStackTrace();
}
return null;
-
}
-
+
+
+ private String getIDQualifier(Feature feature)
+ throws InvalidRelationException
+ {
+ return (String)(feature.getQualifierByName("ID").getValues().get(0));
+ }
+
+ /**
+ * Get the srcfeature residue length
+ * @return
+ */
public int getSeqlen()
{
return seqlen;
}
+ /**
+ * Set the srcfeature residue length
+ * @param seqlen
+ */
public void setSeqlen(int seqlen)
{
this.seqlen = seqlen;