From 47218e272a88aaffd9804b7d283472097aaa4167 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 4 Jul 2006 11:03:06 +0000
Subject: [PATCH] tidy and split out chadoToGFF
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4496 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 325 ++++++++++--------
1 file changed, 173 insertions(+), 152 deletions(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index ac25cd751..82cefdfd3 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -24,7 +24,6 @@
package uk.ac.sanger.artemis.util;
-import com.ibatis.sqlmap.client.SqlMapClient;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.chado.*;
import uk.ac.sanger.artemis.components.DatabaseEntrySource;
@@ -361,7 +360,7 @@ public class DatabaseDocument extends Document
for(int i = 0; i < buffers.length; i++)
buffers[i] = new ByteBuffer();
- String parentFeature = dao.getFeatureName(srcfeature_id, schema);
+ final String parentFeature = dao.getFeatureName(srcfeature_id, schema);
ByteBuffer this_buff;
int feature_size = featList.size();
@@ -376,47 +375,18 @@ public class DatabaseDocument extends Document
id_store.put(feature_id, name);
}
-
- String gff_source;
- // get all dbrefs
+ // get all dbrefs & synonyms
Hashtable dbxrefs = dao.getDbxref(schema, null);
-
- // get all synonyms
Hashtable synonym = dao.getAlias(schema, null);
+ // create gff byte stream
for(int i = 0; i < feature_size; i++)
{
- gff_source = null;
-
+ // select buffer based on feature type
ChadoFeature feat = (ChadoFeature)featList.get(i);
- int fmin = feat.getFeatureloc().getFmin() + 1;
- int fmax = feat.getFeatureloc().getFmax();
long type_id = feat.getCvterm().getCvtermId();
- int strand = feat.getFeatureloc().getStrand();
- int phase = feat.getFeatureloc().getPhase();
- String name = feat.getUniquename();
- String typeName = getCvtermName(type_id);
-
- String timelastmodified = Long.toString(feat.getTimelastmodified().getTime());
- String feature_id = Integer.toString(feat.getId());
-
- String parent_id = null;
- String parent_relationship = null;
- if(feat.getFeature_relationship() != null)
- {
- ChadoFeatureRelationship feat_relationship = feat.getFeature_relationship();
- parent_id = Integer.toString(feat_relationship.getObject_id());
- long parent_type_id = feat_relationship.getCvterm().getCvtermId();
- parent_relationship = getCvtermName(parent_type_id);
- }
-
- if(parent_id != null && id_store.containsKey(parent_id))
- parent_id = (String)id_store.get(parent_id);
-
- // make gff format
-
- // select buffer
+ String typeName = getCvtermName(type_id, dao);
this_buff = buffers[types.length];
for(int j = 0; j < types.length; j++)
{
@@ -424,119 +394,189 @@ public class DatabaseDocument extends Document
this_buff = buffers[j];
}
- Vector dbxref = null;
- // append dbxrefs
- if(dbxrefs != null &&
- dbxrefs.containsKey(new Integer(feature_id)))
+ chadoToGFF(feat, parentFeature,
+ dbxrefs, synonym,
+ id_store, dao, this_buff);
+
+ progress_listener.progressMade("Read from database: " +
+ feat.getUniquename());
+ }
+
+ return buffers;
+ }
+
+ /**
+ * Convert the chado feature into a GFF line
+ * @param feat Chado feature
+ * @param parentFeature parent of this feature
+ * @param dbxrefs hashtable containing dbxrefs
+ * @param synonym hashtable containing synonynms
+ * @param id_store id store for looking up parent names
+ * @param dao chado data access
+ * @param this_buff byte buffer of GFF line
+ */
+ public static void chadoToGFF(final ChadoFeature feat,
+ final String parentFeature,
+ final Hashtable dbxrefs,
+ final Hashtable synonym,
+ final Hashtable id_store,
+ final ChadoDAO dao,
+ final ByteBuffer this_buff)
+ {
+ String gff_source = null;
+
+ int fmin = feat.getFeatureloc().getFmin() + 1;
+ int fmax = feat.getFeatureloc().getFmax();
+ long type_id = feat.getCvterm().getCvtermId();
+ int strand = feat.getFeatureloc().getStrand();
+ int phase = feat.getFeatureloc().getPhase();
+ String name = feat.getUniquename();
+ String typeName = getCvtermName(type_id, dao);
+
+ String timelastmodified = Long.toString(feat.getTimelastmodified().getTime());
+ String feature_id = Integer.toString(feat.getId());
+
+ String parent_id = null;
+ String parent_relationship = null;
+ if(feat.getFeature_relationship() != null)
+ {
+ ChadoFeatureRelationship feat_relationship = feat.getFeature_relationship();
+ parent_id = Integer.toString(feat_relationship.getObject_id());
+ long parent_type_id = feat_relationship.getCvterm().getCvtermId();
+
+ parent_relationship = feat_relationship.getCvterm().getName();
+
+ if(parent_relationship == null)
+ parent_relationship = getCvtermName(parent_type_id, dao);
+ }
+ else if(feat.getFeatureRelationshipsForSubjectId() != null)
+ {
+ List relations = feat.getFeatureRelationshipsForSubjectId();
+ for(int i=0; i<relations.size(); i++)
+ {
+ ChadoFeatureRelationship feat_relationship =
+ (ChadoFeatureRelationship)relations.get(i);
+ parent_id = Integer.toString(feat_relationship.getObject_id());
+ System.out.println("HERE "+i+" "+feat_relationship.getCvterm().getName()+ " "+
+ feat_relationship.getObject_id()+" "+feat_relationship.getSubject_id()+ " parent_id="+ parent_id);
+ parent_relationship = feat_relationship.getCvterm().getName();
+ }
+ }
+
+ if(parent_id != null && id_store != null && id_store.containsKey(parent_id))
+ parent_id = (String)id_store.get(parent_id);
+
+ // make gff format
+
+ Vector dbxref = null;
+ // append dbxrefs
+ if(dbxrefs != null &&
+ dbxrefs.containsKey(new Integer(feature_id)))
+ {
+ dbxref = (Vector)dbxrefs.get(new Integer(feature_id));
+ for(int j=0; j<dbxref.size(); j++)
{
- dbxref = (Vector)dbxrefs.get(new Integer(feature_id));
- for(int j=0; j<dbxref.size(); j++)
+ if(((String)dbxref.get(j)).startsWith("GFF_source:"))
{
- if(((String)dbxref.get(j)).startsWith("GFF_source:"))
- {
- gff_source = ((String)dbxref.get(j)).substring(11);
- dbxref.removeElementAt(j);
- }
+ gff_source = ((String)dbxref.get(j)).substring(11);
+ dbxref.removeElementAt(j);
}
}
+ }
- this_buff.append(parentFeature + "\t"); // seqid
-
- if(gff_source != null)
- this_buff.append(gff_source+"\t"); // source
- else
- this_buff.append("chado\t");
- this_buff.append(typeName + "\t"); // type
- this_buff.append(fmin + "\t"); // start
- this_buff.append(fmax + "\t"); // end
- this_buff.append(".\t"); // score
- if(strand == -1) // strand
- this_buff.append("-\t");
- else if(strand == 1)
- this_buff.append("+\t");
- else
- this_buff.append(".\t");
+ this_buff.append(parentFeature + "\t"); // seqid
+
+ if(gff_source != null)
+ this_buff.append(gff_source+"\t"); // source
+ else
+ this_buff.append("chado\t");
+ this_buff.append(typeName + "\t"); // type
+ this_buff.append(fmin + "\t"); // start
+ this_buff.append(fmax + "\t"); // end
+ this_buff.append(".\t"); // score
+ if(strand == -1) // strand
+ this_buff.append("-\t");
+ else if(strand == 1)
+ this_buff.append("+\t");
+ else
+ this_buff.append(".\t");
- if(phase > 3)
- this_buff.append(".\t"); // phase
- else
- this_buff.append(phase+"\t");
+ if(phase > 3)
+ this_buff.append(".\t"); // phase
+ else
+ this_buff.append(phase+"\t");
- this_buff.append("ID=" + name + ";");
+ this_buff.append("ID=" + name + ";");
-
- if(parent_id != null && !parent_id.equals("0"))
- {
- if(parent_relationship.equals("derives_from"))
- this_buff.append("Derives_from=" + parent_id + ";");
- else
- this_buff.append("Parent=" + parent_id + ";");
- }
+
+ if(parent_id != null && !parent_id.equals("0"))
+ {
+ if(parent_relationship.equals("derives_from"))
+ this_buff.append("Derives_from=" + parent_id + ";");
+ else
+ this_buff.append("Parent=" + parent_id + ";");
+ }
- this_buff.append("timelastmodified=" + timelastmodified + ";");
+ this_buff.append("timelastmodified=" + timelastmodified + ";");
- // attributes
- Hashtable qualifiers = feat.getQualifiers();
- if(qualifiers != null && qualifiers.size() > 0)
+ // attributes
+ Hashtable qualifiers = feat.getQualifiers();
+
+ if(qualifiers != null && qualifiers.size() > 0)
+ {
+ Enumeration e_qualifiers = qualifiers.keys();
+ while(e_qualifiers.hasMoreElements())
{
- Enumeration e_qualifiers = qualifiers.keys();
- while(e_qualifiers.hasMoreElements())
- {
- Long qualifier_type_id = (Long)e_qualifiers.nextElement();
- String qualifier_name = getCvtermName(qualifier_type_id.longValue());
- if(qualifier_name == null)
- continue;
-
- Vector qualifier_value = (Vector)qualifiers.get(qualifier_type_id);
+ Long qualifier_type_id = (Long)e_qualifiers.nextElement();
+ String qualifier_name = getCvtermName(qualifier_type_id.longValue(), dao);
+ if(qualifier_name == null)
+ continue;
- for(int j=0; j<qualifier_value.size(); j++)
- {
- ChadoFeatureProp featprop = (ChadoFeatureProp)qualifier_value.get(j);
- this_buff.append(qualifier_name+ "=" +
- GFFStreamFeature.encode(featprop.getValue())+";");
- }
+ Vector qualifier_value = (Vector)qualifiers.get(qualifier_type_id);
+ for(int j=0; j<qualifier_value.size(); j++)
+ {
+ ChadoFeatureProp featprop = (ChadoFeatureProp)qualifier_value.get(j);
+ this_buff.append(qualifier_name+ "=" +
+ GFFStreamFeature.encode(featprop.getValue())+";");
}
- }
+ }
+ }
- // append dbxrefs
- if(dbxref != null && dbxref.size() > 0)
+ // append dbxrefs
+ if(dbxref != null && dbxref.size() > 0)
+ {
+ this_buff.append("Dbxref=");
+ for(int j=0; j<dbxref.size(); j++)
{
- this_buff.append("Dbxref=");
- for(int j=0; j<dbxref.size(); j++)
- {
- this_buff.append((String)dbxref.get(j));
- if(j<dbxref.size()-1)
- this_buff.append(",");
- }
- this_buff.append(";");
+ this_buff.append((String)dbxref.get(j));
+ if(j<dbxref.size()-1)
+ this_buff.append(",");
}
-
- // append synonyms
- if(synonym != null &&
- synonym.containsKey(new Integer(feature_id)))
- {
- ChadoFeatureSynonym alias;
- Vector v_synonyms = (Vector)synonym.get(new Integer(feature_id));
- for(int j=0; j<v_synonyms.size(); j++)
- {
- alias = (ChadoFeatureSynonym)v_synonyms.get(j);
- this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
- this_buff.append(alias.getSynonym().getName());
-
- if(j<v_synonyms.size()-1)
- this_buff.append(";");
- }
+ this_buff.append(";");
+ }
+
+ // append synonyms
+ if(synonym != null &&
+ synonym.containsKey(new Integer(feature_id)))
+ {
+ ChadoFeatureSynonym alias;
+ Vector v_synonyms = (Vector)synonym.get(new Integer(feature_id));
+ for(int j=0; j<v_synonyms.size(); j++)
+ {
+ alias = (ChadoFeatureSynonym)v_synonyms.get(j);
+ this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
+ this_buff.append(alias.getSynonym().getName());
+
+ if(j<v_synonyms.size()-1)
+ this_buff.append(";");
}
-
- this_buff.append("\n");
-
- progress_listener.progressMade("Read from database: " + name);
}
-
- return buffers;
+
+ this_buff.append("\n");
}
-
+
+
/**
* Look up the cvterm_id for a controlled vocabulary name.
* @param name
@@ -559,29 +599,10 @@ public class DatabaseDocument extends Document
* @param id a cvterm_id
* @return the cvterm name
*/
- private String getCvtermName(long id)
+ private static String getCvtermName(long id, ChadoDAO dao)
{
if(cvterm == null)
- {
- try
- {
- getCvterm(getDAO());
- }
- catch(ConnectException ce)
- {
- ce.printStackTrace();
- }
- catch(SQLException sqle)
- {
- JOptionPane.showMessageDialog(null,
- "Problems Looking Up cvterm Name (cvterm_id="+
- Long.toString(id)+") ...\n" +
- sqle.getMessage(),
- "Cvterm Name Look Up",
- JOptionPane.ERROR_MESSAGE);
- sqle.printStackTrace();
- }
- }
+ getCvterm(dao);
return (String)cvterm.get(new Long(id));
}
@@ -591,7 +612,7 @@ public class DatabaseDocument extends Document
* @param dao the data access object
* @return the cvterm <code>Hashtable</code>
*/
- private Hashtable getCvterm(ChadoDAO dao)
+ private static Hashtable getCvterm(ChadoDAO dao)
{
cvterm = new Hashtable();
@@ -608,7 +629,7 @@ public class DatabaseDocument extends Document
}
catch(SQLException sqle)
{
- System.err.println(this.getClass() + ": SQLException retrieving CvTerms");
+ System.err.println("SQLException retrieving CvTerms");
System.err.println(sqle);
}
@@ -699,7 +720,7 @@ public class DatabaseDocument extends Document
while(it_residue_features.hasNext())
{
ChadoFeature feature = (ChadoFeature)it_residue_features.next();
- String typeName = getCvtermName(feature.getCvterm().getCvtermId());
+ String typeName = getCvtermName(feature.getCvterm().getCvtermId(), getDAO());
db.put(schema + " - " + typeName + " - " + feature.getUniquename(),
Integer.toString(feature.getId()));
--
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