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Commit 47218e27 authored by tjc's avatar tjc
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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
parent 7adabc80
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uk/ac/sanger/artemis/util/DatabaseDocument.java
+ 173
− 152
View file @ 47218e27
......@@ -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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