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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
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uk/ac/sanger/artemis/util/DatabaseDocument.java
+ 173
− 152
View file @ 47218e27
...@@ -24,7 +24,6 @@ ...@@ -24,7 +24,6 @@
package uk.ac.sanger.artemis.util; package uk.ac.sanger.artemis.util;
import com.ibatis.sqlmap.client.SqlMapClient;
import uk.ac.sanger.artemis.io.GFFStreamFeature; import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.chado.*; import uk.ac.sanger.artemis.chado.*;
import uk.ac.sanger.artemis.components.DatabaseEntrySource; import uk.ac.sanger.artemis.components.DatabaseEntrySource;
...@@ -361,7 +360,7 @@ public class DatabaseDocument extends Document ...@@ -361,7 +360,7 @@ public class DatabaseDocument extends Document
for(int i = 0; i < buffers.length; i++) for(int i = 0; i < buffers.length; i++)
buffers[i] = new ByteBuffer(); buffers[i] = new ByteBuffer();
String parentFeature = dao.getFeatureName(srcfeature_id, schema); final String parentFeature = dao.getFeatureName(srcfeature_id, schema);
ByteBuffer this_buff; ByteBuffer this_buff;
int feature_size = featList.size(); int feature_size = featList.size();
...@@ -376,47 +375,18 @@ public class DatabaseDocument extends Document ...@@ -376,47 +375,18 @@ public class DatabaseDocument extends Document
id_store.put(feature_id, name); id_store.put(feature_id, name);
} }
String gff_source;
// get all dbrefs // get all dbrefs & synonyms
Hashtable dbxrefs = dao.getDbxref(schema, null); Hashtable dbxrefs = dao.getDbxref(schema, null);
// get all synonyms
Hashtable synonym = dao.getAlias(schema, null); Hashtable synonym = dao.getAlias(schema, null);
// create gff byte stream
for(int i = 0; i < feature_size; i++) for(int i = 0; i < feature_size; i++)
{ {
gff_source = null; // select buffer based on feature type
ChadoFeature feat = (ChadoFeature)featList.get(i); ChadoFeature feat = (ChadoFeature)featList.get(i);
int fmin = feat.getFeatureloc().getFmin() + 1;
int fmax = feat.getFeatureloc().getFmax();
long type_id = feat.getCvterm().getCvtermId(); long type_id = feat.getCvterm().getCvtermId();
int strand = feat.getFeatureloc().getStrand(); String typeName = getCvtermName(type_id, dao);
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
this_buff = buffers[types.length]; this_buff = buffers[types.length];
for(int j = 0; j < types.length; j++) for(int j = 0; j < types.length; j++)
{ {
...@@ -424,119 +394,189 @@ public class DatabaseDocument extends Document ...@@ -424,119 +394,189 @@ public class DatabaseDocument extends Document
this_buff = buffers[j]; this_buff = buffers[j];
} }
Vector dbxref = null; chadoToGFF(feat, parentFeature,
// append dbxrefs dbxrefs, synonym,
if(dbxrefs != null && id_store, dao, this_buff);
dbxrefs.containsKey(new Integer(feature_id)))
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)); if(((String)dbxref.get(j)).startsWith("GFF_source:"))
for(int j=0; j<dbxref.size(); j++)
{ {
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 this_buff.append(parentFeature + "\t"); // seqid
if(gff_source != null) if(gff_source != null)
this_buff.append(gff_source+"\t"); // source this_buff.append(gff_source+"\t"); // source
else else
this_buff.append("chado\t"); this_buff.append("chado\t");
this_buff.append(typeName + "\t"); // type this_buff.append(typeName + "\t"); // type
this_buff.append(fmin + "\t"); // start this_buff.append(fmin + "\t"); // start
this_buff.append(fmax + "\t"); // end this_buff.append(fmax + "\t"); // end
this_buff.append(".\t"); // score this_buff.append(".\t"); // score
if(strand == -1) // strand if(strand == -1) // strand
this_buff.append("-\t"); this_buff.append("-\t");
else if(strand == 1) else if(strand == 1)
this_buff.append("+\t"); this_buff.append("+\t");
else else
this_buff.append(".\t"); this_buff.append(".\t");
if(phase > 3) if(phase > 3)
this_buff.append(".\t"); // phase this_buff.append(".\t"); // phase
else else
this_buff.append(phase+"\t"); 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_id != null && !parent_id.equals("0"))
{ {
if(parent_relationship.equals("derives_from")) if(parent_relationship.equals("derives_from"))
this_buff.append("Derives_from=" + parent_id + ";"); this_buff.append("Derives_from=" + parent_id + ";");
else else
this_buff.append("Parent=" + parent_id + ";"); this_buff.append("Parent=" + parent_id + ";");
} }
this_buff.append("timelastmodified=" + timelastmodified + ";"); this_buff.append("timelastmodified=" + timelastmodified + ";");
// attributes // attributes
Hashtable qualifiers = feat.getQualifiers(); Hashtable qualifiers = feat.getQualifiers();
if(qualifiers != null && qualifiers.size() > 0)
if(qualifiers != null && qualifiers.size() > 0)
{
Enumeration e_qualifiers = qualifiers.keys();
while(e_qualifiers.hasMoreElements())
{ {
Enumeration e_qualifiers = qualifiers.keys(); Long qualifier_type_id = (Long)e_qualifiers.nextElement();
while(e_qualifiers.hasMoreElements()) String qualifier_name = getCvtermName(qualifier_type_id.longValue(), dao);
{ if(qualifier_name == null)
Long qualifier_type_id = (Long)e_qualifiers.nextElement(); continue;
String qualifier_name = getCvtermName(qualifier_type_id.longValue());
if(qualifier_name == null)
continue;
Vector qualifier_value = (Vector)qualifiers.get(qualifier_type_id);
for(int j=0; j<qualifier_value.size(); j++) 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+ "=" + ChadoFeatureProp featprop = (ChadoFeatureProp)qualifier_value.get(j);
GFFStreamFeature.encode(featprop.getValue())+";"); this_buff.append(qualifier_name+ "=" +
} GFFStreamFeature.encode(featprop.getValue())+";");
} }
} }
}
// append dbxrefs // append dbxrefs
if(dbxref != null && dbxref.size() > 0) if(dbxref != null && dbxref.size() > 0)
{
this_buff.append("Dbxref=");
for(int j=0; j<dbxref.size(); j++)
{ {
this_buff.append("Dbxref="); this_buff.append((String)dbxref.get(j));
for(int j=0; j<dbxref.size(); j++) if(j<dbxref.size()-1)
{ this_buff.append(",");
this_buff.append((String)dbxref.get(j));
if(j<dbxref.size()-1)
this_buff.append(",");
}
this_buff.append(";");
} }
this_buff.append(";");
// append synonyms }
if(synonym != null &&
synonym.containsKey(new Integer(feature_id))) // append synonyms
{ if(synonym != null &&
ChadoFeatureSynonym alias; synonym.containsKey(new Integer(feature_id)))
Vector v_synonyms = (Vector)synonym.get(new Integer(feature_id)); {
for(int j=0; j<v_synonyms.size(); j++) ChadoFeatureSynonym alias;
{ Vector v_synonyms = (Vector)synonym.get(new Integer(feature_id));
alias = (ChadoFeatureSynonym)v_synonyms.get(j); for(int j=0; j<v_synonyms.size(); j++)
this_buff.append(alias.getSynonym().getCvterm().getName()+"="); {
this_buff.append(alias.getSynonym().getName()); alias = (ChadoFeatureSynonym)v_synonyms.get(j);
this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
if(j<v_synonyms.size()-1) this_buff.append(alias.getSynonym().getName());
this_buff.append(";");
} 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. * Look up the cvterm_id for a controlled vocabulary name.
* @param name * @param name
...@@ -559,29 +599,10 @@ public class DatabaseDocument extends Document ...@@ -559,29 +599,10 @@ public class DatabaseDocument extends Document
* @param id a cvterm_id * @param id a cvterm_id
* @return the cvterm name * @return the cvterm name
*/ */
private String getCvtermName(long id) private static String getCvtermName(long id, ChadoDAO dao)
{ {
if(cvterm == null) if(cvterm == null)
{ getCvterm(dao);
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();
}
}
return (String)cvterm.get(new Long(id)); return (String)cvterm.get(new Long(id));
} }
...@@ -591,7 +612,7 @@ public class DatabaseDocument extends Document ...@@ -591,7 +612,7 @@ public class DatabaseDocument extends Document
* @param dao the data access object * @param dao the data access object
* @return the cvterm <code>Hashtable</code> * @return the cvterm <code>Hashtable</code>
*/ */
private Hashtable getCvterm(ChadoDAO dao) private static Hashtable getCvterm(ChadoDAO dao)
{ {
cvterm = new Hashtable(); cvterm = new Hashtable();
...@@ -608,7 +629,7 @@ public class DatabaseDocument extends Document ...@@ -608,7 +629,7 @@ public class DatabaseDocument extends Document
} }
catch(SQLException sqle) catch(SQLException sqle)
{ {
System.err.println(this.getClass() + ": SQLException retrieving CvTerms"); System.err.println("SQLException retrieving CvTerms");
System.err.println(sqle); System.err.println(sqle);
} }
...@@ -699,7 +720,7 @@ public class DatabaseDocument extends Document ...@@ -699,7 +720,7 @@ public class DatabaseDocument extends Document
while(it_residue_features.hasNext()) while(it_residue_features.hasNext())
{ {
ChadoFeature feature = (ChadoFeature)it_residue_features.next(); 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(), db.put(schema + " - " + typeName + " - " + feature.getUniquename(),
Integer.toString(feature.getId())); Integer.toString(feature.getId()));
......
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