*/
package jalview.ext.ensembl;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import org.json.simple.parser.ParseException;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
import jalview.bin.Cache;
import jalview.util.DBRefUtils;
import jalview.util.IntRangeComparator;
import jalview.util.MapList;
-import jalview.util.Platform;
-
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-
-import org.json.simple.parser.ParseException;
/**
* Base class for Ensembl sequence fetchers
EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
EnsemblFeatureType[] features = getFeaturesToFetch();
- Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
-
+ // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
features);
genomicSequence = geneFeatures.getSequenceAt(0);
}
- Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
+ // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
if (genomicSequence != null)
{
* fetch and map protein product, and add it as a cross-reference
* of the retrieved sequence
*/
- Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);
+ // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);
addProteinProduct(querySeq);
}
}
System.err.println(
"Error transferring Ensembl features: " + e.getMessage());
}
- Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
+ // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
}
/**
* copy exon features to protein, compute peptide variants from dna
* variants and add as features on the protein sequence ta-da
*/
- AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
- mapList);
+ // JAL-3187 render on the fly instead
+ // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
}
} catch (Exception e)
{
protected void getCrossReferences(SequenceI seq)
{
- Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
+ // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
while (seq.getDatasetSequence() != null)
seq = seq.getDatasetSequence();
}
- Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);
+ // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);
EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
getEnsemblDataVersion());
seq.addDBRef(self);
- Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
-
+ // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
}
/**
inProgress = false;
throw new JalviewException("ENSEMBL Rest API not available.");
}
- Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
+ // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
List<SequenceI> seqs = parseSequenceJson(ids);
if (seqs == null)
- {
- return alignment;
- }
+ return alignment;
if (seqs.isEmpty())
{
* for now, assumes only one sequence returned; refactor if needed
* in future to handle a JSONArray with more than one
*/
-
- Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
+ // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
if (val == null)
- {
- return null;
- }
+ return null;
Object s = val.get("desc");
String desc = s == null ? null : s.toString();
s = val.get("id");
System.err.println("Error processing JSON response: " + e.toString());
// ignore
}
- Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
+ // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
return result;
}
String comp = complement.toString();
sf.setValue(Gff3Helper.ALLELES, comp);
sf.setDescription(comp);
-
- /*
- * replace value of "alleles=" in sf.ATTRIBUTES as well
- * so 'output as GFF' shows reverse complement alleles
- */
- String atts = sf.getAttributes();
- if (atts != null)
- {
- atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
- Gff3Helper.ALLELES + "=" + comp);
- sf.setAttributes(atts);
- }
}
/**
return false;
}
-
- Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);
-
+ // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);
boolean result = transferFeatures(sfs, targetSequence, mapping,
accessionId);