*/
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);
}
/**
String accId = querySeq.getName();
try
{
- System.out.println("Adding protein product for " + accId);
+ Cache.log.info("Adding protein product for " + accId);
AlignmentI protein = new EnsemblProtein(getDomain())
.getSequenceRecords(accId);
if (protein == null || protein.getHeight() == 0)
{
- System.out.println("No protein product found for " + accId);
+ Cache.log.info("No protein product found for " + accId);
return;
}
SequenceI proteinSeq = protein.getSequenceAt(0);
* 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)
if (seqs.size() != ids.size())
{
- System.out.println(String.format(
+ Cache.log.warn(String.format(
"Only retrieved %d sequences for %d query strings",
seqs.size(), ids.size()));
}
* 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;
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;
}
if (regions.isEmpty())
{
- System.out.println("Failed to identify target sequence for " + accId
+ Cache.log.warn("Failed to identify target sequence for " + accId
+ " from genomic features");
return null;
}
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);
for (int i = 0, n = sfs.size(); i < n; i++)
{
- if ((i%1000) == 0) {
-// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
- Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);
- }
+// if ((i%1000) == 0) {
+//// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
+// Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);
+// }
SequenceFeature sf = sfs.get(i);
if (retainFeature(sf, parentId))