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Merge branch 'develop' into Jalview-JS/develop
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblGene.java
diff --git
a/src/jalview/ext/ensembl/EnsemblGene.java
b/src/jalview/ext/ensembl/EnsemblGene.java
index
dd2547b
..
0e3d84b
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-23,7
+23,6
@@
package jalview.ext.ensembl;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
@@
-63,6
+62,8
@@
public class EnsemblGene extends EnsemblSeqProxy
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ private static final String CHROMOSOME = "chromosome";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
/**
* Default constructor (to use rest.ensembl.org)
*/
@@
-135,29
+136,16
@@
public class EnsemblGene extends EnsemblSeqProxy
@Override
public AlignmentI getSequenceRecords(String query) throws Exception
{
@Override
public AlignmentI getSequenceRecords(String query) throws Exception
{
-
-
-
- Platform.timeCheck("EG " + query, Platform.TIME_MARK);
-
/*
* convert to a non-duplicated list of gene identifiers
*/
List<String> geneIds = getGeneIds(query);
/*
* convert to a non-duplicated list of gene identifiers
*/
List<String> geneIds = getGeneIds(query);
-
-
- Platform.timeCheck("EG genIds " + geneIds.size(), Platform.TIME_MARK);
-
AlignmentI al = null;
for (String geneId : geneIds)
{
/*
* fetch the gene sequence(s) with features and xrefs
*/
AlignmentI al = null;
for (String geneId : geneIds)
{
/*
* fetch the gene sequence(s) with features and xrefs
*/
-
- Platform.timeCheck("EG fetch " + geneId, Platform.TIME_MARK);
-
-
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
if (geneAlignment == null)
{
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
if (geneAlignment == null)
{
@@
-168,15
+156,7
@@
public class EnsemblGene extends EnsemblSeqProxy
{
// ensure id has 'correct' case for the Ensembl identifier
geneId = geneAlignment.getSequenceAt(0).getName();
{
// ensure id has 'correct' case for the Ensembl identifier
geneId = geneAlignment.getSequenceAt(0).getName();
-
-
- Platform.timeCheck("EG loci " + geneId, Platform.TIME_MARK);
-
-
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
-
- Platform.timeCheck("EG transcript " + geneId, Platform.TIME_MARK);
-
getTranscripts(geneAlignment, geneId);
}
if (al == null)
getTranscripts(geneAlignment, geneId);
}
if (al == null)
@@
-188,9
+168,6
@@
public class EnsemblGene extends EnsemblSeqProxy
al.append(geneAlignment);
}
}
al.append(geneAlignment);
}
}
-
- Platform.timeCheck("EG done", Platform.TIME_MARK);
-
return al;
}
return al;
}
@@
-209,7
+186,7
@@
public class EnsemblGene extends EnsemblSeqProxy
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), geneLoci.getMapping());
}
else
{
}
else
{
@@
-231,7
+208,7
@@
public class EnsemblGene extends EnsemblSeqProxy
return false;
}
String[] tokens = description.split(":");
return false;
}
String[] tokens = description.split(":");
- if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+ if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
{
String ref = tokens[1];
String chrom = tokens[2];
{
String ref = tokens[1];
String chrom = tokens[2];
@@
-482,7
+459,7
@@
public class EnsemblGene extends EnsemblSeqProxy
return;
}
return;
}
- MapList geneMapping = loci.getMap();
+ MapList geneMapping = loci.getMapping();
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
@@
-561,10
+538,11
@@
public class EnsemblGene extends EnsemblSeqProxy
@Override
public String getTestQuery()
{
@Override
public String getTestQuery()
{
- return "ENSG00000157764"; // BRAF, 5 transcripts, reverse strand
+ return Platform.isJS() ? "ENSG00000123569" : "ENSG00000157764";
+ // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
+ // ENSG00000157764 // BRAF, 5 transcripts, reverse strand
// ENSG00000090266 // NDUFB2, 15 transcripts, forward strand
// ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand
// ENSG00000090266 // NDUFB2, 15 transcripts, forward strand
// ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand
- // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
}
/**
}
/**