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Jalview-JS/JAL-3253-applet also comments relating to JAL-3268
[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
36b19e2
..
63a6a6c
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-34,6
+34,7
@@
import jalview.io.gff.SequenceOntologyI;
import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
+import jalview.util.Platform;
import java.awt.Color;
import java.io.UnsupportedEncodingException;
import java.awt.Color;
import java.io.UnsupportedEncodingException;
@@
-51,13
+52,11
@@
import com.stevesoft.pat.Regex;
*/
public class EnsemblGene extends EnsemblSeqProxy
{
*/
public class EnsemblGene extends EnsemblSeqProxy
{
- private static final String GENE_PREFIX = "gene:";
-
/*
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
*/
/*
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
*/
- private static final Regex ACCESSION_REGEX = new Regex(".*");
+ private static Regex ACCESSION_REGEX;
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
@@
-140,7
+139,6
@@
public class EnsemblGene extends EnsemblSeqProxy
* 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);
-
AlignmentI al = null;
for (String geneId : geneIds)
{
AlignmentI al = null;
for (String geneId : geneIds)
{
@@
-157,9
+155,7
@@
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();
-
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
-
getTranscripts(geneAlignment, geneId);
}
if (al == null)
getTranscripts(geneAlignment, geneId);
}
if (al == null)
@@
-368,7
+364,7
@@
public class EnsemblGene extends EnsemblSeqProxy
* look for exon features of the transcript, failing that for CDS
* (for example ENSG00000124610 has 1 CDS but no exon features)
*/
* look for exon features of the transcript, failing that for CDS
* (for example ENSG00000124610 has 1 CDS but no exon features)
*/
- String parentId = "transcript:" + accId;
+ String parentId = accId;
List<SequenceFeature> splices = findFeatures(gene,
SequenceOntologyI.EXON, parentId);
if (splices.isEmpty())
List<SequenceFeature> splices = findFeatures(gene,
SequenceOntologyI.EXON, parentId);
if (splices.isEmpty())
@@
-399,7
+395,7
@@
public class EnsemblGene extends EnsemblSeqProxy
* Ensembl has gene name as transcript Name
* EnsemblGenomes doesn't, but has a url-encoded description field
*/
* Ensembl has gene name as transcript Name
* EnsemblGenomes doesn't, but has a url-encoded description field
*/
- String description = (String) transcriptFeature.getValue(NAME);
+ String description = transcriptFeature.getDescription();
if (description == null)
{
description = (String) transcriptFeature.getValue(DESCRIPTION);
if (description == null)
{
description = (String) transcriptFeature.getValue(DESCRIPTION);
@@
-488,7
+484,7
@@
public class EnsemblGene extends EnsemblSeqProxy
*/
protected String getTranscriptId(SequenceFeature feature)
{
*/
protected String getTranscriptId(SequenceFeature feature)
{
- return (String) feature.getValue("transcript_id");
+ return (String) feature.getValue(JSON_ID);
}
/**
}
/**
@@
-510,7
+506,7
@@
public class EnsemblGene extends EnsemblSeqProxy
{
List<SequenceFeature> transcriptFeatures = new ArrayList<>();
{
List<SequenceFeature> transcriptFeatures = new ArrayList<>();
- String parentIdentifier = GENE_PREFIX + accId;
+ String parentIdentifier = accId;
List<SequenceFeature> sfs = geneSequence.getFeatures()
.getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
List<SequenceFeature> sfs = geneSequence.getFeatures()
.getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
@@
-541,10
+537,11
@@
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
}
/**
}
/**
@@
-561,9
+558,8
@@
public class EnsemblGene extends EnsemblSeqProxy
.getFeaturesByOntology(SequenceOntologyI.GENE);
for (SequenceFeature sf : sfs)
{
.getFeaturesByOntology(SequenceOntologyI.GENE);
for (SequenceFeature sf : sfs)
{
- // NB features as gff use 'ID'; rest services return as 'id'
- String id = (String) sf.getValue("ID");
- if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equalsIgnoreCase(id))
{
result.add(sf);
}
{
result.add(sf);
}
@@
-581,7
+577,7
@@
public class EnsemblGene extends EnsemblSeqProxy
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.GENE))
{
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.GENE))
{
@@
-590,7
+586,7
@@
public class EnsemblGene extends EnsemblSeqProxy
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
+ if (!accessionId.equalsIgnoreCase(parent))
{
return false;
}
{
return false;
}
@@
-610,6
+606,10
@@
public class EnsemblGene extends EnsemblSeqProxy
@Override
public Regex getAccessionValidator()
{
@Override
public Regex getAccessionValidator()
{
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex(".*", null);
+ }
return ACCESSION_REGEX;
}
return ACCESSION_REGEX;
}
@@
-628,7
+628,7
@@
public class EnsemblGene extends EnsemblSeqProxy
{
return new FeatureSettingsAdapter()
{
{
return new FeatureSettingsAdapter()
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
@Override
public boolean isFeatureDisplayed(String type)
@Override
public boolean isFeatureDisplayed(String type)