git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
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
dd2547b
..
63a6a6c
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-56,7
+56,7
@@
public class EnsemblGene extends EnsemblSeqProxy
* 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,
@@
-135,29
+135,16
@@
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
+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();
-
-
- 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
+167,6
@@
public class EnsemblGene extends EnsemblSeqProxy
al.append(geneAlignment);
}
}
al.append(geneAlignment);
}
}
-
- Platform.timeCheck("EG done", Platform.TIME_MARK);
-
return al;
}
return al;
}
@@
-561,10
+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
}
/**
}
/**
@@
-600,7
+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))
{
@@
-629,6
+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;
}
@@
-647,7
+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)