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JAL-3438 spotless for 2.11.2.0
[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
cdcfa96
..
75a7154
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;
@@
-34,6
+33,7
@@
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;
@@
-51,8
+51,6
@@
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
@@
-64,6
+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)
*/
@@
-100,6
+100,12
@@
public class EnsemblGene extends EnsemblSeqProxy
return EnsemblSeqType.GENOMIC;
}
return EnsemblSeqType.GENOMIC;
}
+ @Override
+ protected String getObjectType()
+ {
+ return OBJECT_TYPE_GENE;
+ }
+
/**
* Returns an alignment containing the gene(s) for the given gene or
* transcript identifier, or external identifier (e.g. Uniprot id). If given a
/**
* Returns an alignment containing the gene(s) for the given gene or
* transcript identifier, or external identifier (e.g. Uniprot id). If given a
@@
-134,7
+140,6
@@
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)
{
@@
-146,9
+151,11
@@
public class EnsemblGene extends EnsemblSeqProxy
{
continue;
}
{
continue;
}
-
+
if (geneAlignment.getHeight() == 1)
{
if (geneAlignment.getHeight() == 1)
{
+ // ensure id has 'correct' case for the Ensembl identifier
+ geneId = geneAlignment.getSequenceAt(0).getName();
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
getTranscripts(geneAlignment, geneId);
}
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
getTranscripts(geneAlignment, geneId);
}
@@
-179,7
+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
{
@@
-201,7
+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];
@@
-235,7
+242,7
@@
public class EnsemblGene extends EnsemblSeqProxy
*/
List<String> getGeneIds(String accessions)
{
*/
List<String> getGeneIds(String accessions)
{
- List<String> geneIds = new ArrayList<String>();
+ List<String> geneIds = new ArrayList<>();
for (String acc : accessions.split(getAccessionSeparator()))
{
for (String acc : accessions.split(getAccessionSeparator()))
{
@@
-311,8
+318,8
@@
public class EnsemblGene extends EnsemblSeqProxy
SequenceOntologyI.NMD_TRANSCRIPT_VARIANT,
SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON,
SequenceOntologyI.CDS };
SequenceOntologyI.NMD_TRANSCRIPT_VARIANT,
SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON,
SequenceOntologyI.CDS };
- List<SequenceFeature> sfs = gene.getFeatures().getFeaturesByOntology(
- soTerms);
+ List<SequenceFeature> sfs = gene.getFeatures()
+ .getFeaturesByOntology(soTerms);
for (SequenceFeature sf : sfs)
{
gene.deleteFeature(sf);
for (SequenceFeature sf : sfs)
{
gene.deleteFeature(sf);
@@
-358,7
+365,7
@@
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())
@@
-370,7
+377,7
@@
public class EnsemblGene extends EnsemblSeqProxy
int transcriptLength = 0;
final char[] geneChars = gene.getSequence();
int offset = gene.getStart(); // to convert to 0-based positions
int transcriptLength = 0;
final char[] geneChars = gene.getSequence();
int offset = gene.getStart(); // to convert to 0-based positions
- List<int[]> mappedFrom = new ArrayList<int[]>();
+ List<int[]> mappedFrom = new ArrayList<>();
for (SequenceFeature sf : splices)
{
for (SequenceFeature sf : splices)
{
@@
-389,7
+396,7
@@
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);
@@
-412,7
+419,7
@@
public class EnsemblGene extends EnsemblSeqProxy
* transfer features to the new sequence; we use EnsemblCdna to do this,
* to filter out unwanted features types (see method retainFeature)
*/
* transfer features to the new sequence; we use EnsemblCdna to do this,
* to filter out unwanted features types (see method retainFeature)
*/
- List<int[]> mapTo = new ArrayList<int[]>();
+ List<int[]> mapTo = new ArrayList<>();
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
EnsemblCdna cdna = new EnsemblCdna(getDomain());
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
EnsemblCdna cdna = new EnsemblCdna(getDomain());
@@
-452,7
+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<>();
@@
-462,8
+469,9
@@
public class EnsemblGene extends EnsemblSeqProxy
transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
}
transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
}
- List<int[]> transcriptRange = Arrays.asList(new int[] {
- transcript.getStart(), transcript.getEnd() });
+ List<int[]> transcriptRange = Arrays
+ .asList(new int[]
+ { transcript.getStart(), transcript.getEnd() });
MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
@@
-478,7
+486,7
@@
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);
}
/**
}
/**
@@
-498,9
+506,9
@@
public class EnsemblGene extends EnsemblSeqProxy
protected List<SequenceFeature> getTranscriptFeatures(String accId,
SequenceI geneSequence)
{
protected List<SequenceFeature> getTranscriptFeatures(String accId,
SequenceI geneSequence)
{
- List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
+ 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);
@@
-510,7
+518,7
@@
public class EnsemblGene extends EnsemblSeqProxy
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
- if (parentIdentifier.equals(parent))
+ if (parentIdentifier.equalsIgnoreCase(parent))
{
transcriptFeatures.add(sf);
}
{
transcriptFeatures.add(sf);
}
@@
-531,29
+539,34
@@
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
}
/**
}
/**
- * Answers true for a feature of type 'gene' (or a sub-type of gene in the
- * Sequence Ontology), whose ID is the accession we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'gene' (or a
+ * subtype of gene in the Sequence Ontology), and whose ID is the accession we
+ * are retrieving
*/
@Override
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.GENE))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.GENE);
+ for (SequenceFeature sf : sfs)
{
{
- String id = (String) sf.getValue(ID);
- if ((GENE_PREFIX + accId).equals(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equalsIgnoreCase(id))
{
{
- return true;
+ result.add(sf);
}
}
}
}
- return false;
+ return result;
}
/**
}
/**
@@
-575,7
+588,7
@@
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).equals(parent))
+ if (!accessionId.equalsIgnoreCase(parent))
{
return false;
}
{
return false;
}
@@
-584,17
+597,6
@@
public class EnsemblGene extends EnsemblSeqProxy
}
/**
}
/**
- * Answers false. This allows an optimisation - a single 'gene' feature is all
- * that is needed to identify the positions of the gene on the genomic
- * sequence.
- */
- @Override
- protected boolean isSpliceable()
- {
- return false;
- }
-
- /**
* Override to do nothing as Ensembl doesn't return a protein sequence for a
* gene identifier
*/
* Override to do nothing as Ensembl doesn't return a protein sequence for a
* gene identifier
*/
@@
-627,10
+629,10
@@
public class EnsemblGene extends EnsemblSeqProxy
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
@Override
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
@Override
- public boolean isFeatureDisplayed(String type)
+ public boolean isFeatureHidden(String type)
{
{
- return (so.isA(type, SequenceOntologyI.EXON)
- || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
+ return (!so.isA(type, SequenceOntologyI.EXON)
+ && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
}
@Override
}
@Override