X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;fp=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=365c1c24fbc91e429fb08313a8e8487573de541c;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=915fa0aa04e5067731f1ebd8dceae9dc7a79f9d0;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 915fa0a..365c1c2 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -110,7 +110,8 @@ public class EnsemblGene extends EnsemblSeqProxy
*
resolves an external identifier by looking up xref-ed gene ids
* fetches the gene sequence
* fetches features on the sequence
- * identifies "transcript" features whose Parent is the requested gene
+ * identifies "transcript" features whose Parent is the requested
+ * gene
* fetches the transcript sequence for each transcript
* makes a mapping from the gene to each transcript
* copies features from gene to transcript sequences
@@ -313,8 +314,8 @@ public class EnsemblGene extends EnsemblSeqProxy
* the parent gene sequence, with features
* @return
*/
- SequenceI makeTranscript(SequenceFeature transcriptFeature,
- AlignmentI al, SequenceI gene)
+ SequenceI makeTranscript(SequenceFeature transcriptFeature, AlignmentI al,
+ SequenceI gene)
{
String accId = getTranscriptId(transcriptFeature);
if (accId == null)
@@ -363,7 +364,8 @@ public class EnsemblGene extends EnsemblSeqProxy
mappedFrom.add(new int[] { sf.getBegin(), sf.getEnd() });
}
- Sequence transcript = new Sequence(accId, seqChars, 1, transcriptLength);
+ Sequence transcript = new Sequence(accId, seqChars, 1,
+ transcriptLength);
/*
* Ensembl has gene name as transcript Name
@@ -566,8 +568,8 @@ public class EnsemblGene extends EnsemblSeqProxy
@Override
public boolean isFeatureDisplayed(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