X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=e01ad17eaee377a850713e5af6e8fd47582859f1;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=bdfd208dfb98b023d8f69893aa2ae1f5a0a0e6ff;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java index bdfd208..e01ad17 100644 --- a/src/jalview/ext/ensembl/EnsemblCdna.java +++ b/src/jalview/ext/ensembl/EnsemblCdna.java @@ -23,7 +23,6 @@ package jalview.ext.ensembl; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.gff.SequenceOntologyI; -import jalview.util.Platform; import java.util.ArrayList; import java.util.List; @@ -45,7 +44,9 @@ public class EnsemblCdna extends EnsemblSeqProxy * or ENSMUST or similar for other species * or CCDSnnnnn.nn with at least 3 digits */ - private static Regex ACCESSION_REGEX; + private static final Regex ACCESSION_REGEX = new Regex( + "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)"); + /* * fetch exon features on genomic sequence (to identify the cdna regions) * and cds and variation features (to retain) @@ -87,16 +88,6 @@ public class EnsemblCdna extends EnsemblSeqProxy @Override public Regex getAccessionValidator() { - if (ACCESSION_REGEX == null) - { - /* - * accepts ENSG/T/E/P with 11 digits - * or ENSMUSP or similar for other species - * or CCDSnnnnn.nn with at least 3 digits - */ - ACCESSION_REGEX = Platform.newRegex( - "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)", null); - } return ACCESSION_REGEX; }