X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSequenceFetcher.java;h=7454eb627cff9b5bbb76910c3083b1a7e753840a;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=21f9f7e01b87b878f805f38e6f3f93015986877e;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java index 21f9f7e..7454eb6 100644 --- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java +++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java @@ -23,7 +23,6 @@ package jalview.ext.ensembl; import jalview.analysis.AlignmentUtils; import jalview.bin.Cache; import jalview.datamodel.DBRefSource; -import jalview.util.Platform; import jalview.ws.seqfetcher.DbSourceProxyImpl; import com.stevesoft.pat.Regex; @@ -46,7 +45,14 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl // ensemblgenomes REST service merged to ensembl 9th April 2019 protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL; - private static Regex ACCESSION_REGEX; + /* + * accepts ENSG/T/E/P with 11 digits + * or ENSMUSP or similar for other species + * or CCDSnnnnn.nn with at least 3 digits + */ + private static final Regex ACCESSION_REGEX = new Regex( + "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + + "(CCDS[0-9.]{3,}$)"); protected final String ensemblGenomesDomain; @@ -115,17 +121,6 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl @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}|)[GTEP]{1}[0-9]{11}$)" + "|" - + "(CCDS[0-9.]{3,}$)", null); - } return ACCESSION_REGEX; }