X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblProtein.java;h=99006aa0f8e586d7160c289d4d6bfe79ce847508;hb=a2703f9c2948fba9747b304fed02b7bbc5d32b37;hp=97796a5d418a01d6a457cd99a8fc909838e25b14;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java index 97796a5..99006aa 100644 --- a/src/jalview/ext/ensembl/EnsemblProtein.java +++ b/src/jalview/ext/ensembl/EnsemblProtein.java @@ -1,11 +1,28 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ext.ensembl; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceFeature; -import java.util.Arrays; -import java.util.List; - import com.stevesoft.pat.Regex; /** @@ -24,9 +41,6 @@ public class EnsemblProtein extends EnsemblSeqProxy private static final Regex ACCESSION_REGEX = new Regex( "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)"); - private static final List CROSSREFS = Arrays.asList(new String[] { - "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" }); - /** * Default constructor (to use rest.ensembl.org) */ @@ -99,12 +113,6 @@ public class EnsemblProtein extends EnsemblSeqProxy } @Override - protected List getCrossReferenceDatabases() - { - return CROSSREFS; - } - - @Override public Regex getAccessionValidator() { return ACCESSION_REGEX;