X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblProtein.java;h=99006aa0f8e586d7160c289d4d6bfe79ce847508;hb=ff425ad8a4419c01b52734dc4054a509961c15c0;hp=8f23984d9f12759498d4ae93381cb35cdcc1cc31;hpb=46b2bc114452c0e30463214b3e82eb0a5c98d23f;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 8f23984..99006aa 100644
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -1,27 +1,64 @@
+/*
+ * 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;
+/**
+ * A client to fetch protein translated sequence for an Ensembl identifier
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblProtein extends EnsemblSeqProxy
{
- // TODO modify to accept other species e.g. ENSMUSPnnn
+ /*
+ * accepts ENSP 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(
- "((ENSP|CCDS)[0-9.]{3,})");
-
- private static final List CROSSREFS = Arrays.asList(new String[] {
- "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
+ "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblProtein()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblProtein(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
@@ -76,15 +113,33 @@ public class EnsemblProtein extends EnsemblSeqProxy
}
@Override
- protected List getCrossReferenceDatabases()
+ public Regex getAccessionValidator()
{
- return CROSSREFS;
+ return ACCESSION_REGEX;
}
+ /**
+ * Returns an accession id for a query, including conversion of ENST* to
+ * ENSP*. This supports querying for the protein sequence for a transcript
+ * (ENST identifier) and returning the ENSP identifier.
+ */
@Override
- public Regex getAccessionValidator()
+ public String getAccessionIdFromQuery(String query)
{
- return ACCESSION_REGEX;
+ String accId = super.getAccessionIdFromQuery(query);
+
+ /*
+ * ensure last character before (11) digits is P
+ * ENST00000288602 -> ENSP00000288602
+ * ENSMUST00000288602 -> ENSMUSP00000288602
+ */
+ if (accId != null && accId.length() >= 12)
+ {
+ char[] chars = accId.toCharArray();
+ chars[chars.length - 12] = 'P';
+ accId = new String(chars);
+ }
+ return accId;
}
}