X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblProtein.java;h=0280f1613a16c6f17ed32b44ac345364ebd56685;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=db8d9d56fb9543b697c83b16093dd1c7ceb06fa8;hpb=9eec40eae88ae4330adc4d6ae38c513742b9e853;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index db8d9d5..0280f16 100644
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -1,15 +1,68 @@
+/*
+ * 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.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+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
{
+ /*
+ * 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(
+ "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
- public EnsemblProtein() throws Exception
+ /**
+ * 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()
{
@@ -22,4 +75,75 @@ public class EnsemblProtein extends EnsemblSeqProxy
return EnsemblSeqType.PROTEIN;
}
+ /**
+ * Returns false, as this fetcher does not retrieve DNA sequences.
+ */
+ @Override
+ public boolean isDnaCoding()
+ {
+ return false;
+ }
+
+ /**
+ * Test query is to the protein translation of transcript ENST00000288602
+ */
+ @Override
+ public String getTestQuery()
+ {
+ return "ENSP00000288602";
+ }
+
+ /**
+ * Overrides base class method to do nothing - genomic features are not
+ * applicable to the protein product sequence
+ */
+ @Override
+ protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
+ {
+ }
+
+ @Override
+ protected EnsemblFeatureType[] getFeaturesToFetch()
+ {
+ // not applicable - can't fetch genomic features for a protein sequence
+ return null;
+ }
+
+ @Override
+ protected List getIdentifyingFeatures(SequenceI seq,
+ String accId)
+ {
+ return new ArrayList<>();
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ 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 String getAccessionIdFromQuery(String query)
+ {
+ 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;
+ }
+
}