From b5fb170aae86089a49a0529dbb4c04bf36e0499b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 13 Nov 2017 18:57:10 +0000 Subject: [PATCH 1/1] JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs derived from Entry name --- src/jalview/ws/dbsources/Uniprot.java | 21 ++------------------- 1 file changed, 2 insertions(+), 19 deletions(-) diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index 94bc582..73775cf 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -60,11 +60,6 @@ public class Uniprot extends DbSourceProxyImpl private static Mapping map; /** - * configurable parameter controlling prefixing of entry names with accessions - */ - private boolean includeAllIds = false; - - /** * Constructor */ public Uniprot() @@ -208,7 +203,7 @@ public class Uniprot extends DbSourceProxyImpl */ public SequenceI uniprotEntryToSequenceI(UniprotEntry entry) { - String id = getUniprotEntryId(entry, includeAllIds); + String id = getUniprotEntryId(entry); SequenceI sequence = new Sequence(id, entry.getUniprotSequence().getContent()); sequence.setDescription(getUniprotEntryDescription(entry)); @@ -318,21 +313,9 @@ public class Uniprot extends DbSourceProxyImpl * UniprotEntry * @return The accession id(s) and name(s) delimited by '|'. */ - public static String getUniprotEntryId(UniprotEntry entry, - boolean includeAllIds) + public static String getUniprotEntryId(UniprotEntry entry) { StringBuilder name = new StringBuilder(32); - if (includeAllIds) - { - // // use 'canonicalised' name for optimal id matching - name.append(DBRefSource.UNIPROT); - for (String accessionId : entry.getAccession()) - { - name.append(BAR_DELIMITER); - name.append(accessionId); - } - - } for (String n : entry.getName()) { if (name.length() > 0) -- 1.7.10.2