From 9933957d3d6c0a13ccb19e1a83bdc4a5102f10ca Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Aug 2017 19:27:53 +0100 Subject: [PATCH] =?utf8?q?JAL-2425=20remove=20overloaded=20getSequenceRecord?= =?utf8?q?s=20method=20(don=E2=80=99t=20need=20it=20=3F)?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/ws/dbsources/Pfam.java | 36 ------------------------------------ 1 file changed, 36 deletions(-) diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java index 941bf1a..0227e35 100644 --- a/src/jalview/ws/dbsources/Pfam.java +++ b/src/jalview/ws/dbsources/Pfam.java @@ -20,12 +20,7 @@ */ package jalview.ws.dbsources; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; -import jalview.io.DataSourceType; -import jalview.io.FileFormat; -import jalview.io.FormatAdapter; import com.stevesoft.pat.Regex; @@ -111,37 +106,6 @@ abstract public class Pfam extends Xfam /* * (non-Javadoc) * - * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[]) - */ - @Override - public AlignmentI getSequenceRecords(String queries) throws Exception - { - // TODO: this is not a perfect implementation. We need to be able to add - // individual references to each sequence in each family alignment that's - // retrieved. - startQuery(); - AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL() - + queries.trim().toUpperCase(), DataSourceType.URL, - FileFormat.Stockholm); - for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++) - { - rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM, - // getDbSource(), - getDbVersion(), queries.trim().toUpperCase())); - if (!getDbSource().equals(DBRefSource.PFAM)) - { // add the specific ref too - rcds.getSequenceAt(s).addDBRef( - new DBRefEntry(getDbSource(), getDbVersion(), queries - .trim().toUpperCase())); - } - } - stopQuery(); - return rcds; - } - - /* - * (non-Javadoc) - * * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) */ @Override -- 1.7.10.2