From: Jim Procter Date: Mon, 6 Oct 2014 11:38:24 +0000 (+0100) Subject: JAL-654 updated pdb db fetcher test to verify the number of annotation X-Git-Tag: Jalview_2_9~174^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2bf5ab62374818b10dc4842137d02abb57e140aa;p=jalview.git JAL-654 updated pdb db fetcher test to verify the number of annotation rows retrieved for a single chain query --- diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java index 5a9e954..6f0bf26 100644 --- a/test/jalview/ws/PDBSequenceFetcherTest.java +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -1,69 +1,60 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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.ws; - -import static org.junit.Assert.*; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceI; -import jalview.ws.seqfetcher.DbSourceProxy; - -import java.util.List; - -import org.junit.Before; -import org.junit.Test; - -public class PDBSequenceFetcherTest -{ - - SequenceFetcher sf; - - @Before - public void setUp() throws Exception - { - sf = new SequenceFetcher(false); - } - - @Test - public void testPdbPerChainRetrieve() throws Exception - { - List sps = sf.getSourceProxy("PDB"); - AlignmentI response = sps.get(0).getSequenceRecords("1QIPA"); - assertTrue(response != null); - assertTrue(response.getHeight() == 1); - } - - @Test - public void testRnaSeqRetrieve() throws Exception - { - List sps = sf.getSourceProxy("PDB"); - AlignmentI response = sps.get(0).getSequenceRecords("2GIS"); - assertTrue(response != null); - assertTrue(response.getHeight() == 1); - for (SequenceI sq : response.getSequences()) - { - assertTrue("No annotation transfered to sequence.", - sq.getAnnotation().length > 0); - assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0); - assertTrue("No RNA annotation on sequence.", sq.getRNA() != null); - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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.ws; + +import static org.junit.Assert.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.ws.seqfetcher.DbSourceProxy; + +import java.util.List; + +import org.junit.Before; +import org.junit.Test; + +public class PDBSequenceFetcherTest +{ + + SequenceFetcher sf; + + @Before + public void setUp() throws Exception + { + sf = new SequenceFetcher(false); + } + + @Test + public void testRnaSeqRetrieve() throws Exception + { + List sps = sf.getSourceProxy("PDB"); + AlignmentI response = sps.get(0).getSequenceRecords("2GIS"); + assertTrue(response != null); + assertTrue(response.getHeight() == 1); + for (SequenceI sq : response.getSequences()) + { + assertTrue("No annotation transfered to sequence.", + sq.getAnnotation().length > 0); + assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0); + assertTrue("No RNA annotation on sequence.", sq.getRNA() != null); + } + } + +}