From 3e16aae83055354f09b0f9560686d035a5f2e5aa Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 19 Feb 2016 16:59:42 +0000 Subject: [PATCH] JAL-1705 updated for change to CrossRef signature --- test/jalview/ws/SequenceFetcherTest.java | 6 ++++-- test/jalview/ws/seqfetcher/DbRefFetcherTest.java | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java index 7a9b553..d7058d0 100644 --- a/test/jalview/ws/SequenceFetcherTest.java +++ b/test/jalview/ws/SequenceFetcherTest.java @@ -7,6 +7,7 @@ import jalview.datamodel.SequenceI; import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; +import java.util.ArrayList; import java.util.Enumeration; import java.util.List; import java.util.Vector; @@ -116,7 +117,8 @@ public class SequenceFetcherTest System.out.println("Type: " + types[t]); SequenceI[] prod = jalview.analysis.CrossRef .findXrefSequences(al.getSequencesArray(), dna, - types[t]).getSequencesArray(); + types[t], null, new ArrayList()) + .getSequencesArray(); System.out.println("Found " + ((prod == null) ? "no" : "" + prod.length) + " products"); @@ -199,7 +201,7 @@ public class SequenceFetcherTest // sequences. SequenceI[] seqs = al.getSequencesArray(); Alignment prodal = jalview.analysis.CrossRef.findXrefSequences( - seqs, dna, null, ds); + seqs, dna, null, ds, new ArrayList()); System.out.println("Found " + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products"); diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java index fae5778..b9e209f 100644 --- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java +++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java @@ -179,8 +179,8 @@ public class DbRefFetcherTest assertEquals("Expected local reference map to be 3 nucleotides", dr[0] .getMap().getWidth(), 3); AlignmentI sprods = CrossRef.findXrefSequences( - alsq.getSequencesArray(), true, dr[0].getSource(), - alsq.getDataset()); + alsq.getSequencesArray(), true, dr[0].getSource(), alsq, + new ArrayList()); assertNotNull( "Couldn't recover cross reference sequence from dataset. Was it ever added ?", sprods); -- 1.7.10.2