From: Jim Procter Date: Wed, 28 Sep 2016 14:26:52 +0000 (+0100) Subject: JAL-2235 patch tests where self-reference was used for dataset sequence ref X-Git-Tag: Release_2_10_0~20^2~27 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1986948868e6643ea811a70cd0018c8103a7b3f0;p=jalview.git JAL-2235 patch tests where self-reference was used for dataset sequence ref --- diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 9afae37..7fb80fb 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -239,7 +239,7 @@ public class EditCommandTest public void testReplace() { // seem to need a dataset sequence on the edited sequence here - seqs[1].setDatasetSequence(seqs[1]); + seqs[1].createDatasetSequence(); new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] }, 4, 8, al); assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index bad536b..16dfa6b 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -44,7 +44,7 @@ public class StructureChooserTest { seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26); - seq.setDatasetSequence(seq); + seq.createDatasetSequence(); for (int x = 1; x < 5; x++) { DBRefEntry dbRef = new DBRefEntry(); diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java index 625244d..c9b5f4a 100644 --- a/test/jalview/io/AnnotationFileIOTest.java +++ b/test/jalview/io/AnnotationFileIOTest.java @@ -75,8 +75,7 @@ public class AnnotationFileIOTest // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) { - al.getSequenceAt(i).setDatasetSequence( - al.getSequenceAt(i).createDatasetSequence()); + al.getSequenceAt(i).createDatasetSequence(); } assertNotNull("Couldn't read supplied alignment data.", al); return al; diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java index 93fb12b..f75f433 100644 --- a/test/jalview/io/JSONFileTest.java +++ b/test/jalview/io/JSONFileTest.java @@ -114,7 +114,7 @@ public class JSONFileTest for (Sequence seq : seqs) { - seq.setDatasetSequence(seq); + seq.createDatasetSequence(); expectedSeqs.put(seq.getName(), seq); } diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 0e2b630..b635aa3 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -103,7 +103,7 @@ public class StockholmFileTest // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) { - al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i)); + al.getSequenceAt(i).createDatasetSequence(); } String outputfile = rf.formatSequences(ioformat, al, true); System.out.println("Output file in '" + ioformat + "':\n"