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JAL-2235 patch tests where self-reference was used for dataset sequence ref
author
Jim Procter
<jprocter@issues.jalview.org>
Wed, 28 Sep 2016 14:26:52 +0000
(15:26 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Wed, 28 Sep 2016 14:26:52 +0000
(15:26 +0100)
test/jalview/commands/EditCommandTest.java
patch
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test/jalview/gui/StructureChooserTest.java
patch
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test/jalview/io/AnnotationFileIOTest.java
patch
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blob
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test/jalview/io/JSONFileTest.java
patch
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test/jalview/io/StockholmFileTest.java
patch
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diff --git
a/test/jalview/commands/EditCommandTest.java
b/test/jalview/commands/EditCommandTest.java
index
9afae37
..
7fb80fb
100644
(file)
--- 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
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());
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
(file)
--- 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 = 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();
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
(file)
--- 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)
{
// 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;
}
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
(file)
--- a/
test/jalview/io/JSONFileTest.java
+++ b/
test/jalview/io/JSONFileTest.java
@@
-114,7
+114,7
@@
public class JSONFileTest
for (Sequence seq : seqs)
{
for (Sequence seq : seqs)
{
- seq.setDatasetSequence(seq);
+ seq.createDatasetSequence();
expectedSeqs.put(seq.getName(), seq);
}
expectedSeqs.put(seq.getName(), seq);
}
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
0e2b630
..
b635aa3
100644
(file)
--- 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)
{
// 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"
}
String outputfile = rf.formatSequences(ioformat, al, true);
System.out.println("Output file in '" + ioformat + "':\n"