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Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
RNAStructExportImport.java
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
5ea97ff
..
ee07335
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-98,7
+98,7
@@
public class RNAStructExportImport
for (Jws2Instance svc : disc.getServices())
{
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+ if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
{
rnaalifoldws = svc;
}
{
rnaalifoldws = svc;
}
@@
-118,7
+118,7
@@
public class RNAStructExportImport
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
// remove any existing annotation
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
// remove any existing annotation
- List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aal = new ArrayList<>();
for (AlignmentAnnotation rna : af.getViewport().getAlignment()
.getAlignmentAnnotation())
{
for (AlignmentAnnotation rna : af.getViewport().getAlignment()
.getAlignmentAnnotation())
{
@@
-202,7
+202,9
@@
public class RNAStructExportImport
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
} while (af.getViewport().getCalcManager().isWorking());
AlignmentI orig_alig = af.getViewport().getAlignment();
-
+ // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
+ // annotation is mistakenly recognised as an RNA annotation row when read in
+ // as an annotation file.
verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
@@
-257,7
+259,7
@@
public class RNAStructExportImport
@Test(groups = { "Network" })
public void testRnaalifoldSettingsRecovery()
{
@Test(groups = { "Network" })
public void testRnaalifoldSettingsRecovery()
{
- List<Argument> opts = new ArrayList<Argument>();
+ List<Argument> opts = new ArrayList<>();
for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
.getArguments())
{
for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
.getArguments())
{