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JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files
[jalview.git]
/
test
/
jalview
/
io
/
StockholmFileTest.java
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
e4f2abc
..
b1995ab
100644
(file)
--- a/
test/jalview/io/StockholmFileTest.java
+++ b/
test/jalview/io/StockholmFileTest.java
@@
-274,6
+274,11
@@
public class StockholmFileTest
// check Alignment annotation
AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
// check Alignment annotation
AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+ boolean expectProteinSS = !al.isNucleotide();
+ assertTrue(
+ "Alignments not both "
+ + (al.isNucleotide() ? "nucleotide" : "protein"),
+ al_input.isNucleotide() == al.isNucleotide());
// note - at moment we do not distinguish between alignment without any
// annotation rows and alignment with no annotation row vector
// note - at moment we do not distinguish between alignment without any
// annotation rows and alignment with no annotation row vector
@@
-292,6
+297,13
@@
public class StockholmFileTest
assertEqualSecondaryStructure(
"Different alignment annotation at position " + i,
aa_original[i], aa_new[i], allowNullAnnotation);
assertEqualSecondaryStructure(
"Different alignment annotation at position " + i,
aa_original[i], aa_new[i], allowNullAnnotation);
+ if (aa_original[i].hasIcons)
+ {
+ assertTrue(
+ "Secondary structure expected to be "
+ + (expectProteinSS ? "protein" : "nucleotide"),
+ expectProteinSS == !aa_original[i].isRNA());
+ }
// compare graphGroup or graph properties - needed to verify JAL-1299
assertEquals("Graph type not identical.", aa_original[i].graph,
aa_new[i].graph);
// compare graphGroup or graph properties - needed to verify JAL-1299
assertEquals("Graph type not identical.", aa_original[i].graph,
aa_new[i].graph);