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JAL-1665 patch for regression: failing jalview.ws.jabaws.DisorderAnnotExportImport...
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 15 Jun 2015 17:52:02 +0000
(18:52 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 15 Jun 2015 17:52:10 +0000
(18:52 +0100)
test/jalview/io/AnnotationFileIOTest.java
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test/jalview/io/PhylipFileTests.java
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test/jalview/io/StockholmFileTest.java
patch
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test/jalview/ws/jabaws/DisorderAnnotExportImport.java
patch
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test/jalview/ws/jabaws/JpredJabaStructExportImport.java
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test/jalview/ws/jabaws/RNAStructExportImport.java
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diff --git
a/test/jalview/io/AnnotationFileIOTest.java
b/test/jalview/io/AnnotationFileIOTest.java
index
0962452
..
0e066c2
100644
(file)
--- a/
test/jalview/io/AnnotationFileIOTest.java
+++ b/
test/jalview/io/AnnotationFileIOTest.java
@@
-144,7
+144,7
@@
public class AnnotationFileIOTest
FormatAdapter.PASTE));
// test for consistency in io
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{
diff --git
a/test/jalview/io/PhylipFileTests.java
b/test/jalview/io/PhylipFileTests.java
index
70e3f2c
..
e411272
100644
(file)
--- a/
test/jalview/io/PhylipFileTests.java
+++ b/
test/jalview/io/PhylipFileTests.java
@@
-160,7
+160,7
@@
public class PhylipFileTests
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
- StockholmFileTest.testAlignmentEquivalence(al, al_input);
+ StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
}
}
\ No newline at end of file
}
}
\ No newline at end of file
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
3bf0952
..
806e4dc
100644
(file)
--- a/
test/jalview/io/StockholmFileTest.java
+++ b/
test/jalview/io/StockholmFileTest.java
@@
-119,7
+119,7
@@
public class StockholmFileTest
"Identify routine could not recognise output generated by '"
+ ioformat + "' writer",
ioformat.equals(identifyoutput));
"Identify routine could not recognise output generated by '"
+ ioformat + "' writer",
ioformat.equals(identifyoutput));
- testAlignmentEquivalence(al, al_input);
+ testAlignmentEquivalence(al, al_input, false);
int numaliannot = 0, numsqswithali = 0;
for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
{
int numaliannot = 0, numsqswithali = 0;
for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
{
@@
-157,9
+157,11
@@
public class StockholmFileTest
* @param al_input
* 'secondary' or generated alignment from some datapreserving
* transformation
* @param al_input
* 'secondary' or generated alignment from some datapreserving
* transformation
+ * @param ignoreFeatures
+ * when true, differences in seuqence feature annotation are ignored.
*/
public static void testAlignmentEquivalence(AlignmentI al,
*/
public static void testAlignmentEquivalence(AlignmentI al,
- AlignmentI al_input)
+ AlignmentI al_input, boolean ignoreFeatures)
{
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
{
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
@@
-261,8
+263,10
@@
public class StockholmFileTest
+ " are not equal", ss_original.equals(ss_new));
assertTrue(
+ " are not equal", ss_original.equals(ss_new));
assertTrue(
- "Sequence Features were not equivalent",
- (seq_original[i].getSequenceFeatures() == null && seq_new[in]
+ "Sequence Features were not equivalent"
+ + (ignoreFeatures ? " ignoring." : ""),
+ ignoreFeatures
+ || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
.getSequenceFeatures() == null)
|| (seq_original[i].getSequenceFeatures() != null && seq_new[in]
.getSequenceFeatures() != null));
.getSequenceFeatures() == null)
|| (seq_original[i].getSequenceFeatures() != null && seq_new[in]
.getSequenceFeatures() != null));
diff --git
a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index
6076dec
..
e561479
100644
(file)
--- a/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@
-151,7
+151,7
@@
public class DisorderAnnotExportImport
FormatAdapter.PASTE));
// test for consistency in io
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{
diff --git
a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index
c522bc3
..
7afaeed
100644
(file)
--- a/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@
-215,7
+215,7
@@
public class JpredJabaStructExportImport
FormatAdapter.PASTE));
// test for consistency in io
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
665d9c8
..
1475b4e
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-210,7
+210,7
@@
public class RNAStructExportImport
FormatAdapter.PASTE));
// test for consistency in io
FormatAdapter.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{