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JAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testA...
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 15 May 2017 15:43:12 +0000
(16:43 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 15 May 2017 15:43:12 +0000
(16:43 +0100)
test/jalview/io/AnnotationFileIOTest.java
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test/jalview/io/PhylipFileTests.java
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test/jalview/io/RNAMLfileTest.java
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test/jalview/io/StockholmFileTest.java
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test/jalview/ws/jabaws/DisorderAnnotExportImport.java
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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
c3aa13e
..
62bd0b9
100644
(file)
--- a/
test/jalview/io/AnnotationFileIOTest.java
+++ b/
test/jalview/io/AnnotationFileIOTest.java
@@
-153,7
+153,8
@@
public class AnnotationFileIOTest
DataSourceType.PASTE));
// test for consistency in io
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{
diff --git
a/test/jalview/io/PhylipFileTests.java
b/test/jalview/io/PhylipFileTests.java
index
f99c67a
..
d853350
100644
(file)
--- a/
test/jalview/io/PhylipFileTests.java
+++ b/
test/jalview/io/PhylipFileTests.java
@@
-190,7
+190,8
@@
public class PhylipFileTests
DataSourceType.PASTE, FileFormat.Phylip);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
DataSourceType.PASTE, FileFormat.Phylip);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
- StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false,
+ false);
}
}
}
}
diff --git
a/test/jalview/io/RNAMLfileTest.java
b/test/jalview/io/RNAMLfileTest.java
index
1c54980
..
ae72de4
100644
(file)
--- a/
test/jalview/io/RNAMLfileTest.java
+++ b/
test/jalview/io/RNAMLfileTest.java
@@
-53,7
+53,7
@@
public class RNAMLfileTest
{
StockholmFileTest.testFileIOwithFormat(new File(
"examples/testdata/rna-alignment.xml"), FileFormat.Stockholm,
{
StockholmFileTest.testFileIOwithFormat(new File(
"examples/testdata/rna-alignment.xml"), FileFormat.Stockholm,
- -1, -1, true);
+ -1, -1, true, true, true);
}
}
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
1a18fb9
..
228c935
100644
(file)
--- a/
test/jalview/io/StockholmFileTest.java
+++ b/
test/jalview/io/StockholmFileTest.java
@@
-60,7
+60,7
@@
public class StockholmFileTest
public void pfamFileIO() throws Exception
{
testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
public void pfamFileIO() throws Exception
{
testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
- false);
+ false, false, false);
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-86,7
+86,7
@@
public class StockholmFileTest
public void rfamFileIO() throws Exception
{
testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
public void rfamFileIO() throws Exception
{
testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
- false);
+ false, false, false);
}
/**
}
/**
@@
-98,11
+98,14
@@
public class StockholmFileTest
* @param ioformat
* - label for IO class used to write and read back in the data from
* f
* @param ioformat
* - label for IO class used to write and read back in the data from
* f
+ * @param ignoreFeatures
* @param ignoreRowVisibility
* @param ignoreRowVisibility
+ * @param allowNullAnnotations
*/
public static void testFileIOwithFormat(File f, FileFormatI ioformat,
*/
public static void testFileIOwithFormat(File f, FileFormatI ioformat,
- int naliannot, int nminseqann, boolean ignoreRowVisibility)
+ int naliannot, int nminseqann, boolean ignoreFeatures,
+ boolean ignoreRowVisibility, boolean allowNullAnnotations)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
@@
-136,7
+139,8
@@
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, false);
+ testAlignmentEquivalence(al, al_input, ignoreFeatures,
+ ignoreRowVisibility, allowNullAnnotations);
int numaliannot = 0, numsqswithali = 0;
for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
{
int numaliannot = 0, numsqswithali = 0;
for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
{
diff --git
a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index
2714d6c
..
e8b6c2b
100644
(file)
--- a/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@
-177,7
+177,8
@@
public class DisorderAnnotExportImport
DataSourceType.PASTE));
// test for consistency in io
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
+ false);
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
d5b6ed1
..
8326687
100644
(file)
--- a/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@
-218,7
+218,8
@@
public class JpredJabaStructExportImport
DataSourceType.PASTE));
// test for consistency in io
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ 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
4e9741e
..
5ea97ff
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-242,7
+242,8
@@
public class RNAStructExportImport
DataSourceType.PASTE));
// test for consistency in io
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{