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Merge branch 'features/JAL-2447experimentalFlag' into develop
[jalview.git]
/
test
/
jalview
/
io
/
StockholmFileTest.java
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())
{