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JAL-1925 update source version in license
[jalview.git]
/
test
/
jalview
/
io
/
StockholmFileTest.java
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
2537002
..
5ab4297
100644
(file)
--- a/
test/jalview/io/StockholmFileTest.java
+++ b/
test/jalview/io/StockholmFileTest.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-43,13
+43,13
@@
public class StockholmFileTest
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void pfamFileIO() throws Exception
{
testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
}
public void pfamFileIO() throws Exception
{
testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void pfamFileDataExtraction() throws Exception
{
AppletFormatAdapter af = new AppletFormatAdapter();
public void pfamFileDataExtraction() throws Exception
{
AppletFormatAdapter af = new AppletFormatAdapter();
@@
-58,9
+58,9
@@
public class StockholmFileTest
int numpdb = 0;
for (SequenceI sq : al.getSequences())
{
int numpdb = 0;
for (SequenceI sq : al.getSequences())
{
- if (sq.getPDBId() != null)
+ if (sq.getAllPDBEntries() != null)
{
{
- numpdb += sq.getPDBId().size();
+ numpdb += sq.getAllPDBEntries().size();
}
}
assertTrue(
}
}
assertTrue(
@@
-68,7
+68,7
@@
public class StockholmFileTest
numpdb > 0);
}
numpdb > 0);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void rfamFileIO() throws Exception
{
testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
public void rfamFileIO() throws Exception
{
testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
@@
-136,7
+136,7
@@
public class StockholmFileTest
if (naliannot > -1)
{
assertEquals("Number of alignment annotations", naliannot,
if (naliannot > -1)
{
assertEquals("Number of alignment annotations", naliannot,
- numaliannot);
+ numaliannot);
}
assertTrue(
}
assertTrue(
@@
-268,7
+268,7
@@
public class StockholmFileTest
+ (ignoreFeatures ? " ignoring." : ""),
ignoreFeatures
|| (seq_original[i].getSequenceFeatures() == null && seq_new[in]
+ (ignoreFeatures ? " ignoring." : ""),
ignoreFeatures
|| (seq_original[i].getSequenceFeatures() == null && seq_new[in]
- .getSequenceFeatures() == null)
+ .getSequenceFeatures() == null)
|| (seq_original[i].getSequenceFeatures() != null && seq_new[in]
.getSequenceFeatures() != null));
// compare sequence features
|| (seq_original[i].getSequenceFeatures() != null && seq_new[in]
.getSequenceFeatures() != null));
// compare sequence features