git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2480 more efficient contains check on add; tidied comparators
[jalview.git]
/
test
/
jalview
/
io
/
AnnotatedPDBFileInputTest.java
diff --git
a/test/jalview/io/AnnotatedPDBFileInputTest.java
b/test/jalview/io/AnnotatedPDBFileInputTest.java
index
9a07ef7
..
d8ae999
100644
(file)
--- a/
test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/
test/jalview/io/AnnotatedPDBFileInputTest.java
@@
-31,6
+31,7
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
@@
-44,6
+45,13
@@
import org.testng.annotations.Test;
public class AnnotatedPDBFileInputTest
{
public class AnnotatedPDBFileInputTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
AlignmentI al;
String pdbId;
AlignmentI al;
String pdbId;
@@
-85,8
+93,8
@@
public class AnnotatedPDBFileInputTest
{
for (int q = p + 1; q < avec.length; q++)
{
{
for (int q = p + 1; q < avec.length; q++)
{
- assertTrue("Found a duplicate annotation row "
- + avec[p].label, avec[p] != avec[q]);
+ assertTrue("Found a duplicate annotation row " + avec[p].label,
+ avec[p] != avec[q]);
}
}
}
}
}
}
@@
-104,7
+112,7
@@
public class AnnotatedPDBFileInputTest
if (StructureImportSettings.getDefaultPDBFileParser().equals(
StructureParser.JALVIEW_PARSER))
{
if (StructureImportSettings.getDefaultPDBFileParser().equals(
StructureParser.JALVIEW_PARSER))
{
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
}
}
}
@@
-122,9
+130,9
@@
public class AnnotatedPDBFileInputTest
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+ assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
/*
* 1GAQ/B
@@
-132,9
+140,9
@@
public class AnnotatedPDBFileInputTest
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+ assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
assertEquals("RESNUM", sf[97].getType());
assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
/*
* 1GAQ/C
@@
-142,9
+150,9
@@
public class AnnotatedPDBFileInputTest
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+ assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-221,8
+229,8
@@
public class AnnotatedPDBFileInputTest
sq = sq.getDatasetSequence();
}
assertNotNull(sq.getAllPDBEntries());
sq = sq.getDatasetSequence();
}
assertNotNull(sq.getAllPDBEntries());
- assertEquals("Expected only one PDB ID",
- sq.getAllPDBEntries().size(), 1);
+ assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+ .size());
for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
System.err.println("PDB Entry " + pdbentry.getId() + " "
for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
System.err.println("PDB Entry " + pdbentry.getId() + " "