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JAL-2292 squashed bug that breaks feature mapping for different cased residues
[jalview.git]
/
test
/
jalview
/
io
/
AnnotatedPDBFileInputTest.java
diff --git
a/test/jalview/io/AnnotatedPDBFileInputTest.java
b/test/jalview/io/AnnotatedPDBFileInputTest.java
index
62d76a2
..
b8c12c6
100644
(file)
--- a/
test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/
test/jalview/io/AnnotatedPDBFileInputTest.java
@@
-31,6
+31,8
@@
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.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.io.File;
import java.io.File;
@@
-65,6
+67,9
@@
public class AnnotatedPDBFileInputTest
al = af.getViewport().getAlignment();
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
al = af.getViewport().getAlignment();
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-80,8
+85,8
@@
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]);
}
}
}
}
}
}
@@
-96,7
+101,11
@@
public class AnnotatedPDBFileInputTest
{
System.out.println("CalcId: " + aa.getCalcId());
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
}
}
}
@@
-212,8
+221,8
@@
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() + " "