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JAL-2110 cross-refs from protein to show cds not non-coding sequences
[jalview.git]
/
test
/
jalview
/
io
/
StockholmFileTest.java
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
12a8e9c
..
d7a9166
100644
(file)
--- a/
test/jalview/io/StockholmFileTest.java
+++ b/
test/jalview/io/StockholmFileTest.java
@@
-24,6
+24,12
@@
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
@@
-31,37
+37,30
@@
import java.util.Map;
import org.testng.annotations.Test;
import org.testng.annotations.Test;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-
public class StockholmFileTest
{
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
public class StockholmFileTest
{
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
- @Test
+ @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
+ @Test(groups = { "Functional" })
public void pfamFileDataExtraction() throws Exception
{
AppletFormatAdapter af = new AppletFormatAdapter();
AlignmentI al = af.readFile(PfamFile, af.FILE,
public void pfamFileDataExtraction() throws Exception
{
AppletFormatAdapter af = new AppletFormatAdapter();
AlignmentI al = af.readFile(PfamFile, af.FILE,
- new IdentifyFile().Identify(PfamFile, af.FILE));
+ new IdentifyFile().identify(PfamFile, af.FILE));
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(
@@
-69,7
+68,7
@@
public class StockholmFileTest
numpdb > 0);
}
numpdb > 0);
}
- @Test
+ @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);
@@
-95,8
+94,8
@@
public class StockholmFileTest
{
AppletFormatAdapter rf = new AppletFormatAdapter();
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
- new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
assertNotNull("Couldn't read supplied alignment data.", al);
@@
-109,11
+108,11
@@
public class StockholmFileTest
System.out.println("Output file in '" + ioformat + "':\n"
+ outputfile + "\n<<EOF\n");
// test for consistency in io
System.out.println("Output file in '" + ioformat + "':\n"
+ outputfile + "\n<<EOF\n");
// test for consistency in io
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, ioformat);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
AppletFormatAdapter.PASTE, ioformat);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
- String identifyoutput = new IdentifyFile().Identify(outputfile,
+ String identifyoutput = new IdentifyFile().identify(outputfile,
AppletFormatAdapter.PASTE);
assertNotNull("Identify routine failed for outputformat " + ioformat,
identifyoutput);
AppletFormatAdapter.PASTE);
assertNotNull("Identify routine failed for outputformat " + ioformat,
identifyoutput);
@@
-137,7
+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(
@@
-269,7
+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
@@
-352,9
+351,11
@@
public class StockholmFileTest
an_new.displayCharacter.trim())
|| !("" + an_or.secondaryStructure).trim().equals(
("" + an_new.secondaryStructure).trim())
an_new.displayCharacter.trim())
|| !("" + an_or.secondaryStructure).trim().equals(
("" + an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && (an_or.description == null
- || an_new.description == null || !an_or.description
- .equals(an_new.description))))
+ || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+ .trim().length() == 0)
+ || (an_new.description == null && an_or.description
+ .trim().length() == 0) || an_or.description
+ .trim().equals(an_new.description.trim()))))
{
System.err.println("Annotation Element Mismatch\nElement " + i
+ " in original: " + annot_or.annotations[i].toString()
{
System.err.println("Annotation Element Mismatch\nElement " + i
+ " in original: " + annot_or.annotations[i].toString()