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Merge branch 'features/JAL-2393customMatrices' into develop
[jalview.git]
/
test
/
jalview
/
io
/
StockholmFileTest.java
diff --git
a/test/jalview/io/StockholmFileTest.java
b/test/jalview/io/StockholmFileTest.java
index
bdd311b
..
4028913
100644
(file)
--- a/
test/jalview/io/StockholmFileTest.java
+++ b/
test/jalview/io/StockholmFileTest.java
@@
-30,17
+30,26
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Map;
import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class StockholmFileTest
{
import org.testng.annotations.Test;
public class StockholmFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
@@
-103,7
+112,7
@@
public class StockholmFileTest
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+ al.getSequenceAt(i).createDatasetSequence();
}
String outputfile = rf.formatSequences(ioformat, al, true);
System.out.println("Output file in '" + ioformat + "':\n"
}
String outputfile = rf.formatSequences(ioformat, al, true);
System.out.println("Output file in '" + ioformat + "':\n"
@@
-228,7
+237,7
@@
public class StockholmFileTest
}
assertEquals(
"Generated and imported alignment have different annotation sets",
}
assertEquals(
"Generated and imported alignment have different annotation sets",
- aa_new_size, aa_original_size);
+ aa_original_size, aa_new_size);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
@@
-281,8
+290,7
@@
public class StockholmFileTest
assertEquals("different number of features",
seq_original[i].getSequenceFeatures().length,
assertEquals("different number of features",
seq_original[i].getSequenceFeatures().length,
- seq_new[in]
- .getSequenceFeatures().length);
+ seq_new[in].getSequenceFeatures().length);
for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
{
for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
{