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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
test
/
jalview
/
ext
/
paradise
/
TestAnnotate3D.java
diff --git
a/test/jalview/ext/paradise/TestAnnotate3D.java
b/test/jalview/ext/paradise/TestAnnotate3D.java
index
d4f57d8
..
c6c1a29
100644
(file)
--- a/
test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/
test/jalview/ext/paradise/TestAnnotate3D.java
@@
-22,6
+22,14
@@
package jalview.ext.paradise;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FastaFile;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.Reader;
import java.io.BufferedReader;
import java.io.File;
import java.io.Reader;
@@
-29,21
+37,24
@@
import java.util.Iterator;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.Assert;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import MCview.PDBfile;
import compbio.util.FileUtil;
import org.testng.annotations.Test;
import MCview.PDBfile;
import compbio.util.FileUtil;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
-
public class TestAnnotate3D
{
public class TestAnnotate3D
{
- @Test(enabled = false)
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Network" }, enabled = true)
public void test1GIDbyId() throws Exception
{
// use same ID as standard tests given at
public void test1GIDbyId() throws Exception
{
// use same ID as standard tests given at
@@
-53,7
+64,7
@@
public class TestAnnotate3D
testRNAMLcontent(ids, null);
}
testRNAMLcontent(ids, null);
}
- @Test(enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
@@
-97,11
+108,11
@@
public class TestAnnotate3D
*
* @throws Exception
*/
*
* @throws Exception
*/
- @Test(enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
- FormatAdapter.FILE);
+ DataSourceType.FILE);
Assert.assertTrue(pdbf.isValid());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
Assert.assertTrue(pdbf.isValid());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
@@
-111,7
+122,6
@@
public class TestAnnotate3D
testRNAMLcontent(readers, pdbf);
}
testRNAMLcontent(readers, pdbf);
}
- @Test(enabled = false)
private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
throws Exception
{
private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
throws Exception
{
@@
-129,7
+139,7
@@
public class TestAnnotate3D
assertTrue("No data returned by Annotate3D", sb.length() > 0);
final String lines = sb.toString();
AlignmentI al = new FormatAdapter().readFile(lines,
assertTrue("No data returned by Annotate3D", sb.length() > 0);
final String lines = sb.toString();
AlignmentI al = new FormatAdapter().readFile(lines,
- FormatAdapter.PASTE, "RNAML");
+ DataSourceType.PASTE, FileFormat.Rnaml);
if (al == null || al.getHeight() == 0)
{
System.out.println(lines);
if (al == null || al.getHeight() == 0)
{
System.out.println(lines);
@@
-142,12
+152,12
@@
public class TestAnnotate3D
{
{
SequenceI struseq = null;
{
{
SequenceI struseq = null;
- String sq_ = new String(sq.getSequence()).toLowerCase();
+ String sq_ = sq.getSequenceAsString().toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
- if (lowerCase.equals(
- sq_))
+ final String lowerCase = _struseq.getSequenceAsString()
+ .toLowerCase();
+ if (lowerCase.equals(sq_))
{
struseq = _struseq;
break;
{
struseq = _struseq;
break;
@@
-155,11
+165,13
@@
public class TestAnnotate3D
}
if (struseq == null)
{
}
if (struseq == null)
{
- AssertJUnit.fail("Couldn't find this sequence in original input:\n"
- + new FastaFile().print(new SequenceI[]
- { sq })
- + "\n\nOriginal input:\n"
- + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+ AssertJUnit
+ .fail("Couldn't find this sequence in original input:\n"
+ + new FastaFile().print(
+ new SequenceI[] { sq }, true)
+ + "\n\nOriginal input:\n"
+ + new FastaFile().print(
+ pdbf.getSeqsAsArray(), true) + "\n");
}
}
}
}
}
}