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JAL-3438 spotless for 2.11.2.0
[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
679385a
..
6d54f15
100644
(file)
--- a/
test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/
test/jalview/ext/paradise/TestAnnotate3D.java
@@
-20,11
+20,16
@@
*/
package jalview.ext.paradise;
*/
package jalview.ext.paradise;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
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.FastaFile;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import java.io.BufferedReader;
import jalview.io.FormatAdapter;
import java.io.BufferedReader;
@@
-34,16
+39,23
@@
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 org.testng.annotations.Test;
-import MCview.PDBfile;
-
import compbio.util.FileUtil;
import compbio.util.FileUtil;
+import mc_view.PDBfile;
public class TestAnnotate3D
{
public class TestAnnotate3D
{
- @Test(groups = { "Functional" }, 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
@@
-53,19
+65,19
@@
public class TestAnnotate3D
testRNAMLcontent(ids, null);
}
testRNAMLcontent(ids, null);
}
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
assertTrue("Didn't retrieve 2GIS by id.", ids != null);
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
assertTrue("Didn't retrieve 2GIS by id.", ids != null);
- Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
- .readFileToString(new File("examples/2GIS.pdb")));
+ Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(
+ FileUtil.readFileToString(new File("examples/2GIS.pdb")));
assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
int i = 0;
while (ids.hasNext() && files.hasNext())
{
assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
int i = 0;
while (ids.hasNext() && files.hasNext())
{
- BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
- ids.next());
+ BufferedReader file = new BufferedReader(files.next()),
+ id = new BufferedReader(ids.next());
String iline, fline;
do
{
String iline, fline;
do
{
@@
-97,21
+109,19
@@
public class TestAnnotate3D
*
* @throws Exception
*/
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, 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
- Iterator<Reader> readers = Annotate3D
- .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
- "examples/2GIS.pdb")));
+ Iterator<Reader> readers = Annotate3D.getRNAMLForPDBFileAsString(
+ FileUtil.readFileToString(new File("examples/2GIS.pdb")));
testRNAMLcontent(readers, pdbf);
}
testRNAMLcontent(readers, pdbf);
}
- @Test(groups = { "Functional" }, 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);
@@
-142,11
+152,11
@@
public class TestAnnotate3D
{
{
SequenceI struseq = null;
{
{
SequenceI struseq = null;
- String sq_ = new String(sq.getSequence()).toLowerCase();
+ String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- final String lowerCase = new String(_struseq.getSequence())
- .toLowerCase();
+ final String lowerCase = _struseq.getSequenceAsString()
+ .toLowerCase(Locale.ROOT);
if (lowerCase.equals(sq_))
{
struseq = _struseq;
if (lowerCase.equals(sq_))
{
struseq = _struseq;
@@
-155,12
+165,12
@@
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())
+ 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");
}
}
+ "\n");
}
}