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Merge branch 'develop' into releases/Release_2_11_2_Branch
[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
4110863
..
80fffff
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;
@@
-34,15
+39,22
@@
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
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Network" }, enabled = true)
public void test1GIDbyId() throws Exception
{
@Test(groups = { "Network" }, enabled = true)
public void test1GIDbyId() throws Exception
{
@@
-101,7
+113,7
@@
public class TestAnnotate3D
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
@@
-128,7
+140,7
@@
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);
@@
-141,11
+153,11
@@
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;
@@
-156,11
+168,11
@@
public class TestAnnotate3D
{
AssertJUnit
.fail("Couldn't find this sequence in original input:\n"
{
AssertJUnit
.fail("Couldn't find this sequence in original input:\n"
- + new FastaFile()
- .print(new SequenceI[] { sq })
+ + new FastaFile().print(
+ new SequenceI[] { sq }, true)
+ "\n\nOriginal input:\n"
+ "\n\nOriginal input:\n"
- + new FastaFile().print(pdbf.getSeqsAsArray())
- + "\n");
+ + new FastaFile().print(
+ pdbf.getSeqsAsArray(), true) + "\n");
}
}
}
}
}
}