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JAL-2795 added error catching for invalid identifier
[jalview.git]
/
test
/
jalview
/
structure
/
StructureSelectionManagerTest.java
diff --git
a/test/jalview/structure/StructureSelectionManagerTest.java
b/test/jalview/structure/StructureSelectionManagerTest.java
index
ddee3ac
..
a59fbde
100644
(file)
--- a/
test/jalview/structure/StructureSelectionManagerTest.java
+++ b/
test/jalview/structure/StructureSelectionManagerTest.java
@@
-27,23
+27,34
@@
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.util.MapList;
import java.util.ArrayList;
import java.util.List;
import java.util.ArrayList;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import MCview.PDBfile;
-
public class StructureSelectionManagerTest
{
public class StructureSelectionManagerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private StructureSelectionManager ssm;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
private StructureSelectionManager ssm;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
+ StructureImportSettings.setShowSeqFeatures(true);
ssm = new StructureSelectionManager();
}
ssm = new StructureSelectionManager();
}
@@
-51,7
+62,11
@@
public class StructureSelectionManagerTest
public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
ssm.registerMapping(acf1);
assertEquals(1, ssm.getSequenceMappings().size());
ssm.registerMapping(acf1);
assertEquals(1, ssm.getSequenceMappings().size());
@@
-75,8
+90,14
@@
public class StructureSelectionManagerTest
public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
+ new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
set1.add(acf1);
List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
set1.add(acf1);
@@
-112,8
+133,8
@@
public class StructureSelectionManagerTest
StructureSelectionManager sm = new StructureSelectionManager();
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureSelectionManager sm = new StructureSelectionManager();
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
- PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
- new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+ StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
@@
-124,7
+145,7
@@
public class StructureSelectionManagerTest
/*
* Verify a RESNUM sequence feature in the PDBfile sequence
*/
/*
* Verify a RESNUM sequence feature in the PDBfile sequence
*/
- SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+ SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("GLU: 19 1gaqA", sf.getDescription());
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("GLU: 19 1gaqA", sf.getDescription());
@@
-134,7
+155,7
@@
public class StructureSelectionManagerTest
* sequence
*/
StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
* sequence
*/
StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
- sf = map.sequence.getSequenceFeatures()[0];
+ sf = map.sequence.getSequenceFeatures().get(0);
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("ALA: 1 1gaqB", sf.getDescription());
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("ALA: 1 1gaqB", sf.getDescription());