JAL-629 Some refactoring to allow more flexible use of PAE files. Not working as...

[jalview.git] / test / jalview / structure / Mapping.java

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index f1feced..ff17209 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -23,6 +23,11 @@ package jalview.structure;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
@@ -34,11 +39,6 @@ import jalview.io.FileFormat;
 import jalview.io.FileLoader;
 import jalview.io.StructureFile;
 
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class Mapping
 {
 
@@ -80,7 +80,7 @@ public class Mapping
       StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
               new String[]
               { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
-              DataSourceType.FILE);
+              DataSourceType.FILE, null, null);
       assertTrue(pmap != null);
       SequenceI protseq = pmap.getSeqsAsArray()[0];
       AlignmentAnnotation pstra = protseq
@@ -149,7 +149,8 @@ public class Mapping
     // source
     StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
             new String[]
-            { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
+            { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE,
+            null, null);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
     assertTrue("No mappings made.", mp != null && mp.length > 0);
@@ -248,7 +249,7 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[]
-            { null }, "examples/3W5V.pdb", DataSourceType.FILE);
+            { null }, "examples/3W5V.pdb", DataSourceType.FILE, null, null);
     if (pmap == null)
     {
       AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
@@ -278,8 +279,8 @@ public class Mapping
     ssm.setAddTempFacAnnot(true);
     StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[]
-            { null }, "test/jalview/ext/jmol/1QCF.pdb",
-            DataSourceType.FILE);
+            { null }, "test/jalview/ext/jmol/1QCF.pdb", DataSourceType.FILE,
+            null, null);
     assertTrue(pmap != null);
     assertEquals("Original and copied sequence of different lengths.",
             refseq.getLength(), newseq.getLength());