Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 4bee3f5..40715c8 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -75,7 +75,8 @@ public class Mapping
       int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
       { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
 
-      StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+      StructureSelectionManager ssm = StructureSelectionManager
+              .getStructureSelectionManager(null);
       StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
               new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
               DataSourceType.FILE);
@@ -144,7 +145,8 @@ public class Mapping
             "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
     Sequence sq1 = new Sequence(sq);
     String inFile;
-    StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
     StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
@@ -243,7 +245,8 @@ public class Mapping
                     ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
                     DataSourceType.PASTE, FileFormat.Fasta);
     SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
-    StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
     StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "examples/3W5V.pdb",
             DataSourceType.FILE);
@@ -272,7 +275,8 @@ public class Mapping
     // make it harder by shifting the copy vs the reference
     newseq.setStart(refseq.getStart() + 25);
     newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
-    StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
     ssm.setProcessSecondaryStructure(true);
     ssm.setAddTempFacAnnot(true);
     StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },