X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructure%2FMapping.java;h=f8461f8a3fc1b299affda9a7edd8fe84620622b5;hb=a8e0667a62546cdd95d44a45cf14a629cfa416a6;hp=181c27318978b3bde38acfceef7cafa8d0efda84;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 181c273..f8461f8 100644
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,21 +23,37 @@ package jalview.structure;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 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
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.initLogger();
+  }
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
 
   /*
    * more test data
@@ -65,10 +81,11 @@ 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",
-              jalview.io.FormatAdapter.FILE);
+              DataSourceType.FILE);
       assertTrue(pmap != null);
       SequenceI protseq = pmap.getSeqsAsArray()[0];
       AlignmentAnnotation pstra = protseq
@@ -134,12 +151,13 @@ 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 },
-            new String[] { "A" }, inFile = "examples/1gaq.txt",
-            jalview.io.FormatAdapter.FILE);
+            new String[]
+    { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
     assertTrue("No mappings made.", mp != null && mp.length > 0);
@@ -229,14 +247,15 @@ public class Mapping
   public void mapFer1From3W5V() throws Exception
   {
     AlignFrame seqf = new FileLoader(false)
-            .LoadFileWaitTillLoaded(
+            .loadFileWaitTillLoaded(
                     ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
-                    FormatAdapter.PASTE, "FASTA");
+                    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",
-            jalview.io.FormatAdapter.FILE);
+            DataSourceType.FILE);
     if (pmap == null)
     {
       AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
@@ -250,22 +269,25 @@ public class Mapping
   @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
     StructureImportSettings.setShowSeqFeatures(true);
     AlignFrame ref = new FileLoader(false)
             .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
-                    jalview.io.FormatAdapter.FILE);
+                    DataSourceType.FILE);
     SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
     SequenceI newseq = new Sequence(refseq.getName() + "Copy",
             refseq.getSequenceAsString());
     // 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 },
             new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
-            jalview.io.FormatAdapter.FILE);
+            DataSourceType.FILE);
     assertTrue(pmap != null);
     assertEquals("Original and copied sequence of different lengths.",
             refseq.getLength(), newseq.getLength());