X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructure%2FMapping.java;h=85aea4000c0354d1c8ef2f0b4b32ff323be4026d;hb=40bd118644ec4fe8a11b8bee04e1e25ab8699bf8;hp=aae1f3dd29385842d1bfb21d7c6caf77ca795846;hpb=52288466dd1e71946a06fd1e6ea15fa8e652c693;p=jalview.git

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index aae1f3d..85aea40 100644
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.structure;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -8,18 +28,27 @@ 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;
 
-import MCview.PDBfile;
-
 public class Mapping
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /*
    * more test data
    * 
@@ -47,9 +76,9 @@ public class Mapping
       { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
 
       StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-      PDBfile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+      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
@@ -118,8 +147,9 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
-    PDBfile pde = ssm.setMapping(true, new SequenceI[] { sq }, new String[]
-    { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+    StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
+            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);
@@ -211,12 +241,12 @@ public class Mapping
     AlignFrame seqf = new FileLoader(false)
             .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();
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+    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");
@@ -230,9 +260,10 @@ public class Mapping
   @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
+    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());
@@ -242,9 +273,9 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     ssm.setProcessSecondaryStructure(true);
     ssm.setAddTempFacAnnot(true);
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+    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());