Merge branch 'releases/Release_2_10_4_Branch'

[jalview.git] / test / jalview / io / AnnotatedPDBFileInputTest.java

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index c0251b6..c0038a1 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.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.
  * 
@@ -30,9 +30,14 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
+import java.util.List;
 
 import org.junit.Assert;
 import org.testng.annotations.AfterClass;
@@ -43,6 +48,13 @@ import org.testng.annotations.Test;
 public class AnnotatedPDBFileInputTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   AlignmentI al;
 
   String pdbId;
@@ -62,10 +74,13 @@ public class AnnotatedPDBFileInputTest
             Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -81,23 +96,28 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        Assert.assertNotEquals("Found a duplicate annotation row "
-                + avec[p].label, avec[p], avec[q]);
+        assertTrue("Found a duplicate annotation row " + avec[p].label,
+                avec[p] != avec[q]);
       }
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
   public void checkPDBannotationSource()
   {
-
+    Assert.fail(
+            "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
     for (SequenceI asq : al.getSequences())
     {
       for (AlignmentAnnotation aa : asq.getAnnotation())
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        if (StructureImportSettings.getDefaultPDBFileParser()
+                .equals(StructureParser.JALVIEW_PARSER))
+        {
+          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        }
       }
     }
   }
@@ -111,32 +131,35 @@ public class AnnotatedPDBFileInputTest
     /*
      * 1GAQ/A
      */
-    SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
-    assertEquals(296, sf.length);
-    assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:  19  1gaqA", sf[0].getDescription());
-    assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR: 314  1gaqA", sf[295].getDescription());
+    List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
+    SequenceFeatures.sortFeatures(sf, true);
+    assertEquals(296, sf.size());
+    assertEquals("RESNUM", sf.get(0).getType());
+    assertEquals("GLU:  19  1gaqA", sf.get(0).getDescription());
+    assertEquals("RESNUM", sf.get(295).getType());
+    assertEquals("TYR: 314  1gaqA", sf.get(295).getDescription());
 
     /*
      * 1GAQ/B
      */
     sf = al.getSequenceAt(1).getSequenceFeatures();
-    assertEquals(98, sf.length);
-    assertEquals("RESNUM", sf[0].getType());
-    assertEquals("ALA:   1  1gaqB", sf[0].getDescription());
-    assertEquals("RESNUM", sf[97].getType());
-    assertEquals("ALA:  98  1gaqB", sf[97].getDescription());
+    SequenceFeatures.sortFeatures(sf, true);
+    assertEquals(98, sf.size());
+    assertEquals("RESNUM", sf.get(0).getType());
+    assertEquals("ALA:   1  1gaqB", sf.get(0).getDescription());
+    assertEquals("RESNUM", sf.get(97).getType());
+    assertEquals("ALA:  98  1gaqB", sf.get(97).getDescription());
 
     /*
      * 1GAQ/C
      */
     sf = al.getSequenceAt(2).getSequenceFeatures();
-    assertEquals(296, sf.length);
-    assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:  19  1gaqC", sf[0].getDescription());
-    assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
+    SequenceFeatures.sortFeatures(sf, true);
+    assertEquals(296, sf.size());
+    assertEquals("RESNUM", sf.get(0).getType());
+    assertEquals("GLU:  19  1gaqC", sf.get(0).getDescription());
+    assertEquals("RESNUM", sf.get(295).getType());
+    assertEquals("TYR: 314  1gaqC", sf.get(295).getDescription());
   }
 
   @Test(groups = { "Functional" })
@@ -181,7 +204,7 @@ public class AnnotatedPDBFileInputTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
@@ -196,14 +219,14 @@ public class AnnotatedPDBFileInputTest
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
+            inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
     af = null;
     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     assertTrue("Failed to import new project", af != null);
     for (SequenceI asq : af.getViewport().getAlignment().getSequences())
     {
@@ -213,8 +236,8 @@ public class AnnotatedPDBFileInputTest
         sq = sq.getDatasetSequence();
       }
       assertNotNull(sq.getAllPDBEntries());
-      assertEquals("Expected only one PDB ID",
-              sq.getAllPDBEntries().size(), 1);
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
       for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "