X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=beeb52f50587978f1beeed9a5f27d10f825f6c25;hb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;hp=4b10ab80720839dcd17dcb8793072fbc2c4ec39e;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 4b10ab8..beeb52f 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -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;
@@ -56,16 +68,19 @@ public class AnnotatedPDBFileInputTest
   @BeforeMethod(alwaysRun = true)
   public void setup() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+    Cache.setPropertyNoSave("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+    Cache.setPropertyNoSave("ADD_SS_ANN",
             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(mc_view.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" })
@@ -181,10 +204,10 @@ public class AnnotatedPDBFileInputTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
 
   }
 
@@ -196,14 +219,15 @@ 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);
+    af.saveAlignment(tfile, FileFormat.Jalview);
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.isSaveAlignmentSuccessful());
     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 +237,8 @@ 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() + " "
@@ -224,10 +248,10 @@ public class AnnotatedPDBFileInputTest
         {
           System.err.println("CalcId " + ana.getCalcId());
           if (ana.getCalcId() != null
-                  && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
+                  && mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
           {
             exists = true;
-            if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
+            if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
             {
               found = true;
             }