X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=6ea38839957e29eb77d0a5d068b59e4ea84bd48a;hb=b93f8af382bb2fbdb0c974558bcef57750d1bdd6;hp=c40df35d3ae27d6fab00ed3644d220efa202f985;hpb=44f876a4d3b0adfd680ddfa84e14cc7940d6f877;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index c40df35..6ea3883 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.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.io;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -10,14 +30,16 @@ 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.Desktop;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
+import jalview.gui.JvOptionPane;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
+import java.util.List;
 
-import org.testng.Assert;
+import org.junit.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -26,28 +48,42 @@ import org.testng.annotations.Test;
 public class AnnotatedPDBFileInputTest
 {
 
-  AlignmentI al;
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
 
-  String pdbStr = "examples/1gaq.txt";
+  AlignmentI al;
 
   String pdbId;
 
-  @BeforeMethod
+  /**
+   * Ensure 'process secondary structure from PDB and add annotations' are set
+   * in preferences, and load PDB example file 1gaq
+   * 
+   * @throws Exception
+   */
+  @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(pdbStr,
-            FormatAdapter.FILE);
+    AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
+            DataSourceType.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void checkNoDuplicates()
   {
     // not strictly a requirement, but strange things may happen if multiple
@@ -60,24 +96,28 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        Assert.assertNotEquals(
-avec[p], avec[q],
-                "Found a duplicate annotation row " + avec[p].label);
+        assertTrue("Found a duplicate annotation row " + avec[p].label,
+                avec[p] != avec[q]);
       }
     }
   }
 
-  @Test
+  @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));
+        }
       }
     }
   }
@@ -85,46 +125,44 @@ avec[p], avec[q],
   /**
    * Check sequence features have been added
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void checkPDBSequenceFeatures()
   {
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    StructureMapping[] mappings = ssm.getMapping("1gaq");
-    // suspect we really want to make assertions on sequence features
-    // in these mappings' sequencess
     /*
      * 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
+  @Test(groups = { "Functional" })
   public void checkAnnotationWiring()
   {
     assertTrue(al.getAlignmentAnnotation() != null);
@@ -156,24 +194,24 @@ avec[p], avec[q],
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
-    { "-props", "test/src/jalview/io/testProps.jvprops" });
+    jalview.bin.Jalview.main(new String[] { "-props",
+        "test/jalview/io/testProps.jvprops" });
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testJalviewProjectRelocationAnnotation() throws Exception
   {
 
@@ -181,14 +219,15 @@ avec[p], avec[q],
     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())
     {
@@ -197,9 +236,10 @@ avec[p], avec[q],
       {
         sq = sq.getDatasetSequence();
       }
-      assertNotNull(sq.getPDBId());
-      assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-      for (PDBEntry pdbentry : sq.getPDBId())
+      assertNotNull(sq.getAllPDBEntries());
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
+      for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());
@@ -208,11 +248,10 @@ avec[p], avec[q],
         {
           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;
             }