X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fmc_view%2FPDBfileTest.java;fp=test%2Fmc_view%2FPDBfileTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=0e34a24374471abee2700b5afcd3a7e46f5db861;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/mc_view/PDBfileTest.java b/test/mc_view/PDBfileTest.java
deleted file mode 100644
index 0e34a24..0000000
--- a/test/mc_view/PDBfileTest.java
+++ /dev/null
@@ -1,336 +0,0 @@
-/*
- * 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 mc_view;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.structure.StructureImportSettings;
-
-import java.io.IOException;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-public class PDBfileTest
-{
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  @Test(groups = { "Functional" })
-  public void testIsRna()
-  {
-    SequenceI seq = new Sequence("Seq1", "CGAU");
-    assertTrue(PDBfile.isRNA(seq));
-
-    seq.setSequence("CGAu");
-    assertFalse(PDBfile.isRNA(seq));
-
-    seq.setSequence("CGAT");
-    assertFalse(PDBfile.isRNA(seq));
-
-    seq.setSequence("GRSWYFLAVM");
-    assertFalse(PDBfile.isRNA(seq));
-  }
-
-  /**
-   * Test the 'high level' outputs of parsing. More detailed tests in
-   * PDBChainTest.
-   * 
-   * @throws IOException
-   */
-  @Test(groups = { "Functional" })
-  public void testParse() throws IOException
-  {
-    /*
-     * Constructor with file path performs parse()
-     */
-    PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
-            DataSourceType.FILE);
-
-    assertEquals("3W5V", pf.getId());
-    // verify no alignment annotations created
-    assertNull(getAlignmentAnnotations(pf));
-
-    assertEquals(4, pf.getChains().size());
-    assertEquals("A", pf.getChains().get(0).id);
-    assertEquals("B", pf.getChains().get(1).id);
-    assertEquals("C", pf.getChains().get(2).id);
-    assertEquals("D", pf.getChains().get(3).id);
-
-    PDBChain chainA = pf.getChains().get(0);
-    SequenceI seqA = pf.getSeqs().get(0);
-
-    assertEquals(0, chainA.seqstart); // not set
-    assertEquals(0, chainA.seqend); // not set
-    assertEquals(18, chainA.sequence.getStart());
-    assertEquals(314, chainA.sequence.getEnd());
-    assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
-    assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
-    assertEquals("3W5V|A", chainA.sequence.getName());
-    assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, seqA.getAllPDBEntries().size());
-    PDBEntry pdb = seqA.getAllPDBEntries().get(0);
-    assertEquals("A", pdb.getChainCode());
-    assertEquals("PDB", pdb.getType());
-    assertEquals("3W5V", pdb.getId());
-
-    PDBChain chainB = pf.getChains().get(1);
-    assertEquals(1, chainB.sequence.getStart());
-    assertEquals(96, chainB.sequence.getEnd());
-    assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK"));
-    assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT"));
-    assertEquals("3W5V|B", chainB.sequence.getName());
-
-    PDBChain chainC = pf.getChains().get(2);
-    assertEquals(18, chainC.sequence.getStart());
-    assertEquals(314, chainC.sequence.getEnd());
-    assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
-    assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
-    assertEquals("3W5V|C", chainC.sequence.getName());
-
-    PDBChain chainD = pf.getChains().get(3);
-    assertEquals(1, chainD.sequence.getStart());
-    assertEquals(96, chainD.sequence.getEnd());
-    assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
-    assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
-    assertEquals("3W5V|D", chainD.sequence.getName());
-
-    /*
-     * verify PDB-related data in parsed sequences
-     */
-    List<SequenceI> seqs = pf.getSeqs();
-    assertEquals(4, seqs.size());
-    assertEquals("3W5V|A", seqs.get(0).getName());
-    assertEquals("3W5V|B", seqs.get(1).getName());
-    assertEquals("3W5V|C", seqs.get(2).getName());
-    assertEquals("3W5V|D", seqs.get(3).getName());
-    assertEquals(1, seqs.get(0).getAllPDBEntries().size());
-    PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
-    assertEquals("A", pdbe.getChainCode());
-    assertEquals("3W5V", pdbe.getId());
-    assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
-  }
-
-  /**
-   * Test parsing, with annotations added to the alignment but no secondary
-   * structure prediction
-   * 
-   * @throws IOException
-   */
-  @Test(groups = { "Functional" })
-  public void testParse_withAnnotations_noSS() throws IOException
-  {
-    PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
-            DataSourceType.FILE);
-
-    AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
-    assertEquals(4, anns.length);
-
-    /*
-     * Inspect temp factor annotation for chain A
-     */
-    AlignmentAnnotation chainAnnotation = anns[0];
-    assertEquals("Temperature Factor", chainAnnotation.label);
-    // PDBChain constructor changes PDB id to lower case (why?)
-    assertEquals("Temperature Factor for 3w5vA",
-            chainAnnotation.description);
-    assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef);
-    assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph);
-    assertEquals(0f, chainAnnotation.graphMin, 0.001f);
-    assertEquals(40f, chainAnnotation.graphMax, 0.001f);
-    assertEquals(297, chainAnnotation.annotations.length);
-    assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f);
-
-    /*
-     * Chain B temp factor
-     */
-    chainAnnotation = anns[1];
-    assertEquals("Temperature Factor for 3w5vB",
-            chainAnnotation.description);
-    assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef);
-    assertEquals(96, chainAnnotation.annotations.length);
-
-    /*
-     * Chain C temp factor
-     */
-    chainAnnotation = anns[2];
-    assertEquals("Temperature Factor for 3w5vC",
-            chainAnnotation.description);
-    assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef);
-    assertEquals(297, chainAnnotation.annotations.length);
-
-    /*
-     * Chain D temp factor
-     */
-    chainAnnotation = anns[3];
-    assertEquals("Temperature Factor for 3w5vD",
-            chainAnnotation.description);
-    assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef);
-    assertEquals(96, chainAnnotation.annotations.length);
-  }
-
-  /**
-   * Test parsing including secondary structure annotation using JMol; this test
-   * for the case where flag to add annotations to alignment is set false
-   * 
-   * @throws IOException
-   */
-  @Test(groups = { "Functional" })
-  public void testParse_withJmol_noAnnotations() throws IOException
-  {
-    PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
-            DataSourceType.FILE);
-
-    /*
-     * alignment annotations _are_ created anyway (in
-     * AlignSeq.replaceMatchingSeqsWith())
-     */
-    final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
-    assertEquals(4, anns.length);
-
-    /*
-     * no sequence annotations created - tempFactor annotation is not added
-     * unless the flag to 'addAlignmentAnnotations' is set true
-     */
-    for (PDBChain c : pf.getChains())
-    {
-      assertNull(c.sequence.getAnnotation());
-    }
-  }
-
-  /**
-   * Test parsing including secondary structure prediction and annotation using
-   * JMol
-   * 
-   * @throws IOException
-   */
-  @Test(groups = { "Functional" })
-  public void testParse_withJmolAddAlignmentAnnotations()
-          throws IOException
-  {
-    PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
-            DataSourceType.FILE);
-
-    /*
-     * Alignment annotations for TempFactor, SecStruct, per sequence (chain)
-     */
-    AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
-    assertEquals(8, anns.length);
-
-    /*
-     * other tests have detailed assertions for Temp Factor annotations
-     */
-    assertEquals("Temperature Factor for 3w5vA", anns[1].description);
-    assertEquals("Temperature Factor for 3w5vB", anns[3].description);
-    assertEquals("Temperature Factor for 3w5vC", anns[5].description);
-    assertEquals("Temperature Factor for 3w5vD", anns[7].description);
-
-    /*
-     * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
-     */
-    assertEquals("Secondary Structure for 3w5vA", anns[0].description);
-    assertEquals("Secondary Structure for 3w5vB", anns[2].description);
-    assertEquals("Secondary Structure for 3w5vC", anns[4].description);
-    assertEquals("Secondary Structure for 3w5vD", anns[6].description);
-
-    /*
-     * Verify SS annotations are linked to respective sequences (chains)
-     */
-    assertSame(pf.getSeqs().get(0), anns[0].sequenceRef);
-    assertSame(pf.getSeqs().get(1), anns[2].sequenceRef);
-    assertSame(pf.getSeqs().get(2), anns[4].sequenceRef);
-    assertSame(pf.getSeqs().get(3), anns[6].sequenceRef);
-
-    /*
-     * Verify a sample of SS predictions
-     */
-    for (int i = 0; i < 20; i++)
-    {
-      assertNull(anns[0].annotations[i]);
-      assertEquals("E", anns[0].annotations[20].displayCharacter);
-      assertEquals('E', anns[0].annotations[20].secondaryStructure);
-      assertEquals("E", anns[2].annotations[18].displayCharacter);
-      assertEquals("H", anns[2].annotations[23].displayCharacter);
-    }
-  }
-
-  /**
-   * Placeholder for a test of parsing RNA structure with secondary structure
-   * prediction using the Annotate3D service
-   * 
-   * @throws IOException
-   */
-
-  @Test(groups = { "Functional" }, enabled = false)
-  public void testParse_withAnnotate3D() throws IOException
-  {
-    // TODO requires a mock for Annotate3D processing
-    // and/or run as an integration test
-    PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
-            DataSourceType.FILE);
-  }
-
-  /**
-   * Helper method to extract parsed annotations from the PDBfile
-   * 
-   * @param pf
-   * @return
-   */
-  private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)
-  {
-    AlignmentI al = new Alignment(pf.getSeqsAsArray());
-    pf.addAnnotations(al);
-    return al.getAlignmentAnnotation();
-  }
-
-  @BeforeMethod(alwaysRun = true)
-  public void setUp()
-  {
-    Cache.loadProperties("test/jalview/io/testProps.jvprops");
-    Cache.setPropertyNoSave("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    Cache.setPropertyNoSave("ADD_TEMPFACT_ANN",
-            Boolean.TRUE.toString());
-    Cache.setPropertyNoSave("ADD_SS_ANN",
-            Boolean.TRUE.toString());
-    StructureImportSettings.setDefaultStructureFileFormat("PDB");
-  }
-}