+/*
+ * 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.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
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.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class AnnotatedPDBFileInputTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
AlignmentI al;
- @Before
+ String pdbId;
+
+ /**
+ * 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",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("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" })
+ public void checkNoDuplicates()
+ {
+ // not strictly a requirement, but strange things may happen if multiple
+ // instances of the same annotation are placed in the alignment annotation
+ // vector
+ assertNotNull(al.getAlignmentAnnotation());
+ // verify that all sequence annotation is doubly referenced
+ AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
+ for (int p = 0; p < avec.length; p++)
+ {
+ for (int q = p + 1; q < avec.length; q++)
+ {
+ assertTrue("Found a duplicate annotation row " + avec[p].label,
+ avec[p] != avec[q]);
+ }
+ }
}
- @Test
+ @Test(groups = { "Functional" })
+ public void checkPDBannotationSource()
+ {
+
+ for (SequenceI asq : al.getSequences())
+ {
+ for (AlignmentAnnotation aa : asq.getAnnotation())
+ {
+
+ System.out.println("CalcId: " + aa.getCalcId());
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
+ }
+ }
+ }
+
+ /**
+ * Check sequence features have been added
+ */
+ @Test(groups = { "Functional" })
+ public void checkPDBSequenceFeatures()
+ {
+ /*
+ * 1GAQ/A
+ */
+ 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();
+ 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();
+ 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" })
public void checkAnnotationWiring()
{
assertTrue(al.getAlignmentAnnotation() != null);
}
}
}
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ jalview.bin.Jalview.main(new String[] { "-props",
+ "test/jalview/io/testProps.jvprops" });
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testJalviewProjectRelocationAnnotation() throws Exception
+ {
+
+ String inFile = "examples/1gaq.txt";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, DataSourceType.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, FileFormat.Jalview));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ DataSourceType.FILE);
+ assertTrue("Failed to import new project", af != null);
+ for (SequenceI asq : af.getViewport().getAlignment().getSequences())
+ {
+ SequenceI sq = asq;
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ 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());
+ boolean exists = false, found = false;
+ for (AlignmentAnnotation ana : sq.getAnnotation())
+ {
+ System.err.println("CalcId " + ana.getCalcId());
+ if (ana.getCalcId() != null
+ && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
+ {
+ exists = true;
+ if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
+ {
+ found = true;
+ }
+ }
+ }
+ if (exists)
+ {
+ assertTrue("Couldn't find any annotation for " + pdbentry.getId()
+ + " (file handle " + pdbentry.getFile() + ")", found);
+ }
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff