+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-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.gui.AlignFrame;
import java.io.File;
-import java.util.Vector;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class AnnotatedPDBFileInputTest
{
AlignmentI al;
- String pdbStr = "examples/2GIS.pdb";
-
String pdbId;
- @Before
+ /**
+ * 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(pdbStr,
+ AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
FormatAdapter.FILE);
al = af.getViewport().getAlignment();
- pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
- .get(0)).getId();
+ pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
+ .get(0).getId();
}
- @Test
+ @Test(groups = { "Functional" })
public void checkNoDuplicates()
{
// not strictly a requirement, but strange things may happen if multiple
{
for (int q = p + 1; q < avec.length; q++)
{
- assertNotEquals(
- "Found a duplicate annotation row " + avec[p].label,
- avec[p], avec[q]);
+ Assert.assertNotEquals("Found a duplicate annotation row "
+ + avec[p].label, avec[p], avec[q]);
}
}
}
- @Test
+ @Test(groups = { "Functional" })
public void checkPDBannotationSource()
{
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
- @Test
+ /**
+ * Check sequence features have been added
+ */
+ @Test(groups = { "Functional" })
+ public void checkPDBSequenceFeatures()
+ {
+ /*
+ * 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());
+
+ /*
+ * 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());
+
+ /*
+ * 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());
+ }
+
+ @Test(groups = { "Functional" })
public void checkAnnotationWiring()
{
assertTrue(al.getAlignmentAnnotation() != null);
/**
* @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" });
}
/**
}
- @Test
+ @Test(groups = { "Functional" })
public void testJalviewProjectRelocationAnnotation() throws Exception
{
- String inFile = "examples/2GIS.pdb";
+ String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
{
sq = sq.getDatasetSequence();
}
- assertNotNull(sq.getPDBId());
- assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
- for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+ assertNotNull(sq.getAllPDBEntries());
+ assertEquals("Expected only one PDB ID",
+ sq.getAllPDBEntries().size(), 1);
+ for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
System.err.println("PDB Entry " + pdbentry.getId() + " "
+ pdbentry.getFile());
&& MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
{
exists = true;
- if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
- pdbentry.getId()))
+ if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
{
found = true;
}
git://source.jalview.org / jalview.git / blobdiff