+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.ext.paradise;
import static org.junit.Assert.assertTrue;
-
-import jalview.ext.paradise.Annotate3D;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
import java.io.BufferedReader;
import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
+import org.junit.Assert;
import org.junit.Test;
+import MCview.PDBfile;
+
import compbio.util.FileUtil;
public class TestAnnotate3D
{
@Test
- public void testIdVsContent() throws Exception
+ public void test1GIDbyId() throws Exception
{
- BufferedReader id = (BufferedReader) Annotate3D.getRNAMLForPDBId("2GIS");
- assertTrue("Didn't retrieve 2GIS by id.", id != null);
- BufferedReader file = (BufferedReader) Annotate3D.getRNAMLForPDBFileAsString(FileUtil
+ // use same ID as standard tests given at
+ // https://bitbucket.org/fjossinet/pyrna-rest-clients
+ Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
+ assertTrue("Didn't retrieve 1GID by id.", ids != null);
+ testRNAMLcontent(ids, null);
+ }
+
+ @Test
+ public void testIdVsContent2GIS() throws Exception
+ {
+ Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
+ assertTrue("Didn't retrieve 2GIS by id.", ids != null);
+ Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
.readFileToString(new File("examples/2GIS.pdb")));
- assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
- String iline, fline;
- do
+ assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
+ int i = 0;
+ while (ids.hasNext() && files.hasNext())
{
- iline = id.readLine();
- fline = file.readLine();
- if (iline != null)
- System.out.println(iline);
- if (fline != null)
- System.out.println(fline);
-
- assertTrue("Results differ for ID and file upload based retrieval",
- ((iline == fline && iline == null) || (iline != null
- && fline != null && iline.equals(fline))));
-
- } while (iline != null);
+ BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
+ ids.next());
+ String iline, fline;
+ do
+ {
+ iline = id.readLine();
+ fline = file.readLine();
+ if (iline != null)
+ {
+ System.out.println(iline);
+ }
+ if (fline != null)
+ {
+ System.out.println(fline);
+ }
+ // next assert fails for latest RNAview - because the XMLID entries
+ // change between file and ID based RNAML generation.
+ assertTrue(
+ "Results differ for ID and file upload based retrieval (chain entry "
+ + (++i) + ")",
+ ((iline == fline && iline == null) || (iline != null
+ && fline != null && iline.equals(fline))));
+
+ } while (iline != null);
+ }
}
+ /**
+ * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
+ * Annotate3d vs those extracted by Jalview from the originl PDB file
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testPDBfileVsRNAML() throws Exception
+ {
+ PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+ Assert.assertTrue(pdbf.isValid());
+ // Comment - should add new FileParse constructor like new FileParse(Reader
+ // ..). for direct reading
+ Iterator<Reader> readers = Annotate3D
+ .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+ "examples/2GIS.pdb")));
+ testRNAMLcontent(readers, pdbf);
+ }
+
+ private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
+ throws Exception
+ {
+ StringBuffer sb = new StringBuffer();
+ int r = 0;
+ while (readers.hasNext())
+ {
+ System.out.println("Testing RNAML input number " + (++r));
+ BufferedReader br = new BufferedReader(readers.next());
+ String line;
+ while ((line = br.readLine()) != null)
+ {
+ sb.append(line + "\n");
+ }
+ assertTrue("No data returned by Annotate3D", sb.length() > 0);
+ AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ FormatAdapter.PASTE, "RNAML");
+ if (al == null || al.getHeight() == 0)
+ {
+ System.out.println(sb.toString());
+ }
+ assertTrue("No alignment returned.", al != null);
+ assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+ if (pdbf != null)
+ {
+ for (SequenceI sq : al.getSequences())
+ {
+ {
+ SequenceI struseq = null;
+ String sq_ = new String(sq.getSequence()).toLowerCase();
+ for (SequenceI _struseq : pdbf.getSeqsAsArray())
+ {
+ if (new String(_struseq.getSequence()).toLowerCase().equals(
+ sq_))
+ {
+ struseq = _struseq;
+ break;
+ }
+ }
+ if (struseq == null)
+ {
+ Assert.fail("Couldn't find this sequence in original input:\n"
+ + new FastaFile().print(new SequenceI[]
+ { sq })
+ + "\n\nOriginal input:\n"
+ + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+ }
+ }
+ }
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff