2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.paradise;
23 import static org.testng.AssertJUnit.assertTrue;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.FastaFile;
28 import jalview.io.FormatAdapter;
30 import java.io.BufferedReader;
32 import java.io.Reader;
33 import java.util.Iterator;
35 import org.testng.Assert;
36 import org.testng.AssertJUnit;
37 import org.testng.annotations.Test;
39 import MCview.PDBfile;
41 import compbio.util.FileUtil;
43 public class TestAnnotate3D
47 { "Functional" }, enabled = false)
48 public void test1GIDbyId() throws Exception
50 // use same ID as standard tests given at
51 // https://bitbucket.org/fjossinet/pyrna-rest-clients
52 Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
53 assertTrue("Didn't retrieve 1GID by id.", ids != null);
54 testRNAMLcontent(ids, null);
58 { "Functional" }, enabled = false)
59 public void testIdVsContent2GIS() throws Exception
61 Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
62 assertTrue("Didn't retrieve 2GIS by id.", ids != null);
63 Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
64 .readFileToString(new File("examples/2GIS.pdb")));
65 assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
67 while (ids.hasNext() && files.hasNext())
69 BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
74 iline = id.readLine();
75 fline = file.readLine();
78 System.out.println(iline);
82 System.out.println(fline);
84 // next assert fails for latest RNAview - because the XMLID entries
85 // change between file and ID based RNAML generation.
87 "Results differ for ID and file upload based retrieval (chain entry "
89 ((iline == fline && iline == null) || (iline != null
90 && fline != null && iline.equals(fline))));
92 } while (iline != null);
97 * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
98 * Annotate3d vs those extracted by Jalview from the originl PDB file
103 { "Functional" }, enabled = false)
104 public void testPDBfileVsRNAML() throws Exception
106 PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
108 Assert.assertTrue(pdbf.isValid());
109 // Comment - should add new FileParse constructor like new FileParse(Reader
110 // ..). for direct reading
111 Iterator<Reader> readers = Annotate3D
112 .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
113 "examples/2GIS.pdb")));
114 testRNAMLcontent(readers, pdbf);
118 { "Functional" }, enabled = false)
119 private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
122 StringBuffer sb = new StringBuffer();
124 while (readers.hasNext())
126 System.out.println("Testing RNAML input number " + (++r));
127 BufferedReader br = new BufferedReader(readers.next());
129 while ((line = br.readLine()) != null)
131 sb.append(line + "\n");
133 assertTrue("No data returned by Annotate3D", sb.length() > 0);
134 final String lines = sb.toString();
135 AlignmentI al = new FormatAdapter().readFile(lines,
136 FormatAdapter.PASTE, "RNAML");
137 if (al == null || al.getHeight() == 0)
139 System.out.println(lines);
141 assertTrue("No alignment returned.", al != null);
142 assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
145 for (SequenceI sq : al.getSequences())
148 SequenceI struseq = null;
149 String sq_ = new String(sq.getSequence()).toLowerCase();
150 for (SequenceI _struseq : pdbf.getSeqsAsArray())
152 final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
153 if (lowerCase.equals(
162 AssertJUnit.fail("Couldn't find this sequence in original input:\n"
163 + new FastaFile().print(new SequenceI[]
165 + "\n\nOriginal input:\n"
166 + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");