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.gui.JvOptionPane;
28 import jalview.io.FastaFile;
29 import jalview.io.FormatAdapter;
31 import java.io.BufferedReader;
33 import java.io.Reader;
34 import java.util.Iterator;
36 import org.testng.Assert;
37 import org.testng.AssertJUnit;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.Test;
41 import MCview.PDBfile;
43 import compbio.util.FileUtil;
45 public class TestAnnotate3D
48 @BeforeClass(alwaysRun = true)
49 public void setUpJvOptionPane()
51 JvOptionPane.setInteractiveMode(false);
52 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55 @Test(groups = { "Network" }, enabled = true)
56 public void test1GIDbyId() throws Exception
58 // use same ID as standard tests given at
59 // https://bitbucket.org/fjossinet/pyrna-rest-clients
60 Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
61 assertTrue("Didn't retrieve 1GID by id.", ids != null);
62 testRNAMLcontent(ids, null);
65 @Test(groups = { "Network" }, enabled = true)
66 public void testIdVsContent2GIS() throws Exception
68 Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
69 assertTrue("Didn't retrieve 2GIS by id.", ids != null);
70 Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
71 .readFileToString(new File("examples/2GIS.pdb")));
72 assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
74 while (ids.hasNext() && files.hasNext())
76 BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
81 iline = id.readLine();
82 fline = file.readLine();
85 System.out.println(iline);
89 System.out.println(fline);
91 // next assert fails for latest RNAview - because the XMLID entries
92 // change between file and ID based RNAML generation.
94 "Results differ for ID and file upload based retrieval (chain entry "
96 ((iline == fline && iline == null) || (iline != null
97 && fline != null && iline.equals(fline))));
99 } while (iline != null);
104 * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
105 * Annotate3d vs those extracted by Jalview from the originl PDB file
109 @Test(groups = { "Network" }, enabled = true)
110 public void testPDBfileVsRNAML() throws Exception
112 PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
114 Assert.assertTrue(pdbf.isValid());
115 // Comment - should add new FileParse constructor like new FileParse(Reader
116 // ..). for direct reading
117 Iterator<Reader> readers = Annotate3D
118 .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
119 "examples/2GIS.pdb")));
120 testRNAMLcontent(readers, pdbf);
123 private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
126 StringBuffer sb = new StringBuffer();
128 while (readers.hasNext())
130 System.out.println("Testing RNAML input number " + (++r));
131 BufferedReader br = new BufferedReader(readers.next());
133 while ((line = br.readLine()) != null)
135 sb.append(line + "\n");
137 assertTrue("No data returned by Annotate3D", sb.length() > 0);
138 final String lines = sb.toString();
139 AlignmentI al = new FormatAdapter().readFile(lines,
140 FormatAdapter.PASTE, "RNAML");
141 if (al == null || al.getHeight() == 0)
143 System.out.println(lines);
145 assertTrue("No alignment returned.", al != null);
146 assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
149 for (SequenceI sq : al.getSequences())
152 SequenceI struseq = null;
153 String sq_ = new String(sq.getSequence()).toLowerCase();
154 for (SequenceI _struseq : pdbf.getSeqsAsArray())
156 final String lowerCase = new String(_struseq.getSequence())
158 if (lowerCase.equals(sq_))
167 .fail("Couldn't find this sequence in original input:\n"
169 .print(new SequenceI[] { sq })
170 + "\n\nOriginal input:\n"
171 + new FastaFile().print(pdbf.getSeqsAsArray())