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 java.util.Locale;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.JvOptionPane;
30 import jalview.io.DataSourceType;
31 import jalview.io.FastaFile;
32 import jalview.io.FileFormat;
33 import jalview.io.FormatAdapter;
35 import java.io.BufferedReader;
37 import java.io.Reader;
38 import java.util.Iterator;
40 import org.testng.Assert;
41 import org.testng.AssertJUnit;
42 import org.testng.annotations.BeforeClass;
43 import org.testng.annotations.Test;
45 import compbio.util.FileUtil;
46 import mc_view.PDBfile;
48 public class TestAnnotate3D
51 @BeforeClass(alwaysRun = true)
52 public void setUpJvOptionPane()
54 JvOptionPane.setInteractiveMode(false);
55 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58 @Test(groups = { "Network" }, enabled = true)
59 public void test1GIDbyId() throws Exception
61 // use same ID as standard tests given at
62 // https://bitbucket.org/fjossinet/pyrna-rest-clients
63 Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
64 assertTrue("Didn't retrieve 1GID by id.", ids != null);
65 testRNAMLcontent(ids, null);
68 @Test(groups = { "Network" }, enabled = true)
69 public void testIdVsContent2GIS() throws Exception
71 Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
72 assertTrue("Didn't retrieve 2GIS by id.", ids != null);
73 Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(
74 FileUtil.readFileToString(new File("examples/2GIS.pdb")));
75 assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
77 while (ids.hasNext() && files.hasNext())
79 BufferedReader file = new BufferedReader(files.next()),
80 id = new BufferedReader(ids.next());
84 iline = id.readLine();
85 fline = file.readLine();
88 System.out.println(iline);
92 System.out.println(fline);
94 // next assert fails for latest RNAview - because the XMLID entries
95 // change between file and ID based RNAML generation.
97 "Results differ for ID and file upload based retrieval (chain entry "
99 ((iline == fline && iline == null) || (iline != null
100 && fline != null && iline.equals(fline))));
102 } while (iline != null);
107 * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
108 * Annotate3d vs those extracted by Jalview from the originl PDB file
112 @Test(groups = { "Network" }, enabled = true)
113 public void testPDBfileVsRNAML() throws Exception
115 PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
116 DataSourceType.FILE);
117 Assert.assertTrue(pdbf.isValid());
118 // Comment - should add new FileParse constructor like new FileParse(Reader
119 // ..). for direct reading
120 Iterator<Reader> readers = Annotate3D.getRNAMLForPDBFileAsString(
121 FileUtil.readFileToString(new File("examples/2GIS.pdb")));
122 testRNAMLcontent(readers, pdbf);
125 private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
128 StringBuffer sb = new StringBuffer();
130 while (readers.hasNext())
132 System.out.println("Testing RNAML input number " + (++r));
133 BufferedReader br = new BufferedReader(readers.next());
135 while ((line = br.readLine()) != null)
137 sb.append(line + "\n");
139 assertTrue("No data returned by Annotate3D", sb.length() > 0);
140 final String lines = sb.toString();
141 AlignmentI al = new FormatAdapter().readFile(lines,
142 DataSourceType.PASTE, FileFormat.Rnaml);
143 if (al == null || al.getHeight() == 0)
145 System.out.println(lines);
147 assertTrue("No alignment returned.", al != null);
148 assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
151 for (SequenceI sq : al.getSequences())
154 SequenceI struseq = null;
155 String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
156 for (SequenceI _struseq : pdbf.getSeqsAsArray())
158 final String lowerCase = _struseq.getSequenceAsString()
159 .toLowerCase(Locale.ROOT);
160 if (lowerCase.equals(sq_))
169 "Couldn't find this sequence in original input:\n"
170 + new FastaFile().print(new SequenceI[]
171 { sq }, true) + "\n\nOriginal input:\n"
172 + new FastaFile().print(pdbf.getSeqsAsArray(),