X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=1b70e8de026f7fa100528ce7b4b0e1a7572b8248;hb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;hp=702d9ad42a0586d9a49a0def341cfacf150390c3;hpb=9d75efeeb9a6e51bd328f56e376dca4e007b635c;p=jalview.git
diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 702d9ad..1b70e8d 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -1,10 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.paradise;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
+import jalview.gui.JvOptionPane;
import jalview.io.FastaFile;
import jalview.io.FormatAdapter;
@@ -13,8 +33,10 @@ import java.io.File;
import java.io.Reader;
import java.util.Iterator;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
import MCview.PDBfile;
@@ -23,35 +45,58 @@ import compbio.util.FileUtil;
public class TestAnnotate3D
{
- @Test
- public void testIdVsContent() throws Exception
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- Iterator ids = Annotate3D
- .getRNAMLForPDBId("2GIS");
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Network" }, enabled = true)
+ public void test1GIDbyId() throws Exception
+ {
+ // use same ID as standard tests given at
+ // https://bitbucket.org/fjossinet/pyrna-rest-clients
+ Iterator ids = Annotate3D.getRNAMLForPDBId("1GID");
+ assertTrue("Didn't retrieve 1GID by id.", ids != null);
+ testRNAMLcontent(ids, null);
+ }
+
+ @Test(groups = { "Network" }, enabled = true)
+ public void testIdVsContent2GIS() throws Exception
+ {
+ Iterator ids = Annotate3D.getRNAMLForPDBId("2GIS");
assertTrue("Didn't retrieve 2GIS by id.", ids != null);
- Iterator files = Annotate3D
- .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
- "examples/2GIS.pdb")));
+ Iterator files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
+ .readFileToString(new File("examples/2GIS.pdb")));
assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
- int i=0;
+ int i = 0;
while (ids.hasNext() && files.hasNext())
{
- 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))));
+ 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);
+ } while (iline != null);
}
}
@@ -61,21 +106,28 @@ public class TestAnnotate3D
*
* @throws Exception
*/
- @Test
+ @Test(groups = { "Network" }, enabled = true)
public void testPDBfileVsRNAML() throws Exception
{
- PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+ PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+ FormatAdapter.FILE);
Assert.assertTrue(pdbf.isValid());
- StringBuffer sb = new StringBuffer();
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
Iterator readers = Annotate3D
.getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
"examples/2GIS.pdb")));
- int r=0;
+ testRNAMLcontent(readers, pdbf);
+ }
+
+ private void testRNAMLcontent(Iterator readers, PDBfile pdbf)
+ throws Exception
+ {
+ StringBuffer sb = new StringBuffer();
+ int r = 0;
while (readers.hasNext())
{
- System.out.println("Testing RNAML input number "+(++r));
+ System.out.println("Testing RNAML input number " + (++r));
BufferedReader br = new BufferedReader(readers.next());
String line;
while ((line = br.readLine()) != null)
@@ -83,31 +135,42 @@ public class TestAnnotate3D
sb.append(line + "\n");
}
assertTrue("No data returned by Annotate3D", sb.length() > 0);
- AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ final String lines = sb.toString();
+ AlignmentI al = new FormatAdapter().readFile(lines,
FormatAdapter.PASTE, "RNAML");
-
+ if (al == null || al.getHeight() == 0)
+ {
+ System.out.println(lines);
+ }
assertTrue("No alignment returned.", al != null);
assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
- for (SequenceI sq : al.getSequences())
+ 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_))
+ SequenceI struseq = null;
+ String sq_ = new String(sq.getSequence()).toLowerCase();
+ for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- struseq = _struseq;
- break;
+ final String lowerCase = new String(_struseq.getSequence())
+ .toLowerCase();
+ if (lowerCase.equals(sq_))
+ {
+ struseq = _struseq;
+ break;
+ }
+ }
+ if (struseq == null)
+ {
+ AssertJUnit
+ .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");
}
- }
- 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");
}
}
}