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JAL-1749 reinstated the ability to view RNA structures
[jalview.git]
/
test
/
jalview
/
ext
/
paradise
/
TestAnnotate3D.java
diff --git
a/test/jalview/ext/paradise/TestAnnotate3D.java
b/test/jalview/ext/paradise/TestAnnotate3D.java
index
dca7bf8
..
3365c52
100644
(file)
--- a/
test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/
test/jalview/ext/paradise/TestAnnotate3D.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-22,12
+22,6
@@
package jalview.ext.paradise;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.Reader;
import java.io.BufferedReader;
import java.io.File;
import java.io.Reader;
@@
-37,19
+31,24
@@
import org.junit.Assert;
import org.junit.Test;
import MCview.PDBfile;
import org.junit.Test;
import MCview.PDBfile;
-
import compbio.util.FileUtil;
import compbio.util.FileUtil;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
public class TestAnnotate3D
{
@Test
public void test1GIDbyId() throws Exception
{
public class TestAnnotate3D
{
@Test
public void test1GIDbyId() throws Exception
{
- // use same ID as standard tests given at https://bitbucket.org/fjossinet/pyrna-rest-clients
+ // 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);
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
assertTrue("Didn't retrieve 1GID by id.", ids != null);
- testRNAMLcontent(ids,null);
+ testRNAMLcontent(ids, null);
}
@Test
}
@Test
@@
-71,9
+70,13
@@
public class TestAnnotate3D
iline = id.readLine();
fline = file.readLine();
if (iline != null)
iline = id.readLine();
fline = file.readLine();
if (iline != null)
+ {
System.out.println(iline);
System.out.println(iline);
+ }
if (fline != null)
if (fline != null)
+ {
System.out.println(fline);
System.out.println(fline);
+ }
// next assert fails for latest RNAview - because the XMLID entries
// change between file and ID based RNAML generation.
assertTrue(
// next assert fails for latest RNAview - because the XMLID entries
// change between file and ID based RNAML generation.
assertTrue(
@@
-95,7
+98,8
@@
public class TestAnnotate3D
@Test
public void testPDBfileVsRNAML() throws Exception
{
@Test
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());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
Assert.assertTrue(pdbf.isValid());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
@@
-120,10
+124,12
@@
public class TestAnnotate3D
sb.append(line + "\n");
}
assertTrue("No data returned by Annotate3D", sb.length() > 0);
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");
FormatAdapter.PASTE, "RNAML");
- if (al==null || al.getHeight()==0) {
- System.out.println(sb.toString());
+ 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);
}
assertTrue("No alignment returned.", al != null);
assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
@@
-136,7
+142,8
@@
public class TestAnnotate3D
String sq_ = new String(sq.getSequence()).toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
String sq_ = new String(sq.getSequence()).toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- if (new String(_struseq.getSequence()).toLowerCase().equals(
+ final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
+ if (lowerCase.equals(
sq_))
{
struseq = _struseq;
sq_))
{
struseq = _struseq;