import java.io.BufferedReader;
import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
import org.junit.Assert;
import org.junit.Test;
@Test
public void testIdVsContent() throws Exception
{
- BufferedReader id = (BufferedReader) Annotate3D
+ Iterator<Reader> ids = Annotate3D
.getRNAMLForPDBId("2GIS");
- assertTrue("Didn't retrieve 2GIS by id.", id != null);
- BufferedReader file = (BufferedReader) Annotate3D
+ assertTrue("Didn't retrieve 2GIS by id.", ids != null);
+ Iterator<Reader> files = Annotate3D
.getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
"examples/2GIS.pdb")));
- assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
+ assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
+ int i=0;
+ while (ids.hasNext() && files.hasNext())
+ {
+ BufferedReader file=new BufferedReader(files.next()), id=new BufferedReader(ids.next());
String iline, fline;
do
{
System.out.println(iline);
if (fline != null)
System.out.println(fline);
-
- assertTrue("Results differ for ID and file upload based retrieval",
+ // 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);
+ }
}
/**
StringBuffer sb = new StringBuffer();
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
- BufferedReader br = new BufferedReader(
- Annotate3D.getRNAMLForPDBFileAsString(FileUtil
- .readFileToString(new File("examples/2GIS.pdb"))));
- String line;
- while ((line = br.readLine()) != null)
+ Iterator<Reader> readers = Annotate3D
+ .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+ "examples/2GIS.pdb")));
+ int r=0;
+ while (readers.hasNext())
{
- sb.append(line + "\n");
- }
- assertTrue("No data returned by Annotate3D", sb.length() > 0);
- AlignmentI al = new FormatAdapter().readFile(sb.toString(),
- FormatAdapter.PASTE, "RNAML");
+ System.out.println("Testing RNAML input number "+(++r));
+ BufferedReader br = new BufferedReader(readers.next());
+ String line;
+ while ((line = br.readLine()) != null)
+ {
+ sb.append(line + "\n");
+ }
+ assertTrue("No data returned by Annotate3D", sb.length() > 0);
+ AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ FormatAdapter.PASTE, "RNAML");
- assertTrue("No alignment returned.", al != null);
- assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
- for (SequenceI sq : al.getSequences())
- {
+ assertTrue("No alignment returned.", al != null);
+ assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+ 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;
+ if (new String(_struseq.getSequence()).toLowerCase()
+ .equals(sq_))
+ {
+ struseq = _struseq;
+ break;
+ }
+ }
+ 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");
}
- }
- 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");
}
}
}