import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FastaFile;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import java.io.BufferedReader;
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
- FormatAdapter.FILE);
+ DataSourceType.FILE);
Assert.assertTrue(pdbf.isValid());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
assertTrue("No data returned by Annotate3D", sb.length() > 0);
final String lines = sb.toString();
AlignmentI al = new FormatAdapter().readFile(lines,
- FormatAdapter.PASTE, "RNAML");
+ DataSourceType.PASTE, FileFormat.Rnaml);
if (al == null || al.getHeight() == 0)
{
System.out.println(lines);
{
{
SequenceI struseq = null;
- String sq_ = new String(sq.getSequence()).toLowerCase();
+ String sq_ = sq.getSequenceAsString().toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- final String lowerCase = new String(_struseq.getSequence())
+ final String lowerCase = _struseq.getSequenceAsString()
.toLowerCase();
if (lowerCase.equals(sq_))
{
{
AssertJUnit
.fail("Couldn't find this sequence in original input:\n"
- + new FastaFile()
- .print(new SequenceI[] { sq })
+ + new FastaFile().print(
+ new SequenceI[] { sq }, true)
+ "\n\nOriginal input:\n"
- + new FastaFile().print(pdbf.getSeqsAsArray())
- + "\n");
+ + new FastaFile().print(
+ pdbf.getSeqsAsArray(), true) + "\n");
}
}
}