import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
public class StockholmFileTest
{
- public static void main(String argv[])
- {
- try {
- new StockholmFileTest().pfamFileIO();
-
- } catch (Exception x)
- {
- x.printStackTrace();
- }
- }
- static String PfamFile = "examples/PF00111_seed.stk", RfamFile="examples/RF00031_folded.stk";
+ static String PfamFile = "examples/PF00111_seed.stk",
+ RfamFile = "examples/RF00031_folded.stk";
@Test
public void pfamFileIO() throws Exception
{
- test(new File(PfamFile));
- AppletFormatAdapter af = new AppletFormatAdapter();
- AlignmentI al = af.readFile(PfamFile, af.FILE, new IdentifyFile().Identify(PfamFile, af.FILE));
- int numpdb=0;
- for (SequenceI sq:al.getSequences())
+ testFileIOwithFormat(new File(PfamFile), "STH");
+ }
+ @Test
+ public void pfamFileDataExtraction() throws Exception
+ { AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(PfamFile, af.FILE,
+ new IdentifyFile().Identify(PfamFile, af.FILE));
+ int numpdb = 0;
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getPDBId() != null)
{
- if (sq.getPDBId()!=null)
- {
- numpdb+=sq.getPDBId().size();
- }
+ numpdb += sq.getPDBId().size();
}
- assertTrue("PF00111 seed alignment has at least 1 PDB file, but the reader found none.",numpdb>0);
+ }
+ assertTrue(
+ "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
+ numpdb > 0);
}
+
@Test
public void rfamFileIO() throws Exception
{
* 'secondary' or generated alignment from some datapreserving
* transformation
*/
- private static void testAlignmentEquivalence(AlignmentI al,
+ public static void testAlignmentEquivalence(AlignmentI al,
AlignmentI al_input)
{
assertNotNull("Original alignment was null", al);
for (int i = 0; i < aa_original.length; i++)
{
if (aa_new.length>i) {
- assertTrue("Different alignment annotation ordering",
+ assertTrue("Different alignment annotation at position "+i,
equalss(aa_original[i], aa_new[i]));
} else {
System.err.println("No matching annotation row for "+aa_original[i].toString());
System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
return false;
}
+ // TODO: does not compare graphGroup or graph properties
+ // TODO: does not compare visibility
for (int i = 0; i < annot_or.annotations.length; i++)
{
- if (annot_or.annotations[i] != null
- && annot_new.annotations[i] != null)
+ Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
+ if (an_or != null
+ && an_new!= null)
{
- // Jim's comment - shouldn't the conditional here be using || not && for
- // all these clauses ?
- if (!annot_or.annotations[i].displayCharacter
- .equals(annot_new.annotations[i].displayCharacter)
- && annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure
- && !annot_or.annotations[i].description
- .equals(annot_new.annotations[i].description))
+ if (!an_or.displayCharacter
+ .equals(an_new.displayCharacter)
+ || an_or.secondaryStructure != an_new.secondaryStructure
+ || (an_or.description != an_new.description && (an_or.description == null
+ || an_new.description == null || !an_or.description
+ .equals(an_new.description))))
{
System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
return false;