package jalview.io;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.Map;
import org.junit.Test;
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);
// we might want to revise this in future
int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
: aa_original.length);
+ Map<Integer,java.util.BitSet> orig_groups=new HashMap<Integer,java.util.BitSet>(),new_groups=new HashMap<Integer,java.util.BitSet>();
if (aa_new != null && aa_original != null)
{
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]));
+ // compare graphGroup or graph properties - needed to verify JAL-1299
+ assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
+ assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
+ assertTrue(
+ "Threshold line not identical.",
+ aa_original[i].threshold == null ? aa_new[i].threshold == null
+ : aa_original[i].threshold
+ .equals(aa_new[i].threshold));
+ // graphGroup may differ, but pattern should be the same
+ Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
+ BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
+ if (orig_g==null) {
+ orig_groups.put(o_ggrp,orig_g= new BitSet());
+ }
+ if (new_g==null) {
+ new_groups.put(n_ggrp, new_g=new BitSet());
+ }
+ assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
+ orig_g.set(i); new_g.set(i);
} else {
System.err.println("No matching annotation row for "+aa_original[i].toString());
}
.equals(sequenceFeatures_new[feat]));
}
}
-
// compare alignment annotation
if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() != null)
{
annot_original = al.getSequenceAt(i).getAnnotation()[j];
annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
- assertTrue("Different annotation",
+ assertTrue("Different annotation elements",
equalss(annot_original, annot_new));
}
}
}
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.trim()
+ .equals(an_new.displayCharacter.trim())
+ || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
+ || (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;
git://source.jalview.org / jalview.git / blobdiff