{
testFileIOwithFormat(new File(PfamFile), "STH");
}
+
@Test
public void pfamFileDataExtraction() throws Exception
- { AppletFormatAdapter af = new AppletFormatAdapter();
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
AlignmentI al = af.readFile(PfamFile, af.FILE,
new IdentifyFile().Identify(PfamFile, af.FILE));
int numpdb = 0;
al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
}
String outputfile = rf.formatSequences(ioformat, al, true);
- System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n<<EOF\n");
+ System.out.println("Output file in '" + ioformat + "':\n"
+ + outputfile + "\n<<EOF\n");
// test for consistency in io
Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, ioformat);
// 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>();
+ 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 at position "+i,
- equalss(aa_original[i], aa_new[i]));
+ if (aa_new.length > i)
+ {
+ 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("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());
+ 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());
+ 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());
+ 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());
}
}
}
{
if (annot_or.annotations.length != annot_new.annotations.length)
{
- System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
+ System.err.println("Different lengths for annotation row elements: "
+ + annot_or.annotations.length + "!="
+ + annot_new.annotations.length);
return false;
}
for (int i = 0; i < annot_or.annotations.length; i++)
{
- Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
- if (an_or != null
- && an_new!= null)
+ Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
+ if (an_or != null && an_new != null)
{
- if (!an_or.displayCharacter.trim()
- .equals(an_new.displayCharacter.trim())
- || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
+ 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());
+ 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;
}
}
}
else
{
- System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+(annot_or.annotations[i]==null ? "is null" : annot_or.annotations[i].toString())+"\nElement "+i+" in new: "+(annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString()));
+ System.err.println("Annotation Element Mismatch\nElement "
+ + i
+ + " in original: "
+ + (annot_or.annotations[i] == null ? "is null"
+ : annot_or.annotations[i].toString())
+ + "\nElement "
+ + i
+ + " in new: "
+ + (annot_new.annotations[i] == null ? "is null"
+ : annot_new.annotations[i].toString()));
return false;
}
}
git://source.jalview.org / jalview.git / blobdiff