boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
}
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
String content = ContactMatrix.contactToFloatString(dummyMat);
- Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
- float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
- assertEquals(vals[3][4],paevals[3][4]);
- dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat,0.5f, false));
+ Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+ // 1
+ float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+ sq.getLength(), sq.getLength());
+ assertEquals(vals[3][4], paevals[3][4]);
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
// verify store/restore of group bitsets
- for (BitSet gp:dummyMat.getGroups())
+ for (BitSet gp : dummyMat.getGroups())
{
StringBuilder sb = new StringBuilder();
- for (long val:gp.toLongArray())
+ for (long val : gp.toLongArray())
{
- if (sb.length()>0) {
+ if (sb.length() > 0)
+ {
sb.append(",");
}
sb.append(val);
}
String[] longvals = sb.toString().split(",");
long[] newlongvals = new long[longvals.length];
- for (int lv=0;lv<longvals.length;lv++)
+ for (int lv = 0; lv < longvals.length; lv++)
{
- try {
- newlongvals[lv]=Long.valueOf(longvals[lv]);
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
} catch (Exception x)
{
Assert.fail("failed to deserialise bitset element ");
BitSet newGp = BitSet.valueOf(newlongvals);
assertTrue(gp.equals(newGp));
}
-
+
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
".jvp");
new Jalview2XML(false).saveState(tfile);
.getContactMatrixFor(newSeq.getAnnotation()[0]);
Assert.assertNotNull(restoredMat);
MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq);
- MapList newMap = ((MappableContactMatrixI) restoredMat).getMapFor(newSeq);
- Assert.assertEquals(oldMap.getFromRanges(),newMap.getFromRanges());
- Assert.assertEquals(oldMap.getToRanges(),newMap.getToRanges());
- Assert.assertEquals(oldMap.getFromRatio(),newMap.getFromRatio());
- Assert.assertEquals(oldMap.getToRatio(),newMap.getToRatio());
-
+ MapList newMap = ((MappableContactMatrixI) restoredMat)
+ .getMapFor(newSeq);
+ Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges());
+ Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
+ Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
+ Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
+
for (i = sq.getLength() - 1; i >= 0; i--)
{
ContactListI oldCM = dummyMat.getContactList(i),
newCM = restoredMat.getContactList(i);
for (int j = oldCM.getContactHeight(); j >= 0; j--)
{
- double old_j=oldCM.getContactAt(j);
- double new_j=newCM.getContactAt(j);
- Assert.assertEquals(old_j,new_j);
+ double old_j = oldCM.getContactAt(j);
+ double new_j = newCM.getContactAt(j);
+ Assert.assertEquals(old_j, new_j);
}
}
Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
- Assert.assertEquals( restoredMat.getNewick(),dummyMat.getNewick());
-
-
+ Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
}
}