@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
{
paevals[i][j] = ((i - j < 2)
|| ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
- paevals[j][i] = paevals[i][j];
+ paevals[j][i] = -paevals[i][j];
}
}
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
+ assertEquals(vals[4][3], paevals[4][3]);
dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
BitSet newGp = BitSet.valueOf(newlongvals);
assertTrue(gp.equals(newGp));
}
-
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
".jvp");
new Jalview2XML(false).saveState(tfile);
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),
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
-
}
}