Protein Family Alignment Annotation Tool svncode

Updated to start pls module using pls gui start method.
Bug fix - pvalue option must not be passed as argument if permutation test is not selected.

Updated to add fix for the bug - avg coeff class throws exception

Updated to fix the following
1. Added separate start methods for GUI and command line
2. For Gui mode, displayed error message dialog if error or exception occurred.
3. In GUI and command line mode, if pvalue.txt file is not present , bar chart will be displayed in white color without color map column and pvalue data.

Various fixes:
1) Introduction of Zresolution, Zgridvalue and NoofslicesinoneUnit.
2) CalculateRadius
3) Looping through numberofSlicesInOneUnit with zresolution instead of zslice+ZsphereSlice
4) Instead of testing if (atominsideneighbour && circles don't intersect){},
changed to, if (circles intersect) {
if ( isatominsideneighbour) {}
}

Update to be consistent with other programs

print outliers and y values to STDERR

Updated to set pvalues option as optional parameter.

Cosmetic changes to PLSR wizard

Updated to remove commented plsmodule code.

Cancel is modified to Ok.