Protein Family Alignment Annotation Tool svncode

Fix bug where 1st char of line annotation was not being saved to .pfam or .pfaat.

Updated to fix file path shown in file browser dialog

Updated to create residue property file for plsr with only sequences which has selected annotation if selected sequence is checked.

Updated for the following
1. check if any columns is selected
2. check if any sequence is selected
3. Exclude sequences which do not have selected annotation

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Updated to add pls lib files

version with bug fixes

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.