Protein Family Alignment Annotation Tool svncode

1. Renamed File-> Print postscript to File-> Export to Postscript / PDF File... dialog. 2. Renamed several labels in the dialog so they are more intuitive to the user. 3. Reorganized the options into the newly named <MSA options:> and <Column Number Panel Above MSA:> as this is a more intuitive grouping of their functions and facilitates the key functional change (described next). 4. Within the <Column Number Panel Above MSA:> row, the newly created <include panel> checkbox is the main option. When it is unchecked, the other checkboxes on the same row are disabled (even when they are checked). This is necessary as the disabled checkboxes represent components that are part of the top panel and will not be displayed when the <include panel> is unchecked. Prior to this fix, the user would be confused when these components were missing and it appeared that there was a bug as the print function was not behaving as expected. 5. A default output file is now provided in the current working directory. The file name is dervied from the msa file name e.g. ngf.pfaat but has the extension .ps e.g. ngf.ps as this ensures that the file is recognized by the main operating systems and facilitates conversion to pdf. 6. Added a help button for the user. 7. Renamed various methods and variables to reflect their actual function. TO DO: At some point a <column numbering> checkbox should be added to <Column Number Panel Above MSA>. This is somewhat involved as DisplayProperties does not have methods to handle this. For example, it does not have a <setVisibilityOfColumnNumberingTopPanel>. See TODO comment in PrintPSDialog.exportToFile