Protein Family Alignment Annotation Tool svncode

1. Added Find Sequences With The Same Annotation Values... menu item (Currently just finds sequences using pre-existing AlignmentSearchDialog). 2. Extracted a new method named scrollToFoundSequences (Sequence[] seqs) from findSequences() as this will be used by the new menut item described in #1. 3. Changed the 1st letter of each word in the menu items to upper case so most should be consistent now. 4. Several method names related to sequence annotations were renamed as previously referred to as Properties and sometimes tags. Similar renames will appear in the next commit for other files

1. Added more helpful error message when the number of seq annot values in the seqAnnots.csv file are not consistent with the number header values. 2. Added additional journal column-width sizes for .ps export

1. Added more journal column-width options. 2. Append / replace file extension with .ps when user specifies .pdf or nothing when exporting. This ensures the os recognizes the exported file as postscript.

Add additional journal column-width sizes

1. Added new postscript sizes that are equivalent to 1 column-width, 1.5 column-width, and 2 column-width of a journal. This makes it much easier to generate publication ready graphics. Prior to this, all other sizes were much bigger than journal column widths and re-scaling in packages like illustrator and affinity designer does not work well. The aa letters are not scaled properly and the MSA figure was unreadable. 2. Made the export button the default action when the user hits enter on the Export Postscript dialog. 3. Made the help button red and added more details on making publication-ready MSA graphic. 4. Set the 'include panel' checkbox to unchecked by default.

additional changes related to the last commit

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

1. Replace Untitled with resN in residue annotations setting tab so user doesn't feel obligated to set this legacy value. 2. Rename start number to user-defined number as this is what is really being set.

set the 2 checkboxes under the residue annotations settings as checked by default as prior settings of unchecked by default caused confusion among users

Change extension from .txt to .csv . ie percentfile.csv and rawfile.csv so they are automatically opened by excel