added Sort By Distance tool #145
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I'm not sure what the algorithm is supposed to do though
and fixed CLI file
Need to take strand direction into account, and change to upstream-downstream
and changed 'left' and 'right' to upstream and downstream
along with window interface and logging
rename tool to be more precise
add javadocs in standard format with other tools (see dev branch) clean up trailing whitespace
SortByRefCLI - strip out filename extension restrictions - change validation to allow for positive and negative up/downstream bounds and add relational check - clarify up/downstream bounds flag documenation language - rename default filename to have "DistSort" suffix - reorganize method signature to put printstream object last SortByRef - redo implementation to use two large maps instead of parallel sort index array - redo validation logic for identifying closer peak - store search range restriction values such that null indicates no restriction - remove negative/positive-based validation of upstream/downstream restrictions - reorganize method signature to put printstream object last SortByRefOutput - rewrite output filepath construction to use ExtensionFileFilter - add missing stop timestamp on log item - rename default filename to have "DistSort" suffix - reorganize method signature to put printstream object last - comment and clean whitespace SortByRefWindow - restructure option parsing and validation (Task class) - change validation to allow for positive and negative up/downstream bounds and add relational check - make greater use of Exception-based error pop ups - rename execution language to "Sort" rather than "Align" based - reduce scope of variables that don't need large scope (e.g. moved UPSTREAM from class attribute to initialize within Task.doInBackground()) - reorganize options into subpanel - reformat components to leverage "enabled" features for formatting, etc. - separate up and downstream search restrictions - comment and clean whitespace
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merge in new tool from #35 |
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used some methods from the GzipUtilites on the gzip support branch