#       main topics:
UP      arb.hlp
UP      glossary.hlp

#       sub topics:
#SUB     subtopic.hlp

# format described in ../help.readme


TITLE		Track alignment changes

OCCURRENCE	ARB_NT/Sequences/Track alignment changes

DESCRIPTION     When run the first time, a checksum entry is created for every species
                that has data in the chosen alignment.
                For alignment 'ali_16s' the entry is named 'checksum_ali_16s'.

                On subsequent runs, stored checksums are compared with current checksums.
                If a checksum differs, a descriptive line is added to the 'seq_history'
                field for that species.

NOTES           Each 'checksum_xxx' entry stores two checksums:
                - the first checksum ignores gaps and reflects changes to sequence data
                - the second checksum includes gaps and reflects changes to the alignment

EXAMPLES	Use the following recommended workflow to track alignment and sequence changes:

                * Before starting an editing/alignment session, run 'Track changes' on the
                  alignment you plan to work with and supply an identifier (for example your
                  initials 'YN').
                  This records the baseline checksums.
                * Now edit your sequence data using the various aligners or the ARB sequence editor
                  to adjust your alignment or eventually modify the sequence data itself.
                * After finishing, run 'Track changes' again and use a unique suffix such
                  as 'YN-1'. This run compares checksums and adds lines to 'seq_history'
                  for species whose checksums changed.
                * To find species affected by a particular session, search the 'seq_history'
                  field with one of these expressions:

                  Description:                 /Search expression/
                  -                            -
                  alignment-only changes:      /YN-1 ali[^ ]* alignment changed/
                  sequence-data changes:       /YN-1 ali[^ ]* sequence changed/
                  newly imported species:      /YN-1 ali[^ ]* new/

                  Replace 'YN-1' with your actual session identifier (many users prefer a
                  date-based tag like 'YN-20250910').

                'Track changes' inserts a unique timestamp in each run, using the same
                timestamp for ALL entries updated in one run.
                You can use that timestamp for searching as shown in the following examples:

                  Description:                 /Search expression/
                  -                            -
                  all changed by one session   *2025/09/10 12:46 YN ali_16s*
                  alignment-only changes       *2025/09/10 12:46 YN ali_16s alignment changed*

                Note: avoid using wildcards in the middle of expressions, they may match
                unintended text (found in older history lines).

WARNINGS	None

BUGS		No bugs known