positions and ecoli position differ by one for sequence editor and probe match result

[meierh]

positions and ecoli position differ by one for sequence editor and probe match result, i.e.

sequence editor: pos 1007, ecoli 8

probe match: pos 1006, ecoli 7

[meierh]

confirmed for SVN 5990 on Opensuse 10.3 64-bit

[westram]

• positions in editor are correct (first position is 1).
• positions in probe match are not wrong (they just start counting with position 0).

The results in probe match are shown as generated by pt-server

• changing the pt-server-result has wide consequences, so this is no option
• need to change the way the match results are displayed
  • there are 2 classes ProbeMatchParser? and ParsedProbeMatch? to handle probe-match-results, might be useful.
  • think about a way to forward alignment position to editor (when selecting a match result).

[eissler]

probe match is now showing the same position as the editor (svn-version 6000)

(note: only the displaying was changed, so the count is still starting at position 0)

• tested on Ubuntu 9.04 64bit

[westram]

• patch [6000] was no good idea for several reasons
  • the "displaying" is the ONLY output of the pt-server used by ARB_NTREE. By changing it, you broke all parts using ProbeMatchParser?, which parses the output you changed.
  • there are still some parts not even using ProbeMatchParser?
    • e.g. Sonde::get_matching_species() does some parsing on that output
    • probe library also used probe match
  • ptpan uses the same output, now pt-server and ptpan are out-of-sync
  • All position-dependent member functions of ProbeMatchParser? and ParsedProbeMatch? now report wrong position (1…) - they are expected to report (0..). Any dependent code works wrong now (e.g. 'Match SAI' in probe match displays SAIs at the wrong position)

[westram]

misalignment in 'Match SAI'

[eissler]

revoked changes from patch 6000.

[westram]

fixed by [7258]