From 69028f3bc1e7347e2b251fca0a8e731fe0431973 Mon Sep 17 00:00:00 2001 From: Sasha Date: Fri, 28 Jun 2013 17:18:36 +0100 Subject: [PATCH 1/1] JWS-50 refactored the valid AACon method parameters as a series of options in the JABAWS config (cont.) --- conf/settings/AAConParameters.xml | 134 ++++++++++++++++++------------------- conf/settings/AAConPresets.xml | 13 ++-- 2 files changed, 71 insertions(+), 76 deletions(-) diff --git a/conf/settings/AAConParameters.xml b/conf/settings/AAConParameters.xml index ac75e6b..6ebcad4 100644 --- a/conf/settings/AAConParameters.xml +++ b/conf/settings/AAConParameters.xml @@ -1,74 +1,74 @@ - compbio.runner.conservation.AACon - - Normalize - Normalize the results. - Normalized results have values between 0 and 1. Please note however, that - some results cannot be normalized. In such a case, the system returns not - normalized value. The following formula is used for normalization - n = (d - dmin)/(dmax - dmin) - Negative results first converted to positive by adding a greatest absolute - result value. - -n - -n - prog_docs/aacon.txt - - KABAT-m=KABATprog_docs/aacon.txt#KABAT - JORES-m=JORESprog_docs/aacon.txt#JORES - SCHNEIDER-m=SCHNEIDERprog_docs/aacon.txt#SCHNEIDER - SHENKIN-m=SHENKINprog_docs/aacon.txt#SHENKIN-m=SHENKIN - GERSTEIN-m=GERSTEINprog_docs/aacon.txt#GERSTEIN - TAYLOR_GAPS-m=TAYLOR_GAPSprog_docs/aacon.txt#TAYLOR_GAPS - TAYLOR_NO_GAPS-m=TAYLOR_NO_GAPSprog_docs/aacon.txt#TAYLOR_NO_GAPS - ZVELIBIL-m=ZVELIBILprog_docs/aacon.txt#ZVELIBIL - KARLIN-m=KARLINprog_docs/aacon.txt#KARLIN - ARMON-m=ARMONprog_docs/aacon.txt#ARMON - THOMPSON-m=THOMPSONprog_docs/aacon.txt#THOMPSON - NOT_LANCET-m=NOT_LANCETprog_docs/aacon.txt#NOT_LANCET - MIRNY-m=MIRNYprog_docs/aacon.txt#MIRNY - WILLIAMSON-m=WILLIAMSONprog_docs/aacon.txt#WILLIAMSON - LANDGRAF-m=LANDGRAFprog_docs/aacon.txt#LANDGRAF - SANDER-m=SANDERprog_docs/aacon.txt#SANDER - VALDAR-m=VALDARprog_docs/aacon.txt#VALDAR - SMERFS-m=SMERFSprog_docs/aacon.txt#SMERFS - - = - - SMERFS Window Width - The width of the window for SMERFS. Optional, defaults to 7 - -smerfsWW - prog_docs/aacon.txt - 7 - - Integer - 3 - 100 - - - - SMERFS Column Scoring Method - SMERFS Column Score algorithm defines the window scores to - columns allocation, two methods are possible: - MID_SCORE - gives the window score to the middle column - MAX_SCORE - gives the column the highest score of all the windows it - belongs to. Optional defaults to MID_SCORE. - -smerfsCS - prog_docs/aacon.txt - MID_SCORE - MAX_SCORE + compbio.runner.conservation.AACon + + Normalize + + Normalize the results. Normalized results have values between 0 and 1. Please note however, + that some results cannot be normalized. In such a case, the system returns not + normalized value. The following formula is used for normalization n = (d - dmin)/(dmax - dmin) + Negative results first converted to positive by adding a greatest absolute result value. + + -n + -n + prog_docs/aacon.txt + + KABAT-m=KABATprog_docs/aacon.txt#KABAT + JORES-m=JORESprog_docs/aacon.txt#JORES + SCHNEIDER-m=SCHNEIDERprog_docs/aacon.txt#SCHNEIDER + SHENKIN-m=SHENKINprog_docs/aacon.txt#SHENKIN-m=SHENKIN + GERSTEIN-m=GERSTEINprog_docs/aacon.txt#GERSTEIN + TAYLOR_GAPS-m=TAYLOR_GAPSprog_docs/aacon.txt#TAYLOR_GAPS + TAYLOR_NO_GAPS-m=TAYLOR_NO_GAPSprog_docs/aacon.txt#TAYLOR_NO_GAPS + ZVELIBIL-m=ZVELIBILprog_docs/aacon.txt#ZVELIBIL + KARLIN-m=KARLINprog_docs/aacon.txt#KARLIN + ARMON-m=ARMONprog_docs/aacon.txt#ARMON + THOMPSON-m=THOMPSONprog_docs/aacon.txt#THOMPSON + NOT_LANCET-m=NOT_LANCETprog_docs/aacon.txt#NOT_LANCET + MIRNY-m=MIRNYprog_docs/aacon.txt#MIRNY + WILLIAMSON-m=WILLIAMSONprog_docs/aacon.txt#WILLIAMSON + LANDGRAF-m=LANDGRAFprog_docs/aacon.txt#LANDGRAF + SANDER-m=SANDERprog_docs/aacon.txt#SANDER + VALDAR-m=VALDARprog_docs/aacon.txt#VALDAR + SMERFS-m=SMERFSprog_docs/aacon.txt#SMERFS + + = + + SMERFS Window Width + The width of the window for SMERFS. Optional, defaults to 7 + -smerfsWW + prog_docs/aacon.txt + 7 + + Integer + 3 + 100 + + + + + SMERFS Column Scoring Method + SMERFS Column Score algorithm defines the window scores to + columns allocation, two methods are possible: MID_SCORE - gives the window score to the middle column + MAX_SCORE - gives the column the highest score of all the windows it belongs to. Optional defaults to MID_SCORE. + -smerfsCS + prog_docs/aacon.txt + MID_SCORE + MAX_SCORE MID_SCORE - - - SMERFS Gap Threshhold - a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1 - -smerfsGT - prog_docs/aacon.txt - 0.1 - - Float + + + + SMERFS Gap Threshhold + a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1 + -smerfsGT + prog_docs/aacon.txt + 0.1 + + Float 0.001 1 - + + diff --git a/conf/settings/AAConPresets.xml b/conf/settings/AAConPresets.xml index cdf8d37..f2e3cde 100644 --- a/conf/settings/AAConPresets.xml +++ b/conf/settings/AAConPresets.xml @@ -1,30 +1,25 @@ - compbio.runner.conservation.AACon +compbio.runner.conservation.AACon Quick conservation Collection of fast conservation methods - + Slow conservation Collection of most expensive (slow) conservation methods - + Complete conservation Calculate conservation with all supported methods - + - - - - - -- 1.7.10.2