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Created with Raphaël 2.2.021Feb201918157630Jan292827212017161514131011Dec1095413Nov11865431Oct30292825232221181716151411109413Sep1211109532returned rtree as it is still used in edge routingmastermasterfix using get_main_product twice instead of get_main_reactant when identifying reaction for layout recomputationfix averaging of positions for connected species of inserted reactionfix: when laying out ods of inserted reaction, position from reaction layout was used, but this was not updated yetusing distance to known modifiers when laying out modifiers of inserted reactionsonly ODS of the same type are mapped onto each othergui description updateminor upadteimg resizemodified requirementsreadmeDeafult for step sepcification in the export functionStep sepcification in CLIcommented out rtree import which was not usedcommenting out bounding box width and heighttreating long species names (dirty way)storing bounding box dimensions within speciescompartment names in template names separated by double dashdiscrening reaction and species positions when laying outfix issue when no main reactant or product has been laid out when getting position for specieswhen deciding on center of perpendicular line where to place species, distance from center is decided by existing main reactant and product + when center intersects with same type species, it is not extendedwhen placing new species in new reaction and the center of the perpendicular line intersects with existing, first try to move the center furtherusing only main reactant and product id to determine direction of a reactionmaking mapping of inserted reactions' connecting species deterministicadd overal line lengths into strategies comparisontest intersection with forbidden regions when laying out single object on perpendicular linehandling edge casesremoved counting of the number of overlaps in trailing path beautificationworking version of providing mappingproviding-mappingproviding-mappingrefactored providing list of mappings from EDrecovery from disk failuredead-end-insert…dead-end-inserted-reactionslaid_out_rs_tmt in laying out ods replaced with laid_out_rs_tgt which should be the correct wayChanged hadling of joining strategies. Before unrealted strategies were put togetherin progress of joining strtegiesenabling inflation of reactionsremoved debug codey axes in plotting reactiong graph in analyze.py reversename of the output file includes the name of the tempalte file even if splitting by compartment happens and only one template is chosenchange scoring to consider sbo and be symmetric; update mrm testing scriptsfix missing extension of the strategy list when the last reaction list does not have ods