[initial version Ketil Malde **20070809125927] [prettify output (csv-compatible) Ketil Malde **20070809191642] [handle blastx Ketil Malde **20070810202549] [added 2html Ketil Malde **20070822123145] [output fixes: spaces between fields and sequence label only Ketil Malde **20070822123154] [use visible background Ketil Malde **20070822125843] [deal correctly with reverse matches Ketil Malde **20070822130827] [use library flatten function (NB:now lists all matches) Ketil Malde **20070903135227] [README update Ketil Malde **20071025073556] [update for new Strands structure Ketil Malde **20071025073606] [initial version of Xml2Go Ketil Malde **20071025145847] [update README, add Makefile Ketil Malde **20071030140416] [xml2go working (but using lots of memory) Ketil Malde **20071030140430] [added verbose output Ketil Malde **20071031084532] [small output fix Ketil Malde **20071031133801] [parametrized build options in mf Ketil Malde **20071031142721] [slightly stricter still Ketil Malde **20071031142735] [more output fixes Ketil Malde **20071031155728] [TAG 0.0 Ketil Malde **20071101074730] [initialize unified version Ketil Malde **20071101081134] [Using 'real' option handling Ketil Malde **20071101083255] [hihger level option usage, more options added Ketil Malde **20071101085336] [optionally empty term defs db Ketil Malde **20071101100852] [made terms and defs optional Ketil Malde **20071101111821] [refactored annotate flow Ketil Malde **20071101114527] [csv format fix Ketil Malde **20071101114610] [warning elim Ketil Malde **20071101120415] [more csv format improvements Ketil Malde **20071101121500] [cleanups, comments, type sigs Ketil Malde **20071101123930] [output format fixes Ketil Malde **20071101132056] [correctly interpret output formats Ketil Malde **20071101132348] [TAG 0.1 Ketil Malde **20071101133948] [removed obsoleted xml2xls Ketil Malde **20071101141111] [cabalized Ketil Malde **20071101141258] [minor cosmetics in output Ketil Malde **20071101141318] [update README Ketil Malde **20071101143036] [count xml files separately Ketil Malde **20071101152510] [add coordinates to csv output Ketil Malde **20071102112940] [collect GO in a set instead of a list Ketil Malde **20071102113012] [TAG 0.2 Ketil Malde **20071105123523] [support -1 for first match only Ketil Malde **20071106104809] [makefile updates, warn removal Ketil Malde **20071106104941] [refactor top/all output Ketil Malde **20071106150000] [support region output Ketil Malde **20071106153238] [formatting fix, warn elim Ketil Malde **20071106223125] [improved top and renamed long option Ketil Malde **20071106223202] [update readme for new functionality Ketil Malde **20071107092453] [small refactoring of top Ketil Malde **20071107092504] [merge matches against same subject with same e-value Ketil Malde **20071107100232] [summarize GO annotation for --top Ketil Malde **20071107102703] [split GO annots into direct/indirect Ketil Malde **20071107113515] [factor out merge Ketil Malde **20071107122302] [use showTop to summarize regions Ketil Malde **20071107122322 Note that the region will only include the first HSP, maybe this should be fixed to work like 'showTop' and extend to embrace all compatible HSPs. ] [include multiple HSPs in --reg output Ketil Malde **20071107132116] [rewrote protTerms to force GO set - needs testing Ketil Malde **20071107142513] [experiment: save memory by storing GO terms in UArrays Ketil Malde **20071107210602] [strictness fix Ketil Malde **20071107222104] [warning fixes Ketil Malde **20071110145541] [separate field for subject/target name and desc, filter commas Ketil Malde **20071110145627] [showGo performs chopping of UniRef_ from names Ketil Malde **20071110145711] [robust chop Ketil Malde **20071119090538] [moved to Html Ketil Malde **20071119090735] [regions are unidirectional, factor out 'dir' Ketil Malde **20071119142926] [makefile tgt dep on Html Ketil Malde **20071212132217] [chop seqname from hdr Ketil Malde **20071212132331] [moderatly working HTML code Ketil Malde **20071217100603] [fix index brs Ketil Malde **20071217111400] [cleanup html Ketil Malde **20071218095341] [verbose in conjunction with html too Ketil Malde **20071218105858] [refactor stage 1 Ketil Malde **20071218125436] [refactor stage 2 Ketil Malde **20071218130819] [refactor, stage 3: html now with detailed index Ketil Malde **20071218145418] [pts decides if we have GO Ketil Malde **20071219083641] [explicit go boolean Ketil Malde **20071219091306] [fix chopping of Go terms Ketil Malde **20071219093313] [moved quoting to csvFormat Ketil Malde **20071219095238] [new color regime Ketil Malde **20071219113609] [remove gratuitious parameter Ketil Malde **20071219113934] [correct for overlapping HSPs Ketil Malde **20071219191109] [fix identity calc (it is absolute, not percent) Ketil Malde **20071220085316] [ad-hoc length adjustment Ketil Malde **20071220085354] [use bits instead of idents, add comment Ketil Malde **20080110101216] [add directory to deps Ketil Malde **20080110101516] [pre-sort HSP matches Ketil Malde **20080110123658] [bits/pos in comment Ketil Malde **20080114162936] [add more info to htmlheader Ketil Malde **20080114184146] [annotate target with tooltip/anchor Ketil Malde **20080114184846] [remove obsolete comment Ketil Malde **20080116141910] [mem leak fix Ketil Malde **20080117120028 Storing 'up' directly implicitly stores a (possibly huge) chunk of the input file as well. Thanks to dcoutts for helping out. ] [remove debugging print Ketil Malde **20080118063720] [factor out htmldir Ketil Malde **20080121084638] [insignificant perf improvement Ketil Malde **20080121085516] [report incorrect bit scores Ketil Malde **20080123131718] [bits comment Ketil Malde **20080128114453] [link to same name Ketil Malde **20080128145713] [cleanup 'line' function Ketil Malde **20080128145736] [factor out tabulating from html gen Ketil Malde **20080129092221] [Html cleanup/warning removal Ketil Malde **20080129092808] [+LICENSE gwern0@gmail.com**20080308040438] [fmt readme gwern0@gmail.com**20080308040444] [cleanup .hs files gwern0@gmail.com**20080308040448] [improve cabal file for hackage gwern0@gmail.com**20080308040508] [fixed table widths Ketil Malde **20080326115840] [disambiguate readXML Ketil Malde **20080326115854] [rewrote and updated README Ketil Malde **20080416124359] [Attempt at reduced memory consumption Ketil Malde **20080512213329] [add refs to README Ketil Malde **20080707082619] [use style instead of font Ketil Malde **20080707090532] [moved annotation to separate source file Ketil Malde **20080707101609] [comment in html Ketil Malde **20080707103620] [gratuitious imports removed Ketil Malde **20080707103633] [consistencize interface Ketil Malde **20080707103713] [fix headers for HTML Ketil Malde **20080707104239] [mostly doc changes Ketil Malde **20080707112456] [use new interface Ketil Malde **20080725102630] [port to new GO infrastructure, use .obo file, same (non-transitive, non-weigthed) output. Ketil Malde **20080729100540] [refactored showGo Ketil Malde **20080730140903] [hierarchy works, but with duplicates Ketil Malde **20080730143412] [remove duplicated GO annots Ketil Malde **20080730143735] [include primary hits in the hierarchical ones Ketil Malde **20080730144422] [display hierarchy if possible, fix headers Ketil Malde **20080730145850] [eliminate duplicate terms Ketil Malde **20080730145917] [add kegg option Ketil Malde **20080731134942] [partial read_kegg impl. Ketil Malde **20080731141238] [working reading KEGG files Ketil Malde **20080731143349] [add strictness hack to build_kegg Ketil Malde **20080801075658] [add KEGG option to header and tabulate Ketil Malde **20080801075721] [pass kegg to show* functions Ketil Malde **20080801075940] [added Kegg to showAll Ketil Malde **20080801081940] [add kegg to showTop, fix errors in parenthesizing Ketil Malde **20080801084823] [update dependency Ketil Malde **20080801085035] [README updates with KEGG and better references Ketil Malde **20080801085801] [removed superfluous boolean Ketil Malde **20080811095920] [aliased the annotation maps, warning fixes Ketil Malde **20080811130150] [pass blast hits directly to 'showX' functions Ketil Malde **20080811130906] [collect bit-scores for GO annotations Ketil Malde **20080813125644] [buglet: add space between KOs Ketil Malde **20080813135425] [sort GO by decreasing score Ketil Malde **20080813140018]