JAL-2629 hmm match score colour scheme now colours by length

diff --git a/resources/ProbabilityOfMatch b/resources/ProbabilityOfMatch
index 3a0fa09..9e3869f 100644 (file)
--- a/resources/ProbabilityOfMatch
+++ b/resources/ProbabilityOfMatch
@@ -1,138 +1,261 @@
-, A, Q, L, S, R, E, K, T, N, G, M, W, D, H, F, Y, C, I, P, V, 
--7.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.3, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--7.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.3, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--6.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.3, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--5.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.02829164116310036, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.010695823802440853, 0.0, 0.0, 0.0, 0.04208924321147232, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.019635914551440377, 0.0, 0.0, 0.0
--4.3, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
--4.2, 0.0, 0.0, 0.01950088715808336, 0.0, 0.0, 0.0, 0.004055385966837936, 0.0, 0.04657083856751056, 0.061832620711445116, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.12296430262477717, 0.0, 0.0, 0.0
--4.1, 0.08879360675953489, 0.0, 0.0, 0.10995431074443743, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.10431300622971537, 0.0, 0.0, 0.0, 0.03386413551157293, 0.024369797680166727, 0.0, 1.0
--4.0, 0.3689566722305009, 0.0, 0.030009594624555633, 0.0, 0.0810859964183997, 0.003463077970928565, 0.0, 0.0, 0.0, 0.02845876476487721, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.011091944356306106, 0.024369797680166727, 0.011074744236655788, 0.047624494351747315
--3.9, 0.023782180904202643, 0.0, 0.12220730492694099, 0.0, 1.0, 0.04639441442365878, 0.034086873430023944, 0.0, 0.0, 0.019154211577094547, 0.0, 0.01858770249657673, 0.09247973535224101, 0.04475999094154309, 0.0, 0.0, 0.018524058144022394, 0.0, 0.0, 0.0
--3.8, 0.0, 0.0, 0.060650357643932694, 1.0, 0.0, 0.04003196372244064, 0.011626498464401598, 0.0, 0.16344766921789491, 0.013485438989450364, 0.0, 0.0, 0.008658975998176319, 0.0, 0.0, 0.04046447105940979, 0.012339304662932616, 0.0, 1.0, 0.01961015188120082
--3.7, 0.19589295401074644, 0.0, 0.08760338126484823, 0.1395209908570528, 0.04225619088039115, 0.01688127361087505, 0.013919431307936506, 0.01745670307871183, 0.0, 0.2352226440377928, 0.0, 0.036497009439674044, 0.09487133704395254, 0.0, 0.008589307945870255, 0.0, 0.04327024629373948, 0.10439721299122362, 0.02190687543089019, 0.01515330729111168
--3.6, 0.0048486860437526955, 0.0, 0.11821617809720325, 0.0, 0.024591746299820964, 0.005376665836435987, 0.057045704655527135, 0.04658286285692069, 0.03153679064028913, 0.02467377664312319, 0.0, 0.006273642566590675, 0.049797863466474586, 0.0, 0.0, 0.0, 0.010387555511263722, 0.0036868779830590724, 0.21183534863275558, 0.03226181375684487
--3.5, 0.11133859290913524, 0.0, 0.03723265902962619, 0.15633652849901264, 0.012448943783523049, 0.01474892836527587, 0.0, 0.0, 0.08899701167147787, 0.027767051045102954, 0.0, 0.02762481284353547, 0.04813467541481971, 0.04475999094154309, 0.004790123902950727, 0.07778155272944308, 0.02594762955925915, 0.08390336977125232, 1.0, 0.01961015188120082
--3.4, 0.012034190095039215, 0.03322249852715383, 0.053474468644454286, 0.018193535631474262, 0.02269435267853319, 0.008512487621763614, 0.009532740997887394, 0.006931454994480205, 0.30062176091423554, 0.05159346071040341, 0.0, 0.057143866952526955, 0.04184552249134672, 0.21944758587068233, 0.058277319706987574, 0.0, 0.02456377796035574, 0.02323629606844567, 1.0, 0.10448884870730178
--3.3, 0.00461886268047956, 0.0, 0.0390216479953782, 0.0, 0.007958080479154575, 0.1455040163909359, 0.003637389247921454, 0.06828386531864167, 0.3281629653336182, 0.06034283956272431, 0.03163388897118409, 0.02762481284353547, 0.07323948559347689, 0.0, 0.005070467181592201, 0.004097375997032753, 0.03806736353149218, 0.04454938412218862, 0.06296202386528356, 0.14287184886722262
--3.2, 0.026355003287346208, 0.09345769904379421, 0.10900905005333161, 0.0, 0.03955052846705334, 0.007827688606677756, 0.007008492770816025, 0.052885619896659464, 0.020504597265588845, 0.06254823921958845, 0.0, 0.02715332675100986, 0.0389730457034319, 0.03029194975998154, 0.02021100191582733, 0.011120515176494261, 0.06800187967662571, 0.0222797235288159, 0.01652063544887204, 0.056610186916683784
--3.1, 0.008780957809709947, 0.03722074009517412, 0.07754017449792827, 0.0, 0.020577461200741307, 0.02084145274552592, 0.0252719631057375, 0.07529965573727915, 0.04360148651566483, 0.018860571699027263, 0.0, 0.0452087656132568, 0.02829164116310036, 0.0016706800271179848, 0.058277319706987574, 0.02639431423986775, 0.04763215483833094, 0.014072575452935379, 0.012069387768839685, 0.047624494351747315
--3.0, 0.025002579064508895, 0.0, 0.05376950755290202, 0.015207392398806802, 0.03832359911643274, 0.028363002613209905, 0.026594536598103954, 0.0, 0.011702785512497028, 0.019496926236343828, 0.0, 0.011820549895396408, 0.02510918796765158, 0.08568473396689924, 0.01809981185372354, 0.013057334744841264, 0.040723532401874575, 0.04595888736692246, 0.014712015047588428, 0.010240124962036011
--2.9, 0.10165923842396132, 0.01925849138770066, 0.10280532568773196, 0.09030659969055027, 0.040002533313892245, 0.02256781771493697, 0.010049833520510105, 0.058543518716930254, 0.027447298515842, 0.015096030276451577, 0.0, 0.03347340971774025, 0.024029415526062817, 0.01386233177369645, 0.011983857905845214, 0.04883154247724736, 0.03632506151235719, 0.07240601298981855, 0.05636052932384628, 0.03361734667768531
--2.8, 0.052531025940796595, 0.06430850775029018, 0.1626348178740122, 0.06785900401602339, 0.060496654552444275, 0.023527245595209505, 0.03408687343002395, 0.020252412371005103, 0.04463640013348189, 0.044206539181594465, 0.007482198246102163, 0.023215747128816668, 0.021369878103073104, 0.003784862903232261, 0.008107062253890901, 0.05226435462684763, 0.039868467529687805, 0.06826828362594513, 0.010121470189437631, 0.0273875236489425
--2.7, 0.0332492449874311, 0.015379839343212324, 0.0094819857102878, 0.059884592111091026, 0.013975364333812435, 0.02747320325587215, 0.024990976178534782, 0.08901896736539451, 0.06003998506457896, 0.02805049196173922, 0.022115647421607758, 0.008834086370361522, 0.025071369017364065, 0.06637501467563794, 0.01278034182099209, 0.014743249599626527, 0.05694868305881588, 0.037527624809225744, 0.036519311038454766, 0.04569051534486316
--2.6, 0.01851142049541852, 0.06430850775029019, 0.04737803106985519, 0.017566379804295706, 0.012410037290083342, 0.0359867495221175, 0.025205740082693648, 0.16348469591994957, 0.042197735169961975, 0.04173441030708138, 0.030407009090317086, 0.013763526136723185, 0.04815352231784231, 0.03998551989339622, 0.02890459553535015, 0.045502285642742224, 0.03950205051635595, 0.06724240486780662, 0.03372796693235684, 0.031417266844813836
--2.5, 0.03923255526240153, 0.03510815252606944, 0.07427047870277081, 0.04253339434657074, 0.06913497775729868, 0.021574970695644142, 0.010785886769698598, 0.013059789598181252, 0.026708443576734717, 0.05139713957426477, 0.0, 0.01515092856689246, 0.036647702691676894, 0.014212724344809798, 0.01856942714162384, 0.02065003183753786, 0.053324769029336305, 0.035874511879811215, 0.02899741962136608, 0.06732871909476233
--2.4, 0.08311358453970648, 0.01776509435050462, 0.12443647697779268, 0.01125047080020766, 0.026923872354963147, 0.04580415632482146, 0.030017498567789135, 0.01389377153578446, 0.05959116048048238, 0.04035467131299979, 0.016071140827886864, 0.017672332907734307, 0.04581629422051411, 0.037403879835875405, 0.03416577910572242, 0.06482800911628889, 0.06322485879178633, 0.03869238768325982, 0.03027055345729848, 0.07525767742213552
--2.3, 0.034480460164198305, 0.03227690502428549, 0.07828307397825086, 0.03300868588716934, 0.026022201912634265, 0.03392556529243158, 0.02810527506627939, 0.044702560478915986, 0.037294841354115996, 0.04319424647548471, 0.04967144182839176, 0.01765925550459641, 0.03686988261615175, 0.024921581310712794, 0.025638733001976638, 0.03198431543345981, 0.05521322400395561, 0.06050758095172883, 0.01543626087485438, 0.08175593571981533
--2.2, 0.04226928162855123, 0.041755663961279575, 0.07373731608214697, 0.025657424626138153, 0.025288054110848654, 0.04198551016948324, 0.019980479352562995, 0.07020779881682095, 0.041545590655441896, 0.03773302144079488, 0.008100663868861355, 0.022994449476745154, 0.04932523545856454, 0.046433779779943535, 0.03877621149435199, 0.06879794444592742, 0.0742383975128561, 0.07835342334641683, 0.03629692886595023, 0.04217184319315995
--2.1, 0.07045184377103593, 0.032118448968231524, 0.06613606012329647, 0.05893061090363944, 0.040865021862671554, 0.060353957704001905, 0.03465421170074745, 0.0486373025023053, 0.08631206605804465, 0.0567654043284816, 0.017791803121014735, 0.04684955960584719, 0.051976764926009666, 0.016753562631597687, 0.04124067418381241, 0.04060361610317571, 0.08567048506487018, 0.09275835581255626, 0.012453335840940351, 0.0796912536506441
--2.0, 0.06742411609927514, 0.05578022619952826, 0.07937835950580119, 0.0563798286769995, 0.04309455982162019, 0.04304739291933987, 0.05560661571232877, 0.04943351360405592, 0.035150597481930515, 0.04544018039076804, 0.029516636352286643, 0.03324967887154355, 0.058572704120773166, 0.037063377639014905, 0.043994549724330353, 0.02458882267944921, 0.08822721683536476, 0.092877116502672, 0.03109936875068513, 0.07802282294779829
--1.9, 0.08325978929711392, 0.03251451868182044, 0.07449192866734146, 0.035990204930625096, 0.04075863350540484, 0.05639815903541886, 0.043578426415642045, 0.05846149345326845, 0.05724312557785772, 0.05470249284807387, 0.04671199246514356, 0.05859032124499724, 0.07039919628475319, 0.06358363818951468, 0.06785696844834044, 0.04743387744544618, 0.07994137421748179, 0.09589893010474781, 0.02661381221180542, 0.09433352994951928
--1.8, 0.06002309581746732, 0.03312274051992086, 0.09240669531871258, 0.06785900401602339, 0.05774822320879129, 0.04009723216028221, 0.04068510219580195, 0.09616028788342292, 0.09863168007068489, 0.08332004826069814, 0.03252746324302176, 0.05194300524645246, 0.09318071292404347, 0.02110752803125993, 0.08207981912588695, 0.0693306201369613, 0.11063286174209308, 0.09162768947605733, 0.03643645798054579, 0.1266453018134754
--1.7, 0.07532839880730059, 0.03921843872685912, 0.10346325133698366, 0.048455126233623545, 0.04655651900412641, 0.05984619037851527, 0.07728240913052774, 0.0981340873583233, 0.06568856316585131, 0.10749315925484698, 0.040931346307097334, 0.05954876813250768, 0.100429375471394, 0.03488866424042458, 0.10807898623464696, 0.04934639267994535, 0.12102359078032515, 0.1230670119900175, 0.052172065145057706, 0.13364972361241942
--1.6, 0.06413292852312112, 0.05084731813267938, 0.1356325183798371, 0.03877346525407831, 0.07334220556746883, 0.06081806629143686, 0.04801595144472207, 0.07499943063197656, 0.06951215578157782, 0.13342630495608315, 0.07585096144011201, 0.06683844539675281, 0.11040972062872298, 0.04433008363702538, 0.14424263509812715, 0.061198087595813265, 0.14235378521093414, 0.14522389325820145, 0.05105286748606104, 0.13148705615617357
--1.5, 0.05926739383682679, 0.07034778968757303, 0.16379930331129083, 0.06184409029291616, 0.06521060545880578, 0.1196536256744747, 0.07466256706347636, 0.04759886830659513, 0.06903135652454744, 0.1414597325765428, 0.04640193818107075, 0.09102430874585034, 0.12039896224433969, 0.044375795755385826, 0.16473032355285597, 0.06852507286039514, 0.1653038920071332, 0.16727519306815794, 0.0499714217947348, 0.15220710980238833
--1.4, 0.08231738923365092, 0.060507850903448845, 0.2037696063826672, 0.058349939244509, 0.07558156606421074, 0.11546200303829997, 0.07400132979259473, 0.07196486505124003, 0.062365084374836, 0.1545022343308531, 0.07737491494580351, 0.09661569704202352, 0.13468192477050894, 0.07057465189738071, 0.1979636247393688, 0.09042777652690398, 0.16785115948571078, 0.23953434660695522, 0.06436257558042596, 0.17073566469571383
--1.3, 0.06843243908599969, 0.0715205652162853, 0.21761626452134847, 0.08013265438406059, 0.07459192717770596, 0.11429297904363565, 0.08571661619707861, 0.06236033274667358, 0.08495251476710276, 0.17951636173397273, 0.05426786442218258, 0.09917564002949561, 0.15637418758809588, 0.06615127483384402, 0.22297636582534583, 0.11650070258109992, 0.16575918088820024, 0.2439290298634841, 0.08554717832704674, 0.18381340832706633
--1.2, 0.09249269917013553, 0.0879856789570333, 0.2671596726046994, 0.08864299088518895, 0.10556506969247283, 0.10302085679105487, 0.1092978742192447, 0.09432307425333092, 0.0839664774293923, 0.2255248760785672, 0.07734975196725899, 0.14597132745393937, 0.15551332983317057, 0.060107266352475534, 0.21945250710597325, 0.11975666712189477, 0.22443286159697703, 0.2609400050297798, 0.09653139153874761, 0.23971674756418454
--1.1, 0.11876069069519987, 0.09524410195423771, 0.2957908647995533, 0.09593346263556528, 0.11507903111344141, 0.14330200488568748, 0.10362750681709808, 0.11455007290461995, 0.10780653240026329, 0.2421289273328063, 0.08307303987959924, 0.16959539688192585, 0.13540505986353935, 0.07370908294147693, 0.26584875737119523, 0.13922156220679188, 0.2586912245838972, 0.3381487772163038, 0.11724403791016597, 0.2660260610967385
--1.0, 0.10471095215734094, 0.11784389657061581, 0.3559421082891158, 0.09804847657594544, 0.1254109243014077, 0.19146782534905646, 0.1226960864980663, 0.10470187416003479, 0.12486261193624092, 0.26806682266137716, 0.09445119367349221, 0.18831370620444401, 0.14881019457605724, 0.09320810109878575, 0.26287899631928535, 0.16487209810537823, 0.2862301106477413, 0.3569157315337696, 0.14097165971294473, 0.29240151471441245
--0.9, 0.16653176250840415, 0.14261117417047503, 0.3711286203165235, 0.10451447616396557, 0.13672893790369386, 0.17397186461681544, 0.13950618425935557, 0.11962881800650256, 0.13532112249764602, 0.33251624828029747, 0.1333271104292841, 0.1880132880900507, 0.17356597453183156, 0.09600271474776914, 0.2762732845929412, 0.19882810159346917, 0.2946317292022259, 0.3458029824012993, 0.17097243714836555, 0.30519299793894217
--0.8, 0.18216326486601161, 0.1481166126979175, 0.38920137584956127, 0.1448425035965226, 0.17266817596306802, 0.1705475522038679, 0.14543582842744604, 0.1411865991233903, 0.16826523619240086, 0.34969193123052894, 0.13792312205956336, 0.17660006470960948, 0.1508601533241931, 0.13928281436120094, 0.28546912414691944, 0.22205248261772603, 0.28608788036539196, 0.3776271260853456, 0.2085729506292023, 0.3508923664023488
--0.7, 0.20706257983134127, 0.14498923255862617, 0.4039045121758598, 0.16502262534377904, 0.18200747910270168, 0.1796656040959095, 0.1828339831670307, 0.14006430173329298, 0.17722880843648822, 0.40602637804019415, 0.19208870413760687, 0.20103756165517514, 0.16068030422687993, 0.14737917887299626, 0.30017072859565097, 0.2453778124063592, 0.3758434186817855, 0.4166396449582368, 0.2656504380817383, 0.3849966085795739
--0.6, 0.26878520969503195, 0.1898213958783196, 0.3966200351536934, 0.1889243227230277, 0.21840314530861993, 0.18953899044836353, 0.1749524116454863, 0.16954614023894984, 0.18561960124427357, 0.4366361317346378, 0.2533124625236162, 0.2758317864502304, 0.18788493710351753, 0.15635930357987932, 0.28467632269189186, 0.2738579912969273, 0.41712051640679454, 0.4030474580654977, 0.3519208929150796, 0.3956505428542061
--0.5, 0.3266876450603623, 0.1533962969734891, 0.39367532478678585, 0.2097564751741763, 0.22567718877492554, 0.17924636950450673, 0.1876821919084617, 0.1921280471133581, 0.20586932016351703, 0.4231736143678883, 0.2685617078587691, 0.28285423904091667, 0.21793972492497368, 0.19514248243732124, 0.3038077255492445, 0.3006933176247424, 0.40251287875946895, 0.4004315331135224, 0.3765194656115878, 0.41014290750668664
--0.4, 0.36925951658267125, 0.21533522492738663, 0.4130097856368053, 0.26088857593547987, 0.2518087159548277, 0.2027223781883596, 0.21271176273796466, 0.23289600555602044, 0.2249252390716889, 0.4910338710615403, 0.29309953193432364, 0.33297188444900794, 0.24789606843639558, 0.2094778632875902, 0.3193330183262133, 0.3340305130827503, 0.4356538318574331, 0.4010163174505065, 0.3840359100804409, 0.435419535200561
--0.3, 0.39302330598155344, 0.22212166185643983, 0.38509139620484717, 0.2729108203263329, 0.2915040185394449, 0.20336141254369405, 0.22709413988454555, 0.2579383167202503, 0.2497859905932461, 0.48385612870279476, 0.31071055160279265, 0.3401373209903392, 0.28067982852103057, 0.24138580563101125, 0.32927790821294967, 0.34735946077670327, 0.4476935335311523, 0.39413249318859295, 0.4434453454981656, 0.42924807486349675
--0.2, 0.4241820471547197, 0.23741988234538525, 0.4019209106859252, 0.31772330356325984, 0.3308793822409245, 0.23534162361473762, 0.24579431132234678, 0.29680602088929914, 0.2538632670614676, 0.49385335960117327, 0.31568634772895066, 0.3596157490882689, 0.3478466380099695, 0.33407546996346005, 0.32915887765139495, 0.3605751987850893, 0.45302728895271893, 0.39599138055554517, 0.5043961652997092, 0.4254836682349764
--0.1, 0.4682568519400342, 0.2743938488084357, 0.40080783740413134, 0.36536924581726676, 0.35824923339869824, 0.2586707564164095, 0.2851530548226653, 0.3389486344225558, 0.3262928079838116, 0.5246492574566765, 0.32767275945648094, 0.3320887169947781, 0.4036548804953812, 0.35849712530802014, 0.37429386266895315, 0.41177632496929356, 0.5071763405758821, 0.3890180411024422, 0.48317042907980773, 0.43884342535831494
-0, 0.4760066833532794, 0.29142368406424746, 0.4097376655077463, 0.3996139267881248, 0.4129583389940792, 0.2990677692229131, 0.29206264764289325, 0.3979590035325254, 0.3390286026509915, 0.5391106554080464, 0.341473344165919, 0.40574080998755807, 0.4353209347871552, 0.3943150855096053, 0.40704078460962884, 0.4341710841163499, 0.4999329959302685, 0.37701616738559085, 0.4851722658329375, 0.4282225962428927
-0.1, 0.5069523142209985, 0.32045173735894766, 0.43943054067910325, 0.4500783405190095, 0.4463088966061854, 0.33498004021279043, 0.314117238583472, 0.4404494699510325, 0.37720680434478304, 0.5334843150901355, 0.3452645453185921, 0.3872967747572765, 0.48069368022005315, 0.43451533447019514, 0.4042149017841856, 0.44074948337526465, 0.5645105332382124, 0.391301707889661, 0.5381839083090824, 0.42214135730155083
-0.2, 0.5372188183130768, 0.3622253448858164, 0.4537456231757601, 0.4914992646217633, 0.4907496161088513, 0.36869086341462814, 0.3792618840543397, 0.4823919780011589, 0.4213466837302143, 0.5561735277928617, 0.39164035302244277, 0.39850216903169977, 0.5072785198236177, 0.4669456800973856, 0.42266885613250765, 0.44811416131714665, 0.5384354048372217, 0.42350840225167635, 0.5411180431191849, 0.42241346207277225
-0.3, 0.5422590543288226, 0.3936102529834667, 0.4719388562435195, 0.5098135590697281, 0.4846970438365943, 0.42932833384542446, 0.4081766539013263, 0.5271081551467797, 0.46396883586291016, 0.5682552481343182, 0.40012003417370945, 0.4756147601525173, 0.5187093542140269, 0.4852374582287011, 0.46395022142412456, 0.49621518629515043, 0.5746901596778067, 0.4390883586054801, 0.5663538842107534, 0.4449902496781928
-0.4, 0.560786918913391, 0.42729588204858165, 0.4974072417168863, 0.5326671638135232, 0.541282946728411, 0.4571696032356387, 0.4595785308704727, 0.5479170971416253, 0.507481046528753, 0.5852438928764292, 0.4353805511081842, 0.44923696962848636, 0.5566719953208911, 0.5124647328560527, 0.4817546592053216, 0.5044755694919174, 0.5339099620296387, 0.4518425124261185, 0.5272811752260287, 0.4697652716510595
-0.5, 0.5744378045610747, 0.4690055587091403, 0.5219380545725235, 0.563876624342628, 0.5311430270861439, 0.5211497450088437, 0.47491469476433407, 0.5505173062504392, 0.5328593951570615, 0.5722043073232816, 0.45540435331361423, 0.5469810224964171, 0.5643582979572157, 0.5448550325520948, 0.5031907095525162, 0.5278471733893954, 0.5959480619980039, 0.4777369616917495, 0.5553933445411702, 0.47995771734277226
-0.6, 0.5639297737278708, 0.5141003125671755, 0.538703546009715, 0.5623371422633722, 0.5631911492404065, 0.5347987286745954, 0.515029945429449, 0.5678942032743248, 0.5396797724924077, 0.5916863105787228, 0.45337342857859053, 0.49707243384673344, 0.5456535815455144, 0.5774351225346468, 0.5156364805993908, 0.5887550267010188, 0.5307738071181615, 0.4820634764991614, 0.5301369639819945, 0.5041629270466668
-0.7, 0.5711622829629622, 0.5442411383801996, 0.5393131746495888, 0.5747607070128602, 0.5601680761639166, 0.5616802362020841, 0.5516299058815765, 0.5951195049567524, 0.5402077339560376, 0.6042207052861757, 0.5083235023562449, 0.46938577973968715, 0.5537942840638256, 0.5738506023505662, 0.5410075641543021, 0.5870409279898986, 0.6528202070509034, 0.525440279570552, 0.5555769498467394, 0.5159826702420751
-0.8, 0.5532654708771879, 0.5566031972574961, 0.5745650412206081, 0.5906505429991028, 0.5935301173128968, 0.5851100349075697, 0.5571906660780338, 0.6171882752243507, 0.5600362305264932, 0.5919150691087891, 0.5143077549278957, 0.4394284502035009, 0.5738443725638256, 0.5771370958072388, 0.5267032038046119, 0.5621066992588855, 0.6806977035731592, 0.5407670645652837, 0.5710097103045972, 0.5216450516196541
-0.9, 0.5337811487002718, 0.5744269213878807, 0.5928954227491274, 0.6070519839277513, 0.5750995608936055, 0.5880846445545769, 0.5807006786314375, 0.6180757356051656, 0.5493812674459828, 0.5792001693409271, 0.5129275510520633, 0.5299519060200399, 0.5928075432875013, 0.5910413954552426, 0.5626894373127884, 0.5716505854372343, 0.5563717544298727, 0.5386725961954579, 0.5931043039217365, 0.543286997379019
-1.0, 0.6218230293172713, 0.5698786148188568, 0.5843796842641062, 0.6382382250960605, 0.6130237799046254, 0.6033966204269505, 0.6039974080127436, 0.631756393481903, 0.59133648036659, 0.5867655383172455, 0.5746061808817685, 0.5546532752864087, 0.582797069280666, 0.5972469046736386, 0.5668357571299345, 0.5817465041491754, 0.6530790613790189, 0.5626493280098616, 0.6568776230645619, 0.5520551511245354
-1.1, 0.6311034461436135, 0.5740637583679297, 0.5997309155179651, 0.6255823839807453, 0.6183287239533277, 0.6252743384247993, 0.5909485387552802, 0.6630773308408583, 0.5931475401969802, 0.5472081504358964, 0.5782594454016678, 0.49126271826835094, 0.5675287735078935, 0.6030667890908293, 0.5893962034486099, 0.6148888997200117, 0.6101022008992193, 0.5798834292331384, 0.6043943075459104, 0.5809033584508698
-1.2, 0.5979110757454935, 0.6061956298512101, 0.5849477629790879, 0.6479540437565685, 0.6405991994890016, 0.6133586880322605, 0.605403297548792, 0.6904428349494409, 0.6508407358436368, 0.6067516745613201, 0.6064636888987357, 0.5849102108867799, 0.5716938923337361, 0.6631060233835447, 0.6049348349292994, 0.6214559049843502, 0.6786831456764547, 0.5680291409689207, 0.6450682698203796, 0.5893204301507131
-1.3, 0.6120065022824229, 0.5857886433622049, 0.5687164078300544, 0.6227541755231224, 0.6209670992339907, 0.6193866878197734, 0.6147633608023009, 0.6552849509103524, 0.6182558351597499, 0.619746026387359, 0.5945193511103387, 0.620884841644958, 0.5897264169740138, 0.66649735568538, 0.6160968543755698, 0.6361083442656742, 0.547606052503761, 0.5786665043555567, 0.643741069074139, 0.6196412586927049
-1.4, 0.6564445265419007, 0.6374943675970933, 0.5494868671280374, 0.6323629518293681, 0.6683689839646909, 0.6477554794746432, 0.635903090724922, 0.6387613698314176, 0.6696992894418604, 0.5617225678840407, 0.6422570386538097, 0.6152387680812307, 0.6127605645968783, 0.6478187433383954, 0.6034584654246015, 0.6381864706870221, 0.5309823441001336, 0.5527866188327494, 0.5940912040485283, 0.5801941061954019
-1.5, 0.679792304606905, 0.6581187035071405, 0.6021606707107604, 0.6618031046396733, 0.6465726322971244, 0.5941358002947336, 0.6168352700704007, 0.689284307386844, 0.6907017835260635, 0.5845685867101986, 0.6056800111951075, 0.6001453923500057, 0.5504838565458684, 0.706703394205057, 0.6081994505499863, 0.659428436305752, 0.4316613731330781, 0.6002519588553407, 0.5720789615824655, 0.5972826140424782
-1.6, 0.6362556578502566, 0.6906803665094805, 0.6112841972562405, 0.6689567947603224, 0.6529858490213771, 0.6569493469282391, 0.6552581938693522, 0.6965041431992017, 0.6166660762512001, 0.59199199243101, 0.6421951148872854, 0.60234928411176, 0.6147954175399258, 0.6818035505954285, 0.6482290700157093, 0.6600345675995383, 0.4725884862003014, 0.6170079533362501, 0.6741412570387594, 0.6302223768608841
-1.7, 0.6088174702002407, 0.7545966520385297, 0.5734402717441957, 0.6384625010650541, 0.6563573224844883, 0.6523514760454125, 0.6391216749423991, 0.671583436429336, 0.676107952759963, 0.587028665878487, 0.6891516988266855, 0.59354447988984, 0.5669867871715156, 0.7201492632791218, 0.6888464225163634, 0.6628520030493678, 0.4879589415863469, 0.578931760794205, 0.6032112460909805, 0.5993345095129664
-1.8, 0.594740317891928, 0.7612733730105692, 0.6029858813907301, 0.5960090150857972, 0.6577297637477666, 0.6912411867595202, 0.646841146266542, 0.6657079734882466, 0.672091632216141, 0.5743546894161669, 0.70406874951115, 0.6371728013526968, 0.590298625412465, 0.6656314540846276, 0.6487889273867548, 0.6601364557014797, 0.41472505577703245, 0.6460065510988887, 0.637184610055848, 0.610982380460217
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+, 0.061032997065434115, 0.18533639985747144, 0.0145577041202563, 0.010942786101539745, 0.07387934237880509, 0.037536176376309634, 0.02763024311231824, 0.02265328277135838, 0.09520478453610436, 0.1595129075059143, 0.22597260291075094, 0.37063686634929416, 0.4028000965396746, 0.40189585160555535, 0.32174279329124866, 0.37195239626061044, 0.4539851836669101, 0.4666124404448917, 0.5233672984387059, 0.5443786020355682, 0.670588238862655, 0.6746727393780464, 0.774273657653073, 0.8059482440811514, 0.7534118409082837, 0.933769318652744, 0.9199396810574295
+800, -2.0, -1.8, -1.6, -1.4, -1.2, -1.0, -0.8, -0.6, -0.4, -0.2, 0.0, 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4
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+1000, -1.0, -0.8, -0.6, -0.4, -0.2, 0.0, 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2
+, 0.03892955516942246, 0.12043398243351962, 0.2645304545541721, 0.4365200127998329, 0.437088025611357, 0.35702064605615885, 0.4010590154472944, 0.36781079834103564, 0.4587836912312046, 0.39663279275577046, 0.6365005914806564, 0.5655098255829267, 0.593426197811947, 0.6692760067022221, 0.8622693278223753, 0.7184982472426565, 0.7060497525545142
+10000000, -1.4, -1.2, -1.0, -0.8, -0.6, -0.4, -0.2, 0.0, 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 2.0
+, 0.017728944142882157, 0.007167824432547233, 0.08493880095308559, 0.2528489732042521, 0.4813898894916351, 0.36070591557949294, 0.39824076805492237, 0.3119042195275812, 0.32650985724376896, 0.49659876345439163, 0.5211131565504622, 0.4260184611915101, 0.5637321616051639, 0.5428210040346628, 0.7687209074612477, 0.7000895494459963, 0.8891690518938169

diff --git a/src/jalview/schemes/HMMMatchScoreColourScheme.java b/src/jalview/schemes/HMMMatchScoreColourScheme.java
index cc8740b..0ee83a5 100644 (file)
--- a/src/jalview/schemes/HMMMatchScoreColourScheme.java
+++ b/src/jalview/schemes/HMMMatchScoreColourScheme.java
@@ -12,15 +12,22 @@ import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 
+
+
 public class HMMMatchScoreColourScheme extends ResidueColourScheme
 {
   
-  private Map<Character, Map<String, Double>> probabilities;
+  private Map<Character, Map<Integer, Map<String, Double>>> probabilities;
+
+  private List<Integer> ranges;
+
+  private static double binSize;
 
   public class MatchProbReader
   {
@@ -32,6 +39,7 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
               new FileReader("resources/ProbabilityOfMatch"));
     }
     
+    /*
     public Map<Character, Map<String, Double>>  getProbabilities() throws IOException
     {
       Map<Character, Map<String, Double>> probabilities = new HashMap<>();
@@ -55,12 +63,62 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
                           .valueOf(contents[i].replaceAll("\\ ", "")));
         }
         line = reader.readLine();
-
+    
       }
       reader.close();
       return probabilities;
     }
+    */
     
+    public Map<Character, Map<Integer, Map<String, Double>>> getProbabilities()
+            throws IOException
+    {
+
+      Map<Character, Map<Integer, Map<String, Double>>> probabilities = new HashMap<>();
+
+      ranges = new ArrayList<>();
+      ranges.add(0);
+
+      binSize = Double.valueOf((reader.readLine().replaceAll("\\ ", "")));
+      String line = reader.readLine();
+      char c = line.charAt(0);
+
+      while (line != null)
+      {
+        line = reader.readLine();
+        while (line != null && line.split("\\,").length != 1)
+        {
+          String[] llrs = line.split("\\,");
+          String[] counts = reader.readLine().split("\\,");
+          int range = Integer.valueOf(llrs[0]);
+
+          if (!ranges.contains(range))
+          {
+            ranges.add(range);
+          }
+          if (!probabilities.containsKey(c))
+          {
+            probabilities.put(c, new HashMap<>());
+          }
+          probabilities.get(c).put(range, new HashMap<>());
+
+          for (int i = 1; i < llrs.length; i++)
+          {
+            probabilities.get(c).get(range).put(
+                    llrs[i].replaceAll("\\ ", ""),
+                    Double.valueOf(counts[i].replaceAll("\\ ", "")));
+          }
+
+          line = reader.readLine();
+        }
+        if (line != null)
+        {
+          c = line.charAt(0);
+        }
+      }
+
+      return probabilities;
+    }
     
   }
 
@@ -109,10 +167,14 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
   public Color findColour(char symbol, int column, SequenceI seq,
           String consensusResidue, float pid)
   {
-    return findColour(symbol, column);
+    if (seq == null)
+    {
+      return null;
+    }
+    return findColour(symbol, column, seq.gapMap().length);
   }
 
-  // TODO change
+  // TODO change documentation
   /**
    * Returns the colour at a particular symbol at a column in the alignment:
    * <ul>
@@ -126,7 +188,7 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
    * @param column
    * @return
    */
-  private Color findColour(char symbol, int column)
+  private Color findColour(char symbol, int column, int length)
   {
     if (getHmm() == null || Comparison.isGap(symbol))
     {
@@ -144,16 +206,20 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
     double prob = 0;
     if (hmm.getBackgroundFrequencies().containsKey(symbol))
     {
+      int lengthBin = getLengthBin(length);
+
       double llr = Math
               .log(getHmm().getMatchEmissionProbability(column, symbol)
                       / hmm.getBackgroundFrequencies().get(symbol));
 
-      if (!probabilities.get(symbol).containsKey(format(llr)))
+      if (!probabilities.get(symbol).get(lengthBin)
+              .containsKey(format(llr)))
       {
-        return Color.green;
+        return Color.white;
       }
 
-      prob = probabilities.get(symbol).get(format(llr));
+
+      prob = probabilities.get(symbol).get(lengthBin).get(format(llr));
     }
     else
     {
@@ -179,12 +245,25 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
 
   public static String format(Double d)
   {
-    String formatted = String.format("%.1f", d);
+    String formatArg = String.valueOf(binSize);
+
+    // if bin size, need format "%.n" where n is number of decimal places
+    if (binSize < 1)
+    {
+      formatArg = "." + formatArg.split("\\.")[1].length();
+    }
+
+    Double rounded = Math.round(d / binSize) * binSize;
+    String formatted = String.format("%" + formatArg + "f", rounded);
+
+    // format sometimes returns a number rounded to 0 as -0
+    // this ensures output will always be 0
     if (Double.valueOf(formatted) == 0)
     {
       formatted = "0";
     }
     return formatted;
+
   }
 
   /**
@@ -273,7 +352,17 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme
     return JalviewColourScheme.HMMMatchScore.toString();
   }
 
-  
+  private int getLengthBin(int l)
+  {
+    for (int i = 1; i < ranges.size(); i++)
+    {
+      if (l >= ranges.get(i - 1) && l < ranges.get(i))
+      {
+        return ranges.get(i);
+      }
+    }
+    return -1;
+  }
 }