From 940b13e266be76ac186330c615c39989cce654c7 Mon Sep 17 00:00:00 2001 From: tva Date: Tue, 2 Jul 2019 10:31:17 +0100 Subject: [PATCH] JAL-2629 hmm match score colour scheme now colours by length --- resources/ProbabilityOfMatch | 399 +++++++++++++------- src/jalview/schemes/HMMMatchScoreColourScheme.java | 109 +++++- 2 files changed, 360 insertions(+), 148 deletions(-) diff --git a/resources/ProbabilityOfMatch b/resources/ProbabilityOfMatch index 3a0fa09..9e3869f 100644 --- 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, 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0.0, 0.0, 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, 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b/src/jalview/schemes/HMMMatchScoreColourScheme.java index cc8740b..0ee83a5 100644 --- 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> probabilities; + private Map>> probabilities; + + private List ranges; + + private static double binSize; public class MatchProbReader { @@ -32,6 +39,7 @@ public class HMMMatchScoreColourScheme extends ResidueColourScheme new FileReader("resources/ProbabilityOfMatch")); } + /* public Map> getProbabilities() throws IOException { Map> 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>> getProbabilities() + throws IOException + { + + Map>> 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: *
    @@ -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; + } } -- 1.7.10.2