R/privateUtilities.R

Defines functions grid.eti makeLeaveNames getParentNode getPFMid getoffsetPosByIC_old getoffsetPosByIC ungappedScore SWU checkALLR getALLRbyBase getICbyBase getAlignedICWithoutGap UngappedAlignmentAA UngappedAlignment getIE addPseudolog2 coloredSymbols importSVG colalpha hex2psrgb checkInteger

checkInteger <- function(N){
    !length(grep("[^[:digit:]]", as.character(N)))
}

#' @importFrom grDevices col2rgb
hex2psrgb<-function(col){
    col<-col2rgb(col)
    col<-col/255
    col<-paste(col,collapse=" ")
    col
}

#' @importFrom grDevices col2rgb rgb
colalpha <- function(col, alpha){
  col<-col2rgb(col)
  rgb(t(col), alpha = round(alpha*255), maxColorValue = 255)
}

#' @importFrom grDevices svg dev.off
#' @importFrom grid convertHeight stringHeight grid.text gpar polygonGrob
#' @importFrom utils install.packages
importSVG <- function(font, color, ch, fontface="bold", envir=.globals){
  if(capabilities("cairo") && !requireNamespace("grImport2", quietly = TRUE)){
    ## install grImport2
    install.packages("grImport2", repos = "https://cloud.r-project.org",
                     quiet = TRUE)
  }
  if(capabilities("cairo") && requireNamespace("grImport2", quietly = TRUE)){
    psfilename<-tempfile(fileext = ".svg")
    svg(psfilename, width = 1, height = 1, bg = NA, pointsize=72, family = font)
    h <- convertHeight(stringHeight(ch), unitTo = "points", valueOnly = TRUE)
    grid.text(ch, gp = gpar(fontsize=floor(1.05*72*(72/h)), 
                            fontfamily=font, col=color, fontface=fontface))
    dev.off()
    x <- grImport2::readPicture(psfilename)
    unlink(psfilename)
    assign("pictureGrob", grImport2::pictureGrob, envir=envir)
    return(x)
  }
  checkGhost <- function(){
    # get ghostscript path
    gscmd <- Sys.getenv("R_GSCMD")
    if(is.null(gscmd) || !nzchar(gscmd)) {
      if(.Platform$OS.type=="windows"){
        poss <- Sys.which(c("gswin64c.exe",
                            "gswin32c.exe"))
        poss <- poss[nzchar(poss)]
        return(length(poss)>0)
      }else{
        gscmd <- "gs"
      }
    }
    suppressWarnings(rc <- system(paste(shQuote(gscmd), "-help > /dev/null")))
    return(rc == 0) 
  }
  if(checkGhost() && !requireNamespace("grImport", quietly = TRUE)){
    ## install grImport
    install.packages("grImport", repos = "https://cloud.r-project.org",
                     quiet = TRUE)
  }
  if(checkGhost() && requireNamespace("grImport", quietly = TRUE)){
    motifStack_private_fontsize <- 18
    ps<-paste("%!PS\n/",font,
              " findfont\n",motifStack_private_fontsize,
              " scalefont\n",
              hex2psrgb(color),
              " setrgbcolor\nsetfont\nnewpath\n0 0 moveto\n(",
              ch,") show",sep="")
    psfilename<-tempfile()
    psfilename <- gsub("\\", "/", psfilename, fixed=TRUE)
    # step1 create a ps file
    cat(ps,file=paste(psfilename,".ps",sep=""))
    # step2 convert it by grImport::PostScriptTrace
    grImport::PostScriptTrace(paste(psfilename,".ps",sep=""), 
                              paste(psfilename,".xml",sep=""))
    # step3 read by grImport::readPicture
    x<-grImport::readPicture(paste(psfilename,".xml",sep=""))
    unlink(c(paste(psfilename,".ps",sep=""), 
             paste("capture",basename(psfilename),".ps",sep=""), 
             paste(psfilename,".xml",sep="")))
    assign("pictureGrob", grImport::pictureGrob, envir=envir)
    return(x)
  }
  warning("No import funciton (grImport or grImport2) available.",
          "Use predefined fonts.")
  assign("pictureGrob", function(picture, x = .5, y = .5,
                                 width = 1, height = 1, 
                                 just = "centre", distort = TRUE){
    ## plot
    gl <- gList()
    for(i in seq_along(picture)){
      gl <- gList(gl, polygonGrob(picture[[i]]$x*width+x,
                                  picture[[i]]$y*height+y,
                                  gp = gpar(fill=picture[[i]]$color,
                                            col=picture[[i]]$color)))
    }
    return(gl)
  }, envir=envir)
  letterPolygon <- 
    list(A=list(list(color="black", 
                     x=c(0.95,0.734703,0.6673312,0.3334011,0.2660293,
                         0.05,0.3744101,0.6263222,0.95),
                     y=c(0,0,0.2446256,0.2446256,0,0,1,1,0)),
                list(color="white",  
                     x=c(0.5003662,0.5000439,0.4996631,0.4992238,0.4987258,
                         0.4981692,0.4975541,0.4968804,0.4961481,0.4953572,
                         0.4945077,0.4945077,0.4937535,0.4929552,0.4921131,
                         0.491227,0.490297,0.489323,0.4883051,0.4872433,
                         0.4861375,0.4849878,0.4849878,0.4838015,0.4825858,
                         0.4813409,0.4800667,0.4787632,0.4774304,0.4760683,
                         0.474677,0.4732563,0.4718063,0.4718063,0.4704809,
                         0.4691408,0.467786,0.4664166,0.4650325,0.4636338,
                         0.4622205,0.4607925,0.4593499,0.4578926,0.4578926,
                         0.3788039,0.6219284,0.5428397,0.5413751,0.5399105,
                         0.5384459,0.5369813,0.5355167,0.5340521,0.5325875,
                         0.5311229,0.5296583,0.5281937,0.5281937,0.5268828,
                         0.5255867,0.5243051,0.5230382,0.521786,0.5205484,
                         0.5193255,0.5181172,0.5169235,0.5157445,0.5157445,
                         0.5145875,0.5134597,0.5123613,0.5112921,0.5102522,
                         0.5092417,0.5082604,0.5073084,0.5063857,0.5054923,
                         0.5054923,0.5047819,0.5041155,0.5034931,0.5029146,
                         0.50238,0.5018893,0.5014426,0.5010399,0.500681,
                         0.5003662,0.5003662),
                     y=c(0.8650852,0.8634915,0.8616753,0.8596368,0.8573758,
                         0.8548925,0.8521868,0.8492587,0.8461082,0.8427354,
                         0.8391401,0.8391401,0.8353818,0.8315196,0.8275537,
                         0.8234841,0.8193106,0.8150334,0.8106523,0.8061675,
                         0.8015789,0.7968866,0.7968866,0.7920979,0.7872202,
                         0.7822535,0.7771979,0.7720534,0.7668199,0.7614974,
                         0.756086,0.7505856,0.7449963,0.7449963,0.7395182,
                         0.7340549,0.7286064,0.7231727,0.7177539,0.7123499,
                         0.7069607,0.7015864,0.6962268,0.6908821,0.6908821,
                         0.409192,0.409192,0.6908821,0.6962268,0.7015864,
                         0.7069607,0.7123499,0.7177539,0.7231727,0.7286064,
                         0.7340549,0.7395182,0.7449963,0.7449963,0.7505856,
                         0.756086,0.7614974,0.7668199,0.7720534,0.7771979,
                         0.7822535,0.7872202,0.7920979,0.7968866,0.7968866,
                         0.8015789,0.8061675,0.8106523,0.8150334,0.8193106,
                         0.8234841,0.8275537,0.8315196,0.8353818,0.8391401,
                         0.8391401,0.8427354,0.8461082,0.8492587,0.8521868,
                         0.8548925,0.8573758,0.8596368,0.8616753,0.8634915,
                         0.8650852,0.8650852))
                ),
         B=list(list(color="black", 
                     x=c(0.95,0.949674,0.9486959,0.9470658,0.9447836,
                         0.9418494,0.9382631,0.9340248,0.9291344,0.923592,
                         0.9173975,0.9173975,0.910654,0.9034643,0.8958284,
                         0.8877464,0.8792183,0.870244,0.8608236,0.8509571,
                         0.8406444,0.8298856,0.8298856,0.8187235,0.8072011,
                         0.7953184,0.7830753,0.7704719,0.7575081,0.744184,
                         0.7304995,0.7164547,0.7020496,0.7020496,0.68755,
                         0.6728789,0.6580362,0.6430219,0.627836,0.6124786,
                         0.5969495,0.5812488,0.5653765,0.5493327,0.5493327,
                         0.05,0.05,0.500429,0.5180858,0.5353651,
                         0.5522669,0.5687912,0.584938,0.6007073,0.6160991,
                         0.6311134,0.6457502,0.6600095,0.6600095,0.6738656,
                         0.6872927,0.7002908,0.7128599,0.725,0.7367112,
                         0.7479933,0.7588465,0.7692707,0.779266,0.779266,
                         0.7888151,0.7979009,0.8065234,0.8146826,0.8223785,
                         0.8296111,0.8363804,0.8426864,0.8485291,0.8539085,
                         0.8539085,0.8589619,0.8634833,0.8674728,0.8709304,
                         0.8738561,0.8762498,0.8781115,0.8794414,0.8802393,
                         0.8805052,0.8805052,0.879939,0.8782402,0.875409,
                         0.8714452,0.8663489,0.8601201,0.8527588,0.844265,
                         0.8346387,0.8238799,0.8238799,0.8119457,0.7987931,
                         0.7844223,0.7688332,0.7520257,0.734,0.714756,
                         0.6942936,0.672613,0.649714,0.649714,0.6783527,
                         0.7055844,0.731409,0.7558265,0.778837,0.8004404,
                         0.8206368,0.8394261,0.8568084,0.8727836,0.8727836,
                         0.8874547,0.9005815,0.912164,0.9222021,0.9306959,
                         0.9376454,0.9430505,0.9469113,0.9492278,0.95,
                         0.95),
                     y=c(0.2853966,0.2703484,0.255745,0.2415864,0.2278725,
                         0.2146034,0.2017791,0.1893996,0.1774648,0.1659748,
                         0.1549296,0.1549296,0.1442995,0.1340549,0.1241957,
                         0.114722,0.1056338,0.09693106,0.08861379,0.08068199,
                         0.07313566,0.0659748,0.0659748,0.05933284,0.0530467,
                         0.04711638,0.04154188,0.0363232,0.03146034,0.0269533,
                         0.02280208,0.01900667,0.01556709,0.01556709,0.01260934,
                         0.009962936,0.007627872,0.005604151,0.003891772,
                         0.002490734,0.001401038,0.0006226835,0.0001556709,0,0,
                         0,1,1,0.9998443,0.9993773,0.998599,0.9975093,0.9961082,
                         0.9943958,0.9923721,0.9900371,0.9873907,0.9844329,
                         0.9844329,0.9813047,0.9778503,0.9740697,0.9699629,
                         0.96553,0.9607709,0.9556857,0.9502743,0.9445367,
                         0.9384729,0.9384729,0.932083,0.9253669,0.9183247,
                         0.9109563,0.9032617,0.8952409,0.886894,0.8782209,
                         0.8692216,0.8598962,0.8598962,0.8502446,0.8402669,
                         0.8299629,0.8193328,0.8083766,0.7970941,0.7854855,
                         0.7735508,0.7612898,0.7487027,0.7487027,0.7319199,
                         0.7156709,0.6999555,0.6847739,0.670126,0.6560119,
                         0.6424314,0.6293847,0.6168718,0.6048925,0.6048925,
                         0.5936916,0.5832172,0.5734692,0.5644477,0.5561527,
                         0.5485841,0.541742,0.5356264,0.5302372,0.5255745,
                         0.5255745,0.5224166,0.5182802,0.5131653,0.5070719,0.5,
                         0.4919496,0.4829207,0.4729133,0.4619274,0.4499629,
                         0.4499629,0.437109,0.4234544,0.4089993,0.3937435,
                         0.3776872,0.3608302,0.3431727,0.3247146,0.3054559,
                         0.2853966,0.2853966)),
                list(color="white",  
                     x=c(0.6256911,0.6253051,0.6241468,0.6222164,0.6195138,
                         0.6160391,0.6117922,0.6067731,0.6009819,0.5944185,
                         0.5870829,0.5870829,0.5790867,0.5705415,0.5614471,
                         0.5518036,0.5416111,0.5308694,0.5195786,0.5077388,
                         0.4953499,0.4824118,0.4824118,0.3030982,0.3030982,
                         0.4841277,0.4976921,0.5105872,0.5228132,0.5343699,
                         0.5452574,0.5554757,0.5650248,0.5739047,0.5821153,
                         0.5896568,0.5896568,0.5965033,0.6026292,0.6080343,
                         0.6127188,0.6166826,0.6199256,0.622448,0.6242498,
                         0.6253308,0.6256911,0.6256911,NA,0.6951859,
                         0.69504,0.6946025,0.6938732,0.6928522,0.6915396,
                         0.6899352,0.6880391,0.6858513,0.6833718,0.6806006,
                         0.6806006,0.6775806,0.6743546,0.6709228,0.667285,
                         0.6634414,0.6593918,0.6551363,0.6506749,0.6460076,
                         0.6411344,0.6411344,0.636244,0.6311821,0.6259485,
                         0.6205434,0.6149666,0.6092183,0.6032984,0.5972069,
                         0.5909438,0.5845091,0.5845091,0.5781258,0.571674,
                         0.5651535,0.5585643,0.5519066,0.5451802,0.5383851,
                         0.5315214,0.5245891,0.5175882,0.5175882,0.3030982,
                         0.3030982,0.5235939,0.5304233,0.537184,0.5438761,
                         0.5504995,0.5570543,0.5635405,0.5699581,0.576307,
                         0.5825872,0.5887989,0.5887989,0.595062,0.6011535,
                         0.6070734,0.6128217,0.6183985,0.6238036,0.6290372,
                         0.6340991,0.6389895,0.6437083,0.6437083,0.6484099,
                         0.6529056,0.6571954,0.6612793,0.6651573,0.6688294,
                         0.6722955,0.6755558,0.6786101,0.6814585,0.6814585,
                         0.6840667,0.6864004,0.6884595,0.690244,0.6917541,
                         0.6929895,0.6939504,0.6946368,0.6950486,0.6951859,
                         0.6951859),
                     y=c(0.7190511,0.7315715,0.7433358,0.754344,0.764596,
                         0.7740919,0.7828317,0.7908154,0.798043,0.8045145,
                         0.8102298,0.8102298,0.8154411,0.8201038,0.8242179,
                         0.8277835,0.8308006,0.8332691,0.835189,0.8365604,
                         0.8373832,0.8376575,0.8376575,0.8376575,0.6011861,
                         0.6011861,0.6014826,0.6023721,0.6038547,0.6059303,
                         0.608599,0.6118606,0.6157153,0.6201631,0.6252039,
                         0.6308377,0.6308377,0.6370571,0.6438547,0.6512305,
                         0.6591846,0.6677168,0.6768273,0.6865159,0.6967828,
                         0.7076279,0.7190511,0.7190511,NA,0.3039288,
                         0.3115122,0.3188436,0.3259229,0.3327502,0.3393254,
                         0.3456486,0.3517198,0.3575389,0.363106,0.3684211,
                         0.3684211,0.3735063,0.378384,0.3830541,0.3875167,
                         0.3917717,0.3958191,0.399659,0.4032913,0.4067161,
                         0.4099333,0.4099333,0.4130986,0.4160712,0.418851,
                         0.4214381,0.4238325,0.4260341,0.428043,0.4298592,
                         0.4314826,0.4329133,0.4329133,0.4341809,0.435315,
                         0.4363158,0.4371831,0.437917,0.4385174,0.4389844,
                         0.439318,0.4395182,0.4395849,0.4395849,0.4395849,
                         0.1623425,0.1623425,0.1624092,0.1626093,0.1629429,
                         0.1634099,0.1640104,0.1647443,0.1656116,0.1666123,
                         0.1677465,0.1690141,0.1690141,0.1704374,0.1720385,
                         0.1738176,0.1757746,0.1779096,0.1802224,0.1827131,
                         0.1853818,0.1882283,0.1912528,0.1912528,0.1946256,
                         0.1982209,0.2020385,0.2060786,0.210341,0.2148258,
                         0.219533,0.2244626,0.2296145,0.2349889,0.2349889,
                         0.2406153,0.2465234,0.2527131,0.2591846,0.2659377,
                         0.2729726,0.2802891,0.2878873,0.2957672,0.3039288,
                         0.3039288)),
                list(color="white",  
                     x=c(0.6951859,0.69504,0.6946025,0.6938732,0.6928522,
                         0.6915396,0.6899352,0.6880391,0.6858513,0.6833718,
                         0.6806006,0.6806006,0.6775806,0.6743546,0.6709228,
                         0.667285,0.6634414,0.6593918,0.6551363,0.6506749,
                         0.6460076,0.6411344,0.6411344,0.636244,0.6311821,
                         0.6259485,0.6205434,0.6149666,0.6092183,0.6032984,
                         0.5972069,0.5909438,0.5845091,0.5845091,0.5781258,
                         0.571674,0.5651535,0.5585643,0.5519066,0.5451802,
                         0.5383851,0.5315214,0.5245891,0.5175882,0.5175882,
                         0.3030982,0.3030982,0.5235939,0.5304233,0.537184,
                         0.5438761,0.5504995,0.5570543,0.5635405,0.5699581,
                         0.576307,0.5825872,0.5887989,0.5887989,0.595062,
                         0.6011535,0.6070734,0.6128217,0.6183985,0.6238036,
                         0.6290372,0.6340991,0.6389895,0.6437083,0.6437083,
                         0.6484099,0.6529056,0.6571954,0.6612793,0.6651573,
                         0.6688294,0.6722955,0.6755558,0.6786101,0.6814585,
                         0.6814585,0.6840667,0.6864004,0.6884595,0.690244,
                         0.6917541,0.6929895,0.6939504,0.6946368,0.6950486,
                         0.6951859,0.6951859),
                     y=c(0.3039288,0.3115122,0.3188436,0.3259229,0.3327502,
                         0.3393254,0.3456486,0.3517198,0.3575389,0.363106,
                         0.3684211,0.3684211,0.3735063,0.378384,0.3830541,
                         0.3875167,0.3917717,0.3958191,0.399659,0.4032913,
                         0.4067161,0.4099333,0.4099333,0.4130986,0.4160712,
                         0.418851,0.4214381,0.4238325,0.4260341,0.428043,
                         0.4298592,0.4314826,0.4329133,0.4329133,0.4341809,
                         0.435315,0.4363158,0.4371831,0.437917,0.4385174,
                         0.4389844,0.439318,0.4395182,0.4395849,0.4395849,
                         0.4395849,0.1623425,0.1623425,0.1624092,0.1626093,
                         0.1629429,0.1634099,0.1640104,0.1647443,0.1656116,
                         0.1666123,0.1677465,0.1690141,0.1690141,0.1704374,
                         0.1720385,0.1738176,0.1757746,0.1779096,0.1802224,
                         0.1827131,0.1853818,0.1882283,0.1912528,0.1912528,
                         0.1946256,0.1982209,0.2020385,0.2060786,0.210341,
                         0.2148258,0.219533,0.2244626,0.2296145,0.2349889,
                         0.2349889,0.2406153,0.2465234,0.2527131,0.2591846,
                         0.2659377,0.2729726,0.2802891,0.2878873,0.2957672,
                         0.3039288,0.3039288))
                ),
         C=list(list(color="black", 
                     x=c(0.2972527,0.2978297,0.2995604,0.3024451,0.3064835,
                         0.3116758,0.318022,0.325522,0.3341758,0.3439835,
                         0.3549451,0.3549451,0.3670522,0.3802967,0.3946786,
                         0.4101978,0.4268544,0.4446484,0.4635797,0.4836484,
                         0.5048544,0.5271978,0.5271978,0.5345495,0.5417692,
                         0.5488571,0.5558132,0.5626374,0.5693297,0.5758901,
                         0.5823187,0.5886154,0.5947802,0.5947802,0.6008132,
                         0.6067143,0.6124835,0.6181209,0.6236264,0.629,
                         0.6342418,0.6393516,0.6443297,0.6491758,0.6491758,
                         0.6540549,0.6588022,0.6634176,0.6679011,0.6722527,
                         0.6764725,0.6805604,0.6845165,0.6883407,0.692033,
                         0.692033,0.6957747,0.6994176,0.7029615,0.7064066,
                         0.7097527,0.713,0.7161484,0.7191978,0.7221484,
                         0.725,0.725,0.95,0.9447582,0.9392527,
                         0.9334835,0.9274505,0.9211538,0.9145934,0.9077692,
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                         0.2763516,0.2930989,0.3104396,0.3104396,0.3283901,
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                         0.6138681,0.6284396,0.6426154,0.6563956,0.6697802,
                         0.6697802,0.6829588,0.6957912,0.7082775,0.7204176,
                         0.7322115,0.7436593,0.754761,0.7655165,0.7759258,
                         0.785989,0.785989,0.7958874,0.8054725,0.8147445,
                         0.8237033,0.8323489,0.8406813,0.8487005,0.8564066,
                         0.8637995,0.8708791,0.8708791,0.8776703,0.8841978,
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                         0.3426484,0.3331209,0.3247143,0.3174286,0.3112637,
                         0.3062198,0.3022967,0.2994945,0.2978132,0.2972527,
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                         0.2546763,0.2546763,0.238,0.2230791,0.2099137,
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                         0.4167194,0.4379928,0.4596835,0.4817914,0.5043165,
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                         0.617446,0.6383885,0.6587698,0.6785899,0.6978489,
                         0.7165468,0.7165468,0.7346763,0.7522302,0.7692086,
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                         0.9071439,0.9176403,0.927518,0.936777,0.9454173,
                         0.9534388,0.9608417,0.9676259,0.9676259,0.973777,
                         0.9792806,0.9841367,0.9883453,0.9919065,0.9948201,
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                         0.9208633,0.9208633,0.9133741,0.9055827,0.8974892,
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                         0.8425827,0.8323741,0.8323741,0.8220576,0.8115396,
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                         0.7442014,0.7322734,0.7201439,0.7201439,0.6726619,
                         0.679518,0.6862734,0.6929281,0.699482,0.7059353,
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                         0.7642086,0.7692374,0.7741079,0.7788201,0.7833741,
                         0.7877698,0.7877698,0.7919856,0.796,0.7998129,
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                         0.8184604,0.8208633,0.8208633,0.8231871,0.8252662,
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                         0.732295,0.7133525,0.6928129,0.6706763,0.6469424,
                         0.6216115,0.5946835,0.5661583,0.536036,0.5043165,
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                         0.6054438,0.5845858,0.5631953,0.5412722,0.5188166,
                         0.4958284,0.4723077,0.4482544,0.4236686,0.4236686,
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                         0.4516805,0.4774911,0.5026627,0.5271953,0.5510888,
                         0.5743432,0.5969586,0.6189349,0.6189349,0.6402456,
                         0.6608639,0.6807899,0.7000237,0.7185651,0.7364142,
                         0.753571,0.7700355,0.7858077,0.8008876,0.8008876,
                         0.8152574,0.8288994,0.8418136,0.854,0.8654586,
                         0.8761893,0.8861923,0.8954675,0.9040148,0.9118343,
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                         0.9404586,0.9438935,0.9465651,0.9484734,0.9496183,
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                         0.2883617,0.2883617,0.2696887,0.2516234,0.234166,
                         0.2173165,0.2010749,0.1854411,0.1704151,0.155997,
                         0.1421868,0.1289844,0.1289844,0.1165456,0.1047294,
                         0.093536,0.0829652,0.073017,0.0636916,0.0549889,
                         0.0469088,0.0394514,0.0326168,0.0326168,0.0264196,
                         0.0208747,0.0159822,0.011742,0.0081542,0.0052187,
                         0.0029355,0.0013047,0.0003262,0,0,
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                         0.9973981,0.9953744,0.9927724,0.9895923,0.985834,
                         0.9814974,0.9765827,0.9710897,0.9710897,0.9649963,
                         0.9582802,0.9509414,0.94298,0.9343958,0.925189,
                         0.9153595,0.9049073,0.8938325,0.8821349,0.8821349,
                         0.8697924,0.8567828,0.843106,0.828762,0.8137509,
                         0.7980726,0.7817272,0.7647146,0.7470348,0.7286879,
                         0.7286879,0.7097999,0.6902001,0.6698888,0.6488658,
                         0.6271312,0.604685,0.5815271,0.5576575,0.5330764,
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                         0.6553002,0.6553002,0.6673758,0.6789918,0.6901483,
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                         0.5710639,0.5771183,0.5830868,0.5889695,0.5947662,
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                         0.6652977,0.6694542,0.6734733,0.677355,0.6810992,
                         0.6847061,0.6881756,0.6915076,0.6915076,0.6948655,
                         0.6980687,0.7011174,0.7040115,0.706751,0.7093359,
                         0.7117662,0.714042,0.7161632,0.7181298,0.7181298,
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                         0.1883597,0.1899281,0.1899281,0.1916547,0.1933813,
                         0.1951079,0.1968345,0.1985612,0.2002878,0.2020144,
                         0.203741,0.2054676,0.2071942,0.2071942,0.209036,
                         0.2108201,0.2125468,0.2142158,0.2158273,0.2173813,
                         0.2188777,0.2203165,0.2216978,0.2230216,0.2230216,
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                     y=c(0,0.4255004,0.4255004,0,0,
                         1,1,0.6063751,0.6063751,1,
                         1,0,0))
                ),
         I=list(list(color="black", 
                     x=c(0.164878,0.835122,0.835122,0.607561,0.607561,
                         0.835122,0.835122,0.164878,0.164878,0.392439,
                         0.392439,0.164878,0.164878),
                     y=c(1,1,0.8309859,0.8309859,0.1690141,
                         0.1690141,0,0,0.1690141,0.1690141,
                         0.8309859,0.8309859,1))
                ),
         J=list(list(color="black", 
                     x=c(0.5034351,0.4841985,0.4653544,0.4469029,0.4288441,
                         0.4111778,0.393904,0.3770229,0.3605344,0.3444384,
                         0.328735,0.328735,0.313434,0.2985453,0.2840687,
                         0.2700044,0.2563522,0.2431123,0.2302846,0.2178691,
                         0.2058659,0.1942748,0.1942748,0.183096,0.1723293,
                         0.1619749,0.1520327,0.1425027,0.133385,0.1246794,
                         0.116386,0.1085049,0.101036,0.101036,0.0939891,
                         0.087374,0.0811908,0.0754395,0.07012,0.0652323,
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                         0.3356052,0.3397764,0.3444384,0.3495911,0.3552345,
                         0.3613686,0.3679935,0.3751091,0.3827154,0.3908124,
                         0.3994002,0.3994002,0.40841,0.4177732,0.4274896,
                         0.4375594,0.4479826,0.458759,0.4698888,0.4813719,
                         0.4932083,0.505398,0.505398,0.5194329,0.532879,
                         0.5457361,0.5580044,0.5696838,0.5807743,0.5912759,
                         0.6011887,0.6105125,0.6192475,0.6192475,0.6272661,
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                         0.6614504,0.3660305,0.3660305,0.95,0.95,
                         0.9496957,0.948783,0.9472617,0.945132,0.9423937,
                         0.9390469,0.9350916,0.9305278,0.9253555,0.9195747,
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                         0.2654346,0.2793864,0.2936596,0.3082542,0.3082542,
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                         0.2644266,0.2520088,0.2404675,0.2298028,0.2200146,
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                         0.172615,0.1756318,0.1795106,0.1842513,0.1898539,
                         0.1963185,0.203645,0.2118335,0.2118335,0.2208254,
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                         0.2904237,0.3046311,0.3195836,0.3352812,0.3352812,
                         0.8312637,0.8312637,1,1,0.3403944,
                         0.3249087,0.3097151,0.2948137,0.2802045,0.2658875,
                         0.2518627,0.23813,0.2246896,0.2115413,0.1986852,
                         0.1986852,0.1863039,0.1742878,0.162637,0.1513514,
                         0.140431,0.1298758,0.1196859,0.1098612,0.1004018,
                         0.0913075,0.0913075,0.0827392,0.0745654,0.066786,
                         0.059401,0.0524105,0.0458145,0.0396129,0.0338057,
                         0.028393,0.0233747,0.0233747,0.0189335,0.0149598,
                         0.0114536,0.0084149,0.0058437,0.00374,0.0021037,
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                ),
         K=list(list(color="black", 
                     x=c(0.6634492,0.397484,0.2929094,0.2929094,0.05,
                         0.05,0.2929094,0.2929094,0.6519213,0.934355,
                         0.555581,0.95,0.6634492),
                     y=c(0,0.4128984,0.3076353,0,0,
                         1,1,0.5559674,1,1,
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                     x=c(0.05,0.05,0.341438,0.341438,0.95,
                         0.95,0.05),
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                         0.7564869,0.756644,0.7568361,0.757063,0.7573249,
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                         0.7595247,0.7600485,0.7605723,0.761096,0.7616198,
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                         0.6738028,0.6661898,0.6585915,0.6510082,0.6434396,
                         0.6434396,0,0,1,1,
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                         0.5590215,0.5533729,0.5477539,0.5421646,0.5366049,
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                         0.6293551,0.6293551,1,1,0,
                         0))
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                         0.9228483,0.9108696,0.8966548,0.8802041,0.8615173,
                         0.8405945,0.8174357,0.7920408,0.7644099,0.734543,
                         0.7024401,0.6680692,0.6313984,0.5924277,0.5511571,
                         0.5075865,0.435299,0.3685697,0.3073984,0.2517853,
                         0.2017303,0.1578403,0.1207223,0.0903762,0.0668021,
                         0.05,0.2775954,0.2865395,0.2986779,0.3140106,
                         0.3325377,0.3542591,0.3793026,0.4077959,0.4397391,
                         0.4751322,0.5139752,0.5327258,0.550646,0.5677356,
                         0.5839947,0.5994232,0.6143088,0.6282999,0.6413966,
                         0.6535989,0.6649068,0.6752564,0.6845839,0.6928891,
                         0.7001721,0.706433,0.7116078,0.7156327,0.7185075,
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                         0.7469051,0.7902839,0.8276894,0.8594091,0.8854428,
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                         0.703622,0.721063,0.7383762,0.7554339,0.7721083,
                         0.7883993,0.804307,0.8198314,0.8347808,0.8489636,
                         0.8623798,0.8750293,0.8869122,0.8979326,0.9079947,
                         0.9170985,0.925244,0.9324312,0.938756,0.9436752,
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                         0.1776978,0.1566906,0.1368345,0.1181295,0.1005755,
                         0.0841727,0.069036,0.0552806,0.0429065,0.0319137,
                         0.0223022,0.0142734,0.0080288,0.0035683,0.0008921,
                         0,0.0028489,0.0113957,0.0256403,0.0455827,
                         0.071223,0.1023022,0.1385612,0.18,0.2266187,
                         0.2784173,0.305036,0.2791079,0.2554245,0.2339856,
                         0.2147914,0.1978417,0.1838561,0.1729784,0.1652086,
                         0.1605468,0.1589928,0.1592518,0.1600288,0.1613237,
                         0.1631367,0.1654676,0.1683741,0.1719137,0.1760863,
                         0.1808921,0.1863309,0.1924604,0.1993381,0.206964,
                         0.2153381,0.2244604,0.2346475,0.2456403,0.2574388,
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                         0.3810647,0.3877698,0.3941295,0.3999712,0.405295,
                         0.4101007,0.4143885,0.418705,0.4230216,0.4273381,
                         0.4316547,0.4359712,0.4397698,0.4436835,0.4477122,
                         0.4518561,0.4561151,0.4608921,0.4660144,0.471482,
                         0.477295,0.4834532,0.4899856,0.4969209,0.504259,
                         0.512,0.5201439,0.5290935,0.5386763,0.5488921,
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                         0.6239424,0.6388489,0.6548201,0.6716547,0.6893525,
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                         0.8277122,0.8489209,0.8688921,0.8873669,0.9043453,
                         0.9198273,0.9338129,0.9466187,0.9579856,0.9679137,
                         0.9764029,0.9834532,0.9894101,0.9940432,0.9973525,
                         0.9993381,1,0.9974388,0.9897554,0.9769496,
                         0.9590216,0.9359712,0.9078273,0.8740432,0.8346187,
                         0.789554,0.7388489,0.7179856,0.7428777,0.7651799,
                         0.7848921,0.8020144,0.8165468,0.8284604,0.8377266,
                         0.8443453,0.8483165,0.8496403,0.8492662,0.8481439,
                         0.8462734,0.8436547,0.8402878,0.8365468,0.8322302,
                         0.8273381,0.8218705,0.8158273,0.8095827,0.8029353,
                         0.7958849,0.7884317,0.7805755,0.7727194,0.7646906,
                         0.7564892,0.7481151,0.7395683,0.7262158,0.7137842,
                         0.7022734,0.6916835,0.6820144,0.6733813,0.6653237,
                         0.6578417,0.6509353,0.6446043,0.6387338,0.6332086,
                         0.6280288,0.6231942,0.618705,0.6146763,0.6106475,
                         0.6066187,0.6025899,0.5985612,0.594705,0.5906187,
                         0.5863022,0.5817554,0.5769784,0.5721727,0.566964,
                         0.5613525,0.5553381,0.5489209,0.5423309,0.535223,
                         0.5275971,0.5194532,0.5107914,0.5018129,0.4921439,
                         0.4817842,0.4707338,0.4589928,0.4465036,0.4332086,
                         0.4191079,0.4042014,0.3884892,0.3718849,0.3543022,
                         0.335741,0.3162014,0.2956835))
                ),
         T=list(list(color="black", 
                     x=c(0.6199187,0.6199187,0.3800813,0.3800813,0.05,
                         0.05,0.95,0.95,0.6199187),
                     y=c(0.8309859,0,0,0.8309859,0.8309859,
                         1,1,0.8309859,0.8309859))
                ),
         U=list(list(color="black", 
                     x=c(0.4856334,0.465622,0.446,0.4267673,0.4079238,
                         0.3894696,0.3714047,0.3537291,0.3364428,0.3195458,
                         0.3030381,0.3030381,0.2871514,0.2717467,0.2568239,
                         0.2423831,0.2284243,0.2149475,0.2019526,0.1894398,
                         0.1774089,0.1658599,0.1658599,0.1549876,0.1446159,
                         0.1347446,0.1253738,0.1165036,0.1081339,0.1002647,
                         0.092896,0.0860278,0.0796601,0.0796601,0.0740247,
                         0.0689825,0.0645335,0.0606777,0.057415,0.0547456,
                         0.0526694,0.0511864,0.0502966,0.05,0.05,
                         0.05,0.3234295,0.3234295,0.3235221,0.3238002,
                         0.3242636,0.3249125,0.3257467,0.3267662,0.3279712,
                         0.3293615,0.3309372,0.3326982,0.3326982,0.334654,
                         0.3368136,0.3391771,0.3417446,0.344516,0.3474912,
                         0.3506704,0.3540536,0.3576406,0.3614315,0.3614315,
                         0.3656303,0.37007,0.3747508,0.3796725,0.3848352,
                         0.3902389,0.3958836,0.4017693,0.407896,0.4142636,
                         0.4142636,0.4208908,0.4277961,0.4349794,0.4424408,
                         0.4501802,0.4581977,0.4664933,0.4750669,0.4839186,
                         0.4930484,0.4930484,0.5021967,0.511104,0.5197703,
                         0.5281957,0.53638,0.5443234,0.5520257,0.5594871,
                         0.5667075,0.5736869,0.5736869,0.5804346,0.5869598,
                         0.5932626,0.5993429,0.6052008,0.6108363,0.6162492,
                         0.6214398,0.6264078,0.6311535,0.6311535,0.6356674,
                         0.6399403,0.6439722,0.6477631,0.6513131,0.654622,
                         0.65769,0.660517,0.663103,0.665448,0.665448,
                         0.6675613,0.6694521,0.6711205,0.6725664,0.6737899,
                         0.6747909,0.6755695,0.6761256,0.6764593,0.6765705,
                         0.6765705,0.6765705,0.95,0.95,0.9496756,
                         0.9487024,0.9470803,0.9448095,0.9418898,0.9383213,
                         0.934104,0.9292379,0.923723,0.9175592,0.9175592,
                         0.9107837,0.9034336,0.8955088,0.8870093,0.8779351,
                         0.8682863,0.8580628,0.8472647,0.8358919,0.8239444,
                         0.8239444,0.8116354,0.7988074,0.7854604,0.7715942,
                         0.7572091,0.7423048,0.7268816,0.7109392,0.6944779,
                         0.6774974,0.6774974,0.6602297,0.6425355,0.624415,
                         0.6058682,0.586895,0.5674954,0.5476694,0.5274171,
                         0.5067384,0.4856334,0.4856334),
                     y=c(0,0.0001972,0.0007889,0.001775,0.0031556,
                         0.0049306,0.0071001,0.009664,0.0126224,0.0159752,
                         0.0197224,0.0197224,0.0240687,0.0289262,0.0342951,
                         0.0401753,0.0465668,0.0534697,0.0608839,0.0688093,
                         0.0772462,0.0861943,0.0861943,0.0958437,0.106092,
                         0.1169394,0.1283857,0.140431,0.1530752,0.1663185,
                         0.1801607,0.1946019,0.2096421,0.2096421,0.2253543,
                         0.2418115,0.2590139,0.2769613,0.2956538,0.3150913,
                         0.3352739,0.3562016,0.3778744,0.4002922,0.4002922,
                         1,1,0.4024836,0.3896786,0.3772681,
                         0.365252,0.3536304,0.3424032,0.3315705,0.3211322,
                         0.3110884,0.301439,0.2921841,0.2921841,0.2834405,
                         0.2750329,0.2669613,0.2592257,0.2518262,0.2447626,
                         0.2380351,0.2316435,0.225588,0.2198685,0.2198685,
                         0.2146092,0.2096421,0.2049671,0.2005844,0.1964938,
                         0.1926954,0.1891892,0.1859752,0.1830533,0.1804237,
                         0.1804237,0.1782031,0.1762162,0.1744631,0.1729438,
                         0.1716581,0.1706063,0.1697882,0.1692038,0.1688532,
                         0.1687363,0.1687363,0.1688605,0.169233,0.1698539,
                         0.1707232,0.1718408,0.1732067,0.174821,0.1766837,
                         0.1787947,0.1811541,0.1811541,0.1839372,0.187027,
                         0.1904237,0.1941271,0.1981373,0.2024543,0.2070782,
                         0.2120088,0.2172462,0.2227904,0.2227904,0.2286633,
                         0.2348868,0.2414609,0.2483857,0.2556611,0.2632871,
                         0.2712637,0.2795909,0.2882688,0.2972973,0.2972973,
                         0.3067056,0.316523,0.3267495,0.337385,0.3484295,
                         0.3598831,0.3717458,0.3840175,0.3966983,0.4097882,
                         0.4097882,1,1,0.4112491,0.3888093,
                         0.3670709,0.3460336,0.3256976,0.3060628,0.2871293,
                         0.268897,0.251366,0.2345362,0.2184076,0.2184076,
                         0.2030679,0.1883126,0.1741417,0.1605551,0.147553,
                         0.1351351,0.1233017,0.1120526,0.1013879,0.0913075,
                         0.0913075,0.0819284,0.0730752,0.064748,0.0569467,
                         0.0496713,0.0429218,0.0366983,0.0310007,0.0258291,
                         0.0211833,0.0211833,0.0171585,0.0135573,0.0103798,
                         0.007626,0.0052958,0.0033893,0.0019065,0.0008473,
                         0.0002118,0,0))
                ),
         V=list(list(color="black", 
                     x=c(0.6110294,0.3911765,0.05,0.2764706,0.4477941,
                         0.4498456,0.4518824,0.4539044,0.4559118,0.4579044,
                         0.4598824,0.4618456,0.4637941,0.4657279,0.4676471,
                         0.4676471,0.4695441,0.4714118,0.47325,0.4750588,
                         0.4768382,0.4785882,0.4803088,0.482,0.4836618,
                         0.4852941,0.4852941,0.4870515,0.4887941,0.4905221,
                         0.4922353,0.4939338,0.4956176,0.4972868,0.4989412,
                         0.5005809,0.5022059,0.5022059,0.5036838,0.5051765,
                         0.5066838,0.5082059,0.5097426,0.5112941,0.5128603,
                         0.5144412,0.5160368,0.5176471,0.5176471,0.5191397,
                         0.5206765,0.5222574,0.5238824,0.5255515,0.5272647,
                         0.5290221,0.5308235,0.5326691,0.5345588,0.5345588,
                         0.5366176,0.5386765,0.5407353,0.5427941,0.5448529,
                         0.5469118,0.5489706,0.5510294,0.5530882,0.5551471,
                         0.5551471,0.7257353,0.95,0.6110294),
                     y=c(0,0,1,1,0.4255004,
                         0.4188139,0.4120979,0.4053521,0.3985767,0.3917717,
                         0.384937,0.3780726,0.3711787,0.364255,0.3573017,
                         0.3573017,0.3503929,0.3436027,0.3369311,0.3303781,
                         0.3239437,0.3176279,0.3114307,0.3053521,0.2993921,
                         0.2935508,0.2935508,0.2867606,0.2800297,0.273358,
                         0.2667457,0.2601927,0.253699,0.2472646,0.2408895,
                         0.2345738,0.2283173,0.2283173,0.2344255,0.240593,
                         0.2468199,0.253106,0.2594514,0.2658562,0.2723202,
                         0.2788436,0.2854262,0.2920682,0.2920682,0.2977687,
                         0.3036027,0.3095701,0.3156709,0.3219051,0.3282728,
                         0.3347739,0.3414085,0.3481764,0.3550778,0.3550778,
                         0.3621868,0.3692809,0.3763603,0.3834248,0.3904744,
                         0.3975093,0.4045293,0.4115345,0.4185248,0.4255004,
                         0.4255004,1,1,0))
                ),
         W=list(list(color="black", 
                     x=c(0.7960912,0.6143322,0.5674267,0.5659023,0.5642606,
                         0.5625016,0.5606254,0.5586319,0.5565505,0.5544104,
                         0.5522117,0.5499544,0.5476384,0.545557,0.5434169,
                         0.5412182,0.5389609,0.536645,0.5345928,0.5325407,
                         0.5304886,0.5284365,0.5263844,0.5214007,0.5164169,
                         0.5114332,0.5064495,0.5014658,0.4962182,0.4910293,
                         0.485899,0.4808274,0.4758143,0.4737329,0.4715928,
                         0.4693941,0.4671368,0.4648208,0.4627394,0.4605993,
                         0.4584007,0.4561433,0.4538274,0.4517752,0.4497231,
                         0.447671,0.4456189,0.4435668,0.4415733,0.4396971,
                         0.4379381,0.4362964,0.434772,0.3864007,0.2046417,
                         0.05,0.2398208,0.3050489,0.306456,0.3077459,
                         0.3089186,0.3099739,0.3109121,0.3117622,0.3125537,
                         0.3132866,0.3139609,0.3145765,0.3151336,0.3156319,
                         0.3160717,0.3164528,0.3167752,0.3186221,0.320645,
                         0.3228436,0.3252182,0.3277687,0.3301726,0.3326938,
                         0.3353322,0.3380879,0.3409609,0.3439511,0.3470586,
                         0.3502834,0.3536254,0.3570847,0.4296417,0.572557,
                         0.645114,0.6488078,0.6522671,0.6554919,0.6584821,
                         0.6612378,0.6641107,0.6668664,0.6695049,0.6720261,
                         0.67443,0.6769805,0.679355,0.6815537,0.6835765,
                         0.6854235,0.6857166,0.6860098,0.6863029,0.6865961,
                         0.6868893,0.6872117,0.6875928,0.6880326,0.6885309,
                         0.6890879,0.6897036,0.6903779,0.6911107,0.6919023,
                         0.6927524,0.6936906,0.6947459,0.6959186,0.6972085,
                         0.6986156,0.7601792,0.95,0.7960912),
                     y=c(0,0,0.1979244,0.2037658,0.2100222,
                         0.2166938,0.2237806,0.2312824,0.2390808,0.2470571,
                         0.2552113,0.2635434,0.2720534,0.2809785,0.2899629,
                         0.2990067,0.3081097,0.3172721,0.3267013,0.3360119,
                         0.3452039,0.3542772,0.363232,0.384166,0.4054559,
                         0.4271016,0.449103,0.4714603,0.4488362,0.4266271,
                         0.4048332,0.3834544,0.3624907,0.353536,0.3444626,
                         0.3352706,0.32596,0.3165308,0.3073684,0.2982654,
                         0.2892216,0.2802372,0.2713121,0.2628021,0.25447,
                         0.2463158,0.2383395,0.2305411,0.2233062,0.216427,
                         0.2099036,0.2037361,0.1979244,0,0,
                         1,1,0.4848036,0.4730319,0.4608451,
                         0.4482431,0.4352261,0.4217939,0.4083024,0.3951075,
                         0.382209,0.3696071,0.3573017,0.3431282,0.3290734,
                         0.3151371,0.3013195,0.2876205,0.2984136,0.309444,
                         0.3207116,0.3322165,0.3439585,0.3545738,0.3656635,
                         0.3772276,0.3892661,0.4017791,0.4148851,0.4281097,
                         0.4414529,0.4549148,0.4684952,0.7197924,0.7197924,
                         0.4684952,0.4551816,0.4419274,0.4287324,0.4155967,
                         0.4025204,0.3900074,0.3779689,0.3664047,0.355315,
                         0.3446998,0.3329281,0.3213343,0.3099185,0.2986805,
                         0.2876205,0.2884211,0.2908228,0.2948258,0.3004299,
                         0.3076353,0.3160267,0.325189,0.3351223,0.3458265,
                         0.3573017,0.3693403,0.3817346,0.3944848,0.4075908,
                         0.4210526,0.4347517,0.4479763,0.4607265,0.4730022,
                         0.4848036,1,1,0))
                ),
         X=list(list(color="black", 
                     x=c(0.7229862,0.5010985,0.2784784,0.05,0.3861269,
                         0.0800244,0.3085028,0.5010985,0.6929618,0.9199756,
                         0.60655,0.95,0.7229862),
                     y=c(0,0.3654559,0,0,0.5270571,
                         1,1,0.6812454,1,1,
                         0.5270571,0,0))
                ),
         Y=list(list(color="black", 
                     x=c(0.6082651,0.6082651,0.3917349,0.3917349,0.05,
                         0.2775777,0.498527,0.7224223,0.95,0.6082651),
                     y=c(0.4121572,0,0,0.4121572,1,
                         1,0.5804299,1,1,0.4121572))
                ),
         Z=list(list(color="black", 
                     x=c(0.95,0.05,0.05,0.6245956,0.1150809,
                         0.1150809,0.9148906,0.9148906,0.340295,0.95,
                         0.95),
                     y=c(0,0,0.1549296,0.828762,0.828762,
                         1,1,0.8480356,0.171238,0.171238,
                         0))
                )
         )
  x <- letterPolygon[[toupper(ch)]]
  x <- lapply(x, function(.ele){
    if(.ele$color=="black") .ele$color <- color
    .ele
  })
  return(x)
}

coloredSymbols <- function(ncha, font, color, rname, alpha, 
                           fontface="bold", envir = .globals){
  symbols<-list()
  for(i in 1:ncha){
    symbols[[i]]<-importSVG(font, color[i], rname[i], fontface)
  }
  if(!missing(alpha)){
    for(i in 1:ncha){
      symbols[[paste0(i, "_", alpha)]]<-
        importSVG(font, colalpha(color, alpha)[i], rname[i], 
                  fontface, envir = envir)
    }
  }
  symbols
}

addPseudolog2<-function(x){
    x <- round(x, digits=6)
    ifelse(x < .000001, -20, log2(x)) ## !important -10.
}

## get Information Entropy from matrix
getIE<-function(x){
    addPseudolog2(nrow(x))
}

UngappedAlignment<-function(pfms, i, threshold, minimalConsensus=0, 
                            rcpostfix="(RC)", revcomp=TRUE){
    if(!is(pfms[[i]], "pfm")){
        pcms <- pfms
        pfms <- lapply(pfms, pcm2pfm)
    }else{
        pcms <- NULL
    }
    res<-getAlignedICWithoutGap(pfms[[i-1]], pfms[[i]], threshold, revcomp)
    if(!is.null(pcms)) pfms <- pcms
    if(res$max>=minimalConsensus){
        if(res$rev){
            pfms[[i]]<-matrixReverseComplement(pfms[[i]])
            pfms[[i]]@name<-paste(pfms[[i]]@name, rcpostfix, sep="")
        }
        if(res$offset>0){
            pfms[[i]]<-addBlank(pfms[[i]], res$offset, FALSE)
        }else{
            if(res[1]<0){
                pfms[1:(i-1)]<-lapply(pfms[1:(i-1)],function(.ele) 
                  addBlank(.ele, -1*res$offset, FALSE))
            }
        }
    }
    pfms
}

UngappedAlignmentAA<-function(pcms, i, threshold, minimalConsensus){
  pcm1 <- pcms[[i-1]]
  pcm2 <- pcms[[i]]
  offset1 <- 0
  offset2 <- 0
  ## trim pcm
  trimPCMbyIC <- function(pcm, t){
    ic <- getIC(pcm)
    w <- rle(ic < t)
    offL <- offR <- 0
    if(w$values[1]) {
      offL <- w$lengths[1]
    }
    if(w$values[length(w$values)]) {
      offR <- w$lengths[length(w$values)]
    }
    if(offL+1>ncol(pcm@mat)-offR){
      return(pcm=NULL, offL=offL, offR=offR)
    }
    pcm@mat <- pcm@mat[, (offL+1):(ncol(pcm@mat)-offR), drop=FALSE]
    list(pcm=pcm, offL=offL, offR=offR)
  }
  res <- trimPCMbyIC(pcm1, t=threshold)
  if(is.null(res$pcm)){
    return(pcms)
  }
  pcm1 <- res$pcm
  offset1 <- res$offL
  res <- trimPCMbyIC(pcm2, t=threshold)
  if(is.null(res$pcm)){
    return(pcms)
  }
  pcm2 <- res$pcm
  offset2 <- res$offL
  res<-compare2profiles(pcm1, pcm2, method="Smith-Waterman")
  if(res$length>=minimalConsensus){
    of1 <- offset1 + res$i_start
    of2 <- offset2 + res$j_start
    if(of1<of2){
      pcms[seq.int(i-1)] <- lapply(pcms[seq.int(i-1)], function(.ele){
        addBlank(.ele, of2-of1, FALSE)
      })
    }else{
      if(of1>of2){
        pcms[[i]] <- addBlank(pcms[[i]], of1-of2, FALSE)
      }
    }
  }
  pcms
}

getAlignedICWithoutGap<-function(pfm1, pfm2, threshold, revcomp=TRUE){
    if(!is(pfm1, "pfm") | !is(pfm2, "pfm")) 
      stop("class of pfm1 and pfm2 must be pfm")
    offset1<-getoffsetPosByIC(pfm1, pfm2, threshold)
    if(revcomp){
        pfm3<-matrixReverseComplement(pfm2)
        offset2<-getoffsetPosByIC(pfm1, pfm3, threshold)
    }else{
        offset2<-list(k=0,max=0)
    }
    offset<-0
    rev<-FALSE
    if((offset1$max < offset2$max)){
        rev<-TRUE
        max<-offset2$max
        offset<-offset2$k
    }else{
        max<-offset1$max
        offset<-offset1$k
    }
    list(offset=offset,rev=rev,max=max)    
}
getICbyBase<-function(p, pfmj){
    re<-rep(0, 5)
    re[1:4]<-pfmj * (addPseudolog2(pfmj) - addPseudolog2(p))
    re[5]<-sum(re[1:4])
    re
}
getALLRbyBase <- function(b, pfmi, pfmj){##return 2x ALLR
    sum(pfmj * (addPseudolog2(pfmi) - addPseudolog2(b))) + 
        sum(pfmi * (addPseudolog2(pfmj) - addPseudolog2(b)))
}
checkALLR <- function(...){
    getALLRbyBase(...)>0
}
SWU <- function(pattern, subject, b, 
                match=1, mismatch=-1, 
                gap=-1000){## motif length will never longer than 1000
    if(!is(pattern, "matrix") || !is(subject, "matrix")){
        stop("pattern and subject must be numeric matrix")
    }
    m <- ncol(pattern)
    n <- ncol(subject)
    score <- matrix(0, nrow=m+1, ncol=n+1)
    point <- matrix("none", nrow=m+1, ncol=n+1)
    max_i <- 1
    max_j <- 1
    max_score <- 0
    for(i in 1:m){
        for(j in 1:n){
            diagonal_score <- 0
            left_score <- 0
            up_score <- 0
            #calculate match score
            col1 <- subject[, j]
            col2 <- pattern[, i]
            #score by KLLR
            if(checkALLR(b, col1, col2)){
                diagonal_score <- score[i, j] + match
            }else{
                diagonal_score <- score[i, j] + mismatch
            }
            
            #calculate gap scores
            up_score <- score[i, j+1] + gap
            left_score <- score[i+1, j] + gap
            
            if(diagonal_score <=0 && up_score <=0 && left_score <=0){
                score[i+1, j+1] <- 0
                point[i+1, j+1] <- "none"
                next # terminate this iteration of the loop
            }
            
            #choose best score
            if(diagonal_score >= up_score){
                if(diagonal_score >= left_score){
                    score[i+1, j+1] <- diagonal_score
                    point[i+1, j+1] <- "diagonal"
                }else{
                    score[i+1, j+1] <- left_score
                    point[i+1, j+1] <- "left"
                }
            }else{
                if(up_score > left_score){
                    score[i+1, j+1] <- up_score
                    point[i+1, j+1] <- "up"
                }else{
                    score[i+1, j+1] <- left_score
                    point[i+1, j+1] <- "left"
                }
            }
            
            #set maximum score
            if(score[i+1, j+1] > max_score){
                max_i <- i+1
                max_j <- j+1
                max_score <- score[i+1, j+1]
            }
        }
    }
    #trace-back
    align1 <- c()
    align2 <- c()
    
    i <- max_i
    j <- max_j
    while(1){
        if(point[i, j]=="none"){
            break
        }
        
        if(point[i, j]=="diagonal"){
            align1 <- c(align1, j-1)
            align2 <- c(align2, i-1)
            i <- i-1
            j <- j-1
        }else{
            if(point[i, j]=="left"){
                align1 <- c(align1, j-1)
                align2 <- c(align2, 0)
                j <- j-1
            }else{
                if(point[i, j]=="up"){
                    align1 <- c(align1, 0)
                    align2 <- c(align2, i-1)
                    i <- i-1
                }
            }
        }
    }
    align1 <- rev(align1)
    align2 <- rev(align2)
    if(length(align1)<1 | length(align2)<1){
        k <- 0
    }else{
        k=align1[1]-align2[1]
    }
    list(k=k, max=max_score)
}
ungappedScore <- function(query, subject, b, threshold){
    if(!is(query, "matrix") || !is(subject, "matrix")){
        stop("query and subject must be numeric matrix")
    }
    m <- ncol(query)
    n <- ncol(subject)
    score <- matrix(0, nrow=m+1, ncol=n+1)
    for(i in 1:m){
        for(j in 1:n){
            ic1 <- getICbyBase(b, query[, i])[5]
            ic2 <- getICbyBase(b, subject[, j])[5]
            if(ic1>=threshold && ic2>=threshold){
                value <- getICbyBase(b, c(query[, i]+subject[, j])/2)[5]
            }else{
                value <- 0
            }
            score[i+1, j+1] <- score[i, j] + value
        }
    }
    score[1:m, 1:n] <- 0
    max_score <- max(score)
    if(max_score==0){
        return(list(k=0, max=0))
    }
    idx <- which(score==max_score, arr.ind=TRUE)
    
    if(nrow(idx)>1){
        idxn <- apply(idx, 1, min)
        idx <- idx[which(idxn==min(idxn))[1], , drop=FALSE]
    }
    max_r <- idx[, "row"]
    max_c <- idx[, "col"]
    k <- max_r - max_c
    list(k=as.numeric(k), max=max_score)
}
getoffsetPosByIC<-function(pfm1, pfm2, threshold){
    if(!is(pfm1, "pfm") | !is(pfm2, "pfm")) 
      stop("class of pfm1 and pfm2 must be pfm")
    res <- ungappedScore(pfm1$mat, pfm2$mat, b=pfm1$background, threshold)
    res
}

#' @importFrom stats sd cor
getoffsetPosByIC_old<-function(pfm1, pfm2, threshold){
    if(!is(pfm1, "pfm") | !is(pfm2, "pfm")) 
      stop("class of pfm1 and pfm2 must be pfm")
    score1<-rep(0, ncol(pfm1@mat))
    score2<-rep(0, ncol(pfm2@mat))
    value1<-rep(0, ncol(pfm1@mat))
    value2<-rep(0, ncol(pfm2@mat))
    for(i in 1:ncol(pfm1@mat)){
        J<-ifelse(ncol(pfm1@mat)+1-i>ncol(pfm2@mat),
                  ncol(pfm2@mat),ncol(pfm1@mat)+1-i)
        for(j in 1:J){
            ic1<-getICbyBase(pfm1@background, pfm1@mat[,i+j-1])
            ic2<-getICbyBase(pfm2@background, pfm2@mat[,j])
            #ic3<-getALLRbyBase(pfm1@background, pfm1@mat[,i+j-1], pfm2@mat[,j])
            ic3 <- getICbyBase(pfm1@background, 
                               (pfm1@mat[,i+j-1]+pfm2@mat[,j])/2)
            if(sd(pfm1@mat[,i+j-1])==0 || sd(pfm2@mat[,j])==0){
                corr <- 0
            }else{
                corr <- cor(pfm1@mat[,i+j-1], pfm2@mat[,j], method="spearman")
            }
            if(ic1[5]>threshold & ic2[5]>threshold){
                #a<-ic1[1:4]>mean(ic1[1:4])
                #b<-ic2[1:4]>mean(ic2[1:4])
                #if(ic3>0) score1[i]<-score1[i]+1
                #if(ic3>0.25) {
                #if(any(a&b)){
                if(corr>0){
                    score1[i]<-score1[i]+1
                    value1[i] <- value1[i]+ic3[5]
                }
            }
        }
    }
    for(i in 1:ncol(pfm2@mat)){
        J<-ifelse(ncol(pfm2@mat)+1-i>ncol(pfm1@mat),
                  ncol(pfm1@mat),ncol(pfm2@mat)+1-i)
        for(j in 1:J){
            ic2<-getICbyBase(pfm2@background, pfm2@mat[,i+j-1])
            ic1<-getICbyBase(pfm1@background, pfm1@mat[,j])
            #ic3<-getALLRbyBase(pfm1@background, pfm1@mat[,j], pfm2@mat[,i+j-1])
            ic3 <- getICbyBase(pfm1@background, 
                               (pfm2@mat[,i+j-1]+pfm1@mat[,j])/2)
            if(sd(pfm1@mat[,j])==0 || sd(pfm2@mat[,i+j-1])==0){
                corr <- 0
            }else{
                corr <- cor(pfm1@mat[,j], pfm2@mat[,i+j-1], method="spearman")
            }
            if(ic1[5]>threshold & ic2[5]>threshold){
                #a<-ic1[1:4]>mean(ic1[1:4])
                #b<-ic2[1:4]>mean(ic2[1:4])
                #if(ic3>0) score2[i]<-score2[i]+1
                #if(ic3>0.25) {
                #if(any(a&b)){
                if(corr>0){
                    score2[i]<-score2[i]+1
                    value2[i] <- value2[i]+ic3[5]
                }
            }
        }
    }
    k1<-match(max(score1),score1)
    k2<-match(max(score2),score2)
    sc <- (score1[k1] < score2[k2]) || ((score1[k1] == score2[k2]) && 
                                            (value1[k1] < value2[k2]))
    k <- ifelse(sc, -1*(k2-1), (k1-1))
    max <- ifelse(sc, score2[k2], score1[k1])
    val <- ifelse(sc, value2[k2], value1[k1])
    list(k=k,max=max,val=val)
}

setClass("Rect", 
         representation(x="numeric", y="numeric",
                        width="numeric", height="numeric"), 
         prototype=prototype(x=0, y=0, width=0, height=0)
)

setGeneric("isContainedIn", function(a, b) standardGeneric("isContainedIn"))

setMethod("isContainedIn", signature(a="Rect", b="Rect"), function(a, b){
    a@x >= b@x && a@y >= b@y && 
      a@x+a@width <= b@x+b@width && a@y+a@height <= b@y+b@height
})

setClass("pos",
         representation(box="Rect", beta="numeric", sig="pfm", 
                        freq="numeric", norm="numeric")
)

getPFMid <- function(pfms, nodename, rcpostfix="(RC)"){
    pfmNames <- as.character(unlist(lapply(pfms, function(.ele) .ele@name)))
    pfmNames <- gsub(rcpostfix,"",pfmNames, fixed=TRUE)
    which(pfmNames==nodename)
}

getParentNode <- function(nodelist, nodename){
    for(i in 1:length(nodelist)){
        currNode <- nodelist[[i]]
        if(currNode@left==nodename) return(c(currNode@parent, "left"))
        if(currNode@right==nodename) return(c(currNode@parent, "right"))
    }
    NULL
}

makeLeaveNames <- function(ch){
    gsub(".", "_", make.names(ch), fixed=TRUE)
}

#' @importFrom graphics par
#' @importFrom grid stringWidth stringHeight grid.rect gpar grid.text
grid.eti <- function(x, y, label, clabel, boxes=FALSE, 
                     coul = rep(1, length(x)), 
                     bg = "white"){
  if (length(label) == 0) 
    return(invisible())
  if (is.null(label)) 
    return(invisible())
  if (any(label == "")) 
    return(invisible())
  cex0 <- par("cex") * clabel
  for (i in 1:(length(x))) {
    cha <- as.character(label[i])
    cha <- paste(" ", cha, " ", sep = "")
    x1 <- x[i]
    y1 <- y[i]
    xh <- cex0*stringWidth(cha)
    yh <- cex0*stringHeight(cha) * 1.66666666667
    if (boxes) {
      grid.rect(x=x1, y=y1, width=xh, height=yh, 
           gp=gpar(fill = bg, col = coul[i]), 
           default.units = "native")
    }
    grid.text(x=x1, y=y1, label=cha, 
              gp=gpar(cex = cex0, col = coul[i]), 
              default.units = "native")
  }
} 

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motifStack documentation built on Nov. 8, 2020, 7:43 p.m.