diff options
Diffstat (limited to 'Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua')
| -rw-r--r-- | Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua | 624 |
1 files changed, 362 insertions, 262 deletions
diff --git a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua index 59d500cc0c0..4919aeab702 100644 --- a/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua +++ b/Master/texmf-dist/tex/lualatex/pgfmolbio/pgfmolbio.chromatogram.lua @@ -6,7 +6,7 @@ -- -- pgfmolbio.dtx (with options: `pmb-chr-lua') -- --- Copyright (C) 2011 by Wolfgang Skala +-- Copyright (C) 2012 by Wolfgang Skala -- -- This work may be distributed and/or modified under the -- conditions of the LaTeX Project Public License, either version 1.3 @@ -18,27 +18,29 @@ -- module("pgfmolbio.chromatogram", package.seeall) + +if luatexbase then + luatexbase.provides_module{ + name = "pgfmolbio.chromatogram", + version = 0.2, + date = "2012/10/01", + description = "DNA sequencing chromatograms", + author = "Wolfgang Skala", + copyright = "Wolfgang Skala", + license = "LPPL", + } +end + local ALL_BASES = {"A", "C", "G", "T"} local PGFKEYS_PATH = "/pgfmolbio/chromatogram/" -local header, samples, - peaks, parms, - selectedPeaks, - lastScfFile - -local function baseToSampleIndex (baseIndex) - local result = tonumber(baseIndex) - if result then - return result - else - result = string.match(baseIndex, "base%s*(%d+)") - if tonumber(result) then - return peaks[tonumber(result)].offset - end - end -end +local stringToDim = pgfmolbio.stringToDim +local dimToString = pgfmolbio.dimToString +local packageError = pgfmolbio.packageError +local packageWarning = pgfmolbio.packageWarning +local getRange = pgfmolbio.getRange -local function stdProbStyle (prob) +local function stdProbStyle(prob) local color = "" if prob >= 0 and prob < 10 then color = "black" @@ -52,21 +54,85 @@ local function stdProbStyle (prob) return "ultra thick, " .. color end -local function findBasesInStr (target) +local function findBasesInStr(target) if not target then return end local result = {} for _, v in ipairs(ALL_BASES) do - if string.find(string.upper(target), v) then + if target:upper():find(v) then table.insert(result, v) end end return result end -function getMinMaxProbability () +local function readInt(file, n, offset) + if offset then file:seek("set", offset) end + local result = 0 + for i = 1, n do + result = result * 0x100 + file:read(1):byte() + end + return result +end + +Chromatogram = {} + +function Chromatogram:new() + newChromatogram = { + sampleMin = 1, + sampleMax = 500, + sampleStep = 1, + peakMin = -1, + peakMax = -1, + xUnit = stringToDim("0.2mm"), + yUnit = stringToDim("0.01mm"), + samplesPerLine = 500, + baselineSkip = stringToDim("3cm"), + canvasHeight = stringToDim("2cm"), + traceStyle = { + A = PGFKEYS_PATH .. "trace A style", + C = PGFKEYS_PATH .. "trace C style", + G = PGFKEYS_PATH .. "trace G style", + T = PGFKEYS_PATH .. "trace T style" + }, + tickStyle = { + A = PGFKEYS_PATH .. "tick A style", + C = PGFKEYS_PATH .. "tick C style", + G = PGFKEYS_PATH .. "tick G style", + T = PGFKEYS_PATH .. "tick T style" + }, + tickLength = stringToDim("1mm"), + baseLabelText = { + A = "\\pgfkeysvalueof{" .. PGFKEYS_PATH .. "base label A text}", + C = "\\pgfkeysvalueof{" .. PGFKEYS_PATH .. "base label C text}", + G = "\\pgfkeysvalueof{" .. PGFKEYS_PATH .. "base label G text}", + T = "\\pgfkeysvalueof{" .. PGFKEYS_PATH .. "base label T text}" + }, + baseLabelStyle = { + A = PGFKEYS_PATH .. "base label A style", + C = PGFKEYS_PATH .. "base label C style", + G = PGFKEYS_PATH .. "base label G style", + T = PGFKEYS_PATH .. "base label T style" + }, + showBaseNumbers = true, + baseNumberMin = -1, + baseNumberMax = -1, + baseNumberStep = 10, + probDistance = stringToDim("0.8cm"), + probStyle = stdProbStyle, + tracesDrawn = ALL_BASES, + ticksDrawn = "ACGT", + baseLabelsDrawn = "ACGT", + probabilitiesDrawn = "ACGT", + } + setmetatable(newChromatogram, self) + self.__index = self + return newChromatogram +end + +function Chromatogram:getMinMaxProbability() local minProb = 0 local maxProb = 0 - for _, currPeak in ipairs(selectedPeaks) do + for _, currPeak in ipairs(self.selectedPeaks) do for __, currProb in pairs(currPeak.prob) do if currProb > maxProb then maxProb = currProb end if currProb < minProb then minProb = currProb end @@ -75,232 +141,266 @@ function getMinMaxProbability () return minProb, maxProb end -local function getRange (rangeInput, regExp) - local lower, upper = string.match(rangeInput, regExp) - local step = string.match(rangeInput, "step%s*(%d*)") - return lower, upper, step -end +function Chromatogram:getSampleAndPeakIndex(baseIndex, isLowerLimit) + local sampleId, peakId -local function readInt (file, n, offset) - if offset then file:seek("set", offset) end - local result = 0 - for i = 1, n do - result = result * 0x100 + string.byte(file:read(1)) + sampleId = tonumber(baseIndex) + if sampleId then + for i, v in ipairs(self.peaks) do + if isLowerLimit then + if v.offset >= sampleId then + peakId = i + break + end + else + if v.offset == sampleId then + peakId = i + break + elseif v.offset > sampleId then + peakId = i - 1 + break + end + end + end + else + peakId = tonumber(baseIndex:match("base%s*(%d+)")) + if peakId then + sampleId = self.peaks[peakId].offset + end end - return result + return sampleId, peakId end -local function evaluateScfFile (file) - samples = {A = {}, C = {}, G = {}, T = {}} - peaks = {} - header = { - magicNumber = readInt(file, 4, 0), - samplesNumber = readInt(file, 4), - samplesOffset = readInt(file, 4), - basesNumber = readInt(file, 4), - leftClip = readInt(file, 4), - rightClip = readInt(file, 4), - basesOffset = readInt(file, 4), - comments = readInt(file, 4), - commentsOffset = readInt(file, 4), - version = readInt(file, 4), - sampleSize = readInt(file, 4), - codeSet = readInt(file, 4), - privateSize = readInt(file, 4), - privateOffset = readInt(file, 4) - } - if header.magicNumber ~= 0x2E736366 then - tex.error("Magic number in scf file '" .. lastScfFile .. "' corrupt!") - end - if header.version ~= 0x332E3030 then - tex.error("Scf file '" .. lastScfFile .. "' is not version 3.00!") - end - - file:seek("set", header.samplesOffset) - for baseIndex, baseName in ipairs(ALL_BASES) do - for i = 1, header.samplesNumber do - samples[baseName][i] = readInt(file, header.sampleSize) +function Chromatogram:readScfFile(filename) + if filename ~= self.lastScfFile then + self.lastScfFile = filename + local scfFile, errorMsg = io.open(filename, "rb") + if not scfFile then packageError(errorMsg) end + + self.samples = {A = {}, C = {}, G = {}, T = {}} + self.peaks = {} + self.header = { + magicNumber = readInt(scfFile, 4, 0), + samplesNumber = readInt(scfFile, 4), + samplesOffset = readInt(scfFile, 4), + basesNumber = readInt(scfFile, 4), + leftClip = readInt(scfFile, 4), + rightClip = readInt(scfFile, 4), + basesOffset = readInt(scfFile, 4), + comments = readInt(scfFile, 4), + commentsOffset = readInt(scfFile, 4), + version = readInt(scfFile, 4), + sampleSize = readInt(scfFile, 4), + codeSet = readInt(scfFile, 4), + privateSize = readInt(scfFile, 4), + privateOffset = readInt(scfFile, 4) + } + if self.header.magicNumber ~= 0x2E736366 then + packageError( + "Magic number in scf scfFile '" .. + self.lastScfFile .. + "' corrupt!" + ) end + if self.header.version ~= 0x332E3030 then + packageError( + "Scf scfFile '" .. + self.lastScfFile .. + "' is not version 3.00!" + ) + end + scfFile:seek("set", self.header.samplesOffset) + for baseIndex, baseName in ipairs(ALL_BASES) do + for i = 1, self.header.samplesNumber do + self.samples[baseName][i] = + readInt(scfFile, self.header.sampleSize) + end - for _ = 1, 2 do - local preValue = 0 - for i = 1, header.samplesNumber do - samples[baseName][i] = samples[baseName][i] + preValue - if samples[baseName][i] > 0xFFFF then - samples[baseName][i] = samples[baseName][i] - 0x10000 + for _ = 1, 2 do + local preValue = 0 + for i = 1, self.header.samplesNumber do + self.samples[baseName][i] = self.samples[baseName][i] + preValue + if self.samples[baseName][i] > 0xFFFF then + self.samples[baseName][i] = self.samples[baseName][i] - 0x10000 + end + preValue = self.samples[baseName][i] end - preValue = samples[baseName][i] end end - end - - for i = 1, header.basesNumber do - peaks[i] = { - offset = readInt(file, 4), - prob = {A, C, G, T}, - base - } - end + for i = 1, self.header.basesNumber do + self.peaks[i] = { + offset = readInt(scfFile, 4), + prob = {A, C, G, T}, + base + } + end - for i = 1, header.basesNumber do - peaks[i].prob.A = readInt(file, 1) - end + for i = 1, self.header.basesNumber do + self.peaks[i].prob.A = readInt(scfFile, 1) + end - for i = 1, header.basesNumber do - peaks[i].prob.C = readInt(file, 1) - end + for i = 1, self.header.basesNumber do + self.peaks[i].prob.C = readInt(scfFile, 1) + end - for i = 1, header.basesNumber do - peaks[i].prob.G = readInt(file, 1) - end + for i = 1, self.header.basesNumber do + self.peaks[i].prob.G = readInt(scfFile, 1) + end - for i = 1, header.basesNumber do - peaks[i].prob.T = readInt(file, 1) - end + for i = 1, self.header.basesNumber do + self.peaks[i].prob.T = readInt(scfFile, 1) + end - for i = 1, header.basesNumber do - peaks[i].base = string.char(readInt(file, 1)) - end -end + for i = 1, self.header.basesNumber do + self.peaks[i].base = string.char(readInt(scfFile, 1)) + end -function readScfFile (filename) - if filename ~= lastScfFile then - lastScfFile = filename - local scfFile, errorMsg = io.open(filename, "rb") - if not scfFile then tex.error(errorMsg) end - evaluateScfFile(scfFile) scfFile:close() end end -function setParameters (newParms) - local sampleRangeMin, sampleRangeMax, sampleRangeStep = - getRange( - newParms.sampleRange or "1 to 500 step 1", - "([base]*%s*%d+)%s*to%s*([base]*%s*%d+)" - ) - local baseNumberRangeMin, baseNumberRangeMax, baseNumberRangeStep = - getRange( - newParms.baseNumberRange or "auto to auto step 10", - "([auto%d]*)%s+to%s+([auto%d]*)" - ) - - parms = { - sampleMin = baseToSampleIndex(sampleRangeMin) or 1, - sampleMax = baseToSampleIndex(sampleRangeMax) or 500, - sampleStep = sampleRangeStep or 1, - xUnit = newParms.xUnit or dimen("0.2mm")[1], - yUnit = newParms.yUnit or dimen("0.01mm")[1], - samplesPerLine = newParms.samplesPerLine or 500, - baselineSkip = newParms.baselineSkip or dimen("3cm")[1], - canvasHeight= newParms.canvasHeight or dimen("2cm")[1], - traceStyle = { - A = PGFKEYS_PATH .. "trace A style@style", - C = PGFKEYS_PATH .. "trace C style@style", - G = PGFKEYS_PATH .. "trace G style@style", - T = PGFKEYS_PATH .. "trace T style@style" - }, - tickStyle = { - A = PGFKEYS_PATH .. "tick A style@style", - C = PGFKEYS_PATH .. "tick C style@style", - G = PGFKEYS_PATH .. "tick G style@style", - T = PGFKEYS_PATH .. "tick T style@style" - }, - tickLength = newParms.tickLength or dimen("1mm")[1], - baseLabelText = { - A = "\\csname pmb@chr@base label A text\\endcsname", - C = "\\csname pmb@chr@base label C text\\endcsname", - G = "\\csname pmb@chr@base label G text\\endcsname", - T = "\\csname pmb@chr@base label T text\\endcsname" - }, - baseLabelStyle = { - A = PGFKEYS_PATH .. "base label A style@style", - C = PGFKEYS_PATH .. "base label C style@style", - G = PGFKEYS_PATH .. "base label G style@style", - T = PGFKEYS_PATH .. "base label T style@style" - }, - showBaseNumbers = newParms.showBaseNumbers, - baseNumberMin = tonumber(baseNumberRangeMin) or -1, - baseNumberMax = tonumber(baseNumberRangeMax) or -1, - baseNumberStep = tonumber(baseNumberRangeStep) or 10, - probDistance = newParms.probDistance or dimen("0.8cm")[1], - probStyle = newParms.probStyle or stdProbStyle, - tracesDrawn = findBasesInStr(newParms.tracesDrawn) or ALL_BASES, - ticksDrawn = newParms.ticksDrawn or "ACGT", - baseLabelsDrawn = newParms.baseLabelsDrawn or "ACGT", - probabilitiesDrawn = newParms.probabilitiesDrawn or "ACGT", - coordUnit = "mm", - coordFmtStr = "%s%s" +function Chromatogram:setParameters(newParms) + local keyHash = { + sampleRange = function(v) + local sampleRangeMin, sampleRangeMax, sampleRangeStep = + getRange( + v:trim(), + "^([base]*%s*%d+)%s*%-", + "%-%s*([base]*%s*%d+)", + "step%s*(%d+)$" + ) + self.sampleMin, self.peakMin = + self:getSampleAndPeakIndex(sampleRangeMin, true) + self.sampleMax, self.peakMax = + self:getSampleAndPeakIndex(sampleRangeMax, false) + if self.sampleMin >= self.sampleMax then + packageError("Sample range is smaller than 1.") + end + self.sampleStep = sampleRangeStep or self.sampleStep + end, + xUnit = stringToDim, + yUnit = stringToDim, + samplesPerLine = tonumber, + baselineSkip = stringToDim, + canvasHeight = stringToDim, + tickLength = stringToDim, + showBaseNumbers = function(v) + if v == "true" then return true else return false end + end, + baseNumberRange = function(v) + local baseNumberRangeMin, baseNumberRangeMax, baseNumberRangeStep = + getRange( + v:trim(), + "^([auto%d]*)%s+%-", + "%-%s+([auto%d]*$)" + ) + if tonumber(baseNumberRangeMin) then + self.baseNumberMin = tonumber(baseNumberRangeMin) + else + self.baseNumberMin = self.peakMin + end + if tonumber(baseNumberRangeMax) then + self.baseNumberMax = tonumber(baseNumberRangeMax) + else + self.baseNumberMax = self.peakMax + end + if self.baseNumberMin >= self.baseNumberMax then + packageError("Base number range is smaller than 1.") + end + if self.baseNumberMin < self.peakMin then + self.baseNumberMin = self.peakMin + packageWarning("Lower base number range is smaller than lower sample range. It was adjusted to " .. self.baseNumberMin .. ".") + end + if self.baseNumberMax > self.peakMax then + self.baseNumberMax = self.peakMax + packageWarning("Upper base number range exceeds upper sample range. It was adjusted to " .. self.baseNumberMax .. ".") + end + self.baseNumberStep = tonumber(baseNumberRangeStep) + or self.baseNumberStep + end, + probDistance = stringToDim, + probStyle = function(v) return v end, + tracesDrawn = findBasesInStr, + ticksDrawn = function(v) return v end, + baseLabelsDrawn = function(v) return v end, + probabilitiesDrawn = function(v) return v end, + probStyle = function(v) return v end } + for key, value in pairs(newParms) do + if keyHash[key] then + self[key] = keyHash[key](value) + end + end end -function printTikzChromatogram () - selectedPeaks = {} +function Chromatogram:printTikzChromatogram() + if pgfmolbio.errorCatched then return end + self.selectedPeaks = {} local tIndex = 1 - for rPeakIndex, currPeak in ipairs(peaks) do - if currPeak.offset >= parms.sampleMin - and currPeak.offset <= parms.sampleMax then - selectedPeaks[tIndex] = { - offset = currPeak.offset + 1 - parms.sampleMin, + for rPeakIndex, currPeak in ipairs(self.peaks) do + if currPeak.offset >= self.sampleMin + and currPeak.offset <= self.sampleMax then + self.selectedPeaks[tIndex] = { + offset = currPeak.offset + 1 - self.sampleMin, base = currPeak.base, prob = currPeak.prob, baseIndex = rPeakIndex, - probXRight = parms.sampleMax + 1 - parms.sampleMin + probXRight = self.sampleMax + 1 - self.sampleMin } if tIndex > 1 then - selectedPeaks[tIndex-1].probXRight = - (selectedPeaks[tIndex-1].offset - + selectedPeaks[tIndex].offset) / 2 + self.selectedPeaks[tIndex-1].probXRight = + (self.selectedPeaks[tIndex-1].offset + + self.selectedPeaks[tIndex].offset) / 2 end tIndex = tIndex + 1 end end if tIndex > 1 then - if parms.baseNumberMin == -1 then - parms.baseNumberMin = selectedPeaks[1].baseIndex + if self.baseNumberMin == -1 then + self.baseNumberMin = self.selectedPeaks[1].baseIndex end - if parms.baseNumberMax == -1 then - parms.baseNumberMax = selectedPeaks[tIndex-1].baseIndex + if self.baseNumberMax == -1 then + self.baseNumberMax = self.selectedPeaks[tIndex-1].baseIndex end end - local samplesLeft = parms.sampleMax - parms.sampleMin + 1 + local samplesLeft = self.sampleMax - self.sampleMin + 1 local currLine = 0 while samplesLeft > 0 do - local yLower = -currLine * parms.baselineSkip - local yUpper = -currLine * parms.baselineSkip + parms.canvasHeight + local yLower = -currLine * self.baselineSkip + local yUpper = -currLine * self.baselineSkip + self.canvasHeight local xRight = - (math.min(parms.samplesPerLine, samplesLeft) - 1) * parms.xUnit + (math.min(self.samplesPerLine, samplesLeft) - 1) * self.xUnit tex.sprint( - "\\draw[" .. PGFKEYS_PATH .. "canvas style@style] (" .. - number.todimen(0, parms.coordUnit, parms.coordFmtStr) .. + "\n\t\\draw [" .. PGFKEYS_PATH .. "canvas style] (" .. + dimToString(0) .. ", " .. - number.todimen(yLower, parms.coordUnit, parms.coordFmtStr) .. + dimToString(yLower) .. ") rectangle (" .. - number.todimen(xRight, parms.coordUnit, parms.coordFmtStr) .. + dimToString(xRight) .. ", " .. - number.todimen(yUpper, parms.coordUnit, parms.coordFmtStr) .. - ");\n" + dimToString(yUpper) .. + ");" ) - samplesLeft = samplesLeft - parms.samplesPerLine + samplesLeft = samplesLeft - self.samplesPerLine currLine = currLine + 1 end - for _, baseName in ipairs(parms.tracesDrawn) do - tex.sprint("\\draw[" .. parms.traceStyle[baseName] .. "] ") - local currSampleIndex = parms.sampleMin + for _, baseName in ipairs(self.tracesDrawn) do + tex.sprint("\n\t\\draw [" .. self.traceStyle[baseName] .. "] ") + local currSampleIndex = self.sampleMin local sampleX = 1 local x = 0 local y = 0 local currLine = 0 local firstPointInLine = true - while currSampleIndex <= parms.sampleMax do - x = ((sampleX - 1) % parms.samplesPerLine) * parms.xUnit - y = samples[baseName][currSampleIndex] * parms.yUnit - - currLine * parms.baselineSkip - if sampleX % parms.sampleStep == 0 then + while currSampleIndex <= self.sampleMax do + x = ((sampleX - 1) % self.samplesPerLine) * self.xUnit + y = self.samples[baseName][currSampleIndex] * self.yUnit + - currLine * self.baselineSkip + if sampleX % self.sampleStep == 0 then if not firstPointInLine then tex.sprint(" -- ") else @@ -308,20 +408,20 @@ function printTikzChromatogram () end tex.sprint( "(" .. - number.todimen(x, parms.coordUnit, parms.coordFmtStr) .. + dimToString(x) .. ", " .. - number.todimen(y, parms.coordUnit, parms.coordFmtStr) .. + dimToString(y) .. ")" ) end - if sampleX ~= parms.sampleMax + 1 - parms.sampleMin then - if sampleX >= (currLine + 1) * parms.samplesPerLine then + if sampleX ~= self.sampleMax + 1 - self.sampleMin then + if sampleX >= (currLine + 1) * self.samplesPerLine then currLine = currLine + 1 - tex.sprint(";\n\\draw[" .. parms.traceStyle[baseName] .. "] ") + tex.sprint(";\n\t\\draw [" .. self.traceStyle[baseName] .. "] ") firstPointInLine = true end else - tex.sprint(";\n") + tex.sprint(";") end sampleX = sampleX + 1 currSampleIndex = currSampleIndex + 1 @@ -332,127 +432,127 @@ function printTikzChromatogram () local lastProbX = 1 local probRemainder = false - for _, currPeak in ipairs(selectedPeaks) do - while currPeak.offset > (currLine + 1) * parms.samplesPerLine do + for _, currPeak in ipairs(self.selectedPeaks) do + while currPeak.offset > (currLine + 1) * self.samplesPerLine do currLine = currLine + 1 end - local x = ((currPeak.offset - 1) % parms.samplesPerLine) * parms.xUnit - local yUpper = -currLine * parms.baselineSkip - local yLower = -currLine * parms.baselineSkip - parms.tickLength + local x = ((currPeak.offset - 1) % self.samplesPerLine) * self.xUnit + local yUpper = -currLine * self.baselineSkip + local yLower = -currLine * self.baselineSkip - self.tickLength local tickOperation = "" - if string.find(string.upper(parms.ticksDrawn), currPeak.base) then + if self.ticksDrawn:upper():find(currPeak.base) then tickOperation = "--" end tex.sprint( - "\\draw[" .. - parms.tickStyle[currPeak.base] .. + "\n\t\\draw [" .. + self.tickStyle[currPeak.base] .. "] (" .. - number.todimen(x, parms.coordUnit, parms.coordFmtStr) .. + dimToString(x) .. ", " .. - number.todimen(yUpper, parms.coordUnit, parms.coordFmtStr) .. + dimToString(yUpper) .. ") " .. tickOperation .. " (" .. - number.todimen(x, parms.coordUnit, parms.coordFmtStr) .. + dimToString(x) .. ", " .. - number.todimen(yLower, parms.coordUnit, parms.coordFmtStr) .. + dimToString(yLower) .. ")" ) - if string.find(string.upper(parms.baseLabelsDrawn), currPeak.base) then + if self.baseLabelsDrawn:upper():find(currPeak.base) then tex.sprint( - " node[" .. - parms.baseLabelStyle[currPeak.base] .. + " node [" .. + self.baseLabelStyle[currPeak.base] .. "] {" .. - parms.baseLabelText[currPeak.base] .. + self.baseLabelText[currPeak.base] .. "}" ) end - if parms.showBaseNumbers - and currPeak.baseIndex >= parms.baseNumberMin - and currPeak.baseIndex <= parms.baseNumberMax - and (currPeak.baseIndex - parms.baseNumberMin) - % parms.baseNumberStep == 0 then + if self.showBaseNumbers + and currPeak.baseIndex >= self.baseNumberMin + and currPeak.baseIndex <= self.baseNumberMax + and (currPeak.baseIndex - self.baseNumberMin) + % self.baseNumberStep == 0 then tex.sprint( - " node[" .. PGFKEYS_PATH .. "base number style@style] {\\strut " .. + " node [" .. + PGFKEYS_PATH .. + "base number style] {\\strut " .. currPeak.baseIndex .. "}" ) end - tex.sprint(";\n") + tex.sprint(";") if probRemainder then tex.sprint(probRemainder) probRemainder = false end - local drawCurrProb = string.find( - string.upper(parms.probabilitiesDrawn), - currPeak.base - ) - local xLeft = lastProbX - 1 - currLine * parms.samplesPerLine + local drawCurrProb = + self.probabilitiesDrawn:upper():find(currPeak.base) + local xLeft = lastProbX - 1 - currLine * self.samplesPerLine if xLeft < 0 then - local xLeftPrev = (parms.samplesPerLine + xLeft) * parms.xUnit - local xRightPrev = (parms.samplesPerLine - 1) * parms.xUnit - local yPrev = -(currLine-1) * parms.baselineSkip - parms.probDistance + local xLeftPrev = (self.samplesPerLine + xLeft) * self.xUnit + local xRightPrev = (self.samplesPerLine - 1) * self.xUnit + local yPrev = -(currLine-1) * self.baselineSkip - self.probDistance if drawCurrProb then tex.sprint( - "\\draw[" .. - parms.probStyle(currPeak.prob[currPeak.base]) .. - " ] (" .. - number.todimen(xLeftPrev, parms.coordUnit, parms.coordFmtStr) .. + "\n\t\\draw [" .. + self.probStyle(currPeak.prob[currPeak.base]) .. + "] (" .. + dimToString(xLeftPrev) .. ", " .. - number.todimen(yPrev, parms.coordUnit, parms.coordFmtStr) .. + dimToString(yPrev) .. ") -- (" .. - number.todimen(xRightPrev, parms.coordUnit, parms.coordFmtStr) .. + dimToString(xRightPrev) .. ", " .. - number.todimen(yPrev, parms.coordUnit, parms.coordFmtStr) .. - ");\n" + dimToString(yPrev) .. + ");" ) end xLeft = 0 else - xLeft = xLeft * parms.xUnit + xLeft = xLeft * self.xUnit end - local xRight = currPeak.probXRight - 1 - currLine * parms.samplesPerLine - if xRight >= parms.samplesPerLine then + local xRight = currPeak.probXRight - 1 - currLine * self.samplesPerLine + if xRight >= self.samplesPerLine then if drawCurrProb then - local xRightNext = (xRight - parms.samplesPerLine) * parms.xUnit - local yNext = -(currLine+1) * parms.baselineSkip - parms.probDistance + local xRightNext = (xRight - self.samplesPerLine) * self.xUnit + local yNext = -(currLine+1) * self.baselineSkip - self.probDistance probRemainder = - "\\draw[" .. - parms.probStyle(currPeak.prob[currPeak.base]) .. - " ] (" .. - number.todimen(0, parms.coordUnit, parms.coordFmtStr) .. + "\n\t\\draw [" .. + self.probStyle(currPeak.prob[currPeak.base]) .. + "] (" .. + dimToString(0) .. ", " .. - number.todimen(yNext, parms.coordUnit, parms.coordFmtStr) .. + dimToString(yNext) .. ") -- (" .. - number.todimen(xRightNext, parms.coordUnit, parms.coordFmtStr) .. + dimToString(xRightNext) .. ", " .. - number.todimen(yNext, parms.coordUnit, parms.coordFmtStr) .. - ");\n" + dimToString(yNext) .. + ");" end - xRight = (parms.samplesPerLine - 1) * parms.xUnit + xRight = (self.samplesPerLine - 1) * self.xUnit else - xRight = xRight * parms.xUnit + xRight = xRight * self.xUnit end - local y = -currLine * parms.baselineSkip - parms.probDistance + local y = -currLine * self.baselineSkip - self.probDistance if drawCurrProb then tex.sprint( - "\\draw[" .. - parms.probStyle(currPeak.prob[currPeak.base]) .. - " ] (" .. - number.todimen(xLeft, parms.coordUnit, parms.coordFmtStr) .. + "\n\t\\draw [" .. + self.probStyle(currPeak.prob[currPeak.base]) .. + "] (" .. + dimToString(xLeft) .. ", " .. - number.todimen(y, parms.coordUnit, parms.coordFmtStr) .. + dimToString(y) .. ") -- (" .. - number.todimen(xRight, parms.coordUnit, parms.coordFmtStr) .. + dimToString(xRight) .. ", " .. - number.todimen(y, parms.coordUnit, parms.coordFmtStr) .. - ");\n" + dimToString(y) .. + ");" ) end lastProbX = currPeak.probXRight |