[CHNOSZ-commits] r123 - in pkg/CHNOSZ: . R inst man tests/testthat
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jan 28 09:29:14 CET 2017
Author: jedick
Date: 2017-01-28 09:29:14 +0100 (Sat, 28 Jan 2017)
New Revision: 123
Removed:
pkg/CHNOSZ/R/msgout.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/EOSregress.R
pkg/CHNOSZ/R/affinity.R
pkg/CHNOSZ/R/buffer.R
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/equilibrate.R
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/R/findit.R
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/iprotein.R
pkg/CHNOSZ/R/more.aa.R
pkg/CHNOSZ/R/mosaic.R
pkg/CHNOSZ/R/nonideal.R
pkg/CHNOSZ/R/protein.info.R
pkg/CHNOSZ/R/read.expr.R
pkg/CHNOSZ/R/revisit.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/R/util.affinity.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/R/util.fasta.R
pkg/CHNOSZ/R/util.program.R
pkg/CHNOSZ/R/util.water.R
pkg/CHNOSZ/R/water.R
pkg/CHNOSZ/R/wjd.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/util.program.Rd
pkg/CHNOSZ/tests/testthat/test-equilibrate.R
pkg/CHNOSZ/tests/testthat/test-protein.info.R
Log:
remove msgout()
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/DESCRIPTION 2017-01-28 08:29:14 UTC (rev 123)
@@ -1,6 +1,6 @@
-Date: 2017-01-22
+Date: 2017-01-28
Package: CHNOSZ
-Version: 1.0.8-11
+Version: 1.0.8-13
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/EOSregress.R
===================================================================
--- pkg/CHNOSZ/R/EOSregress.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/EOSregress.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -167,7 +167,7 @@
}
# plot regression line at a single P
P <- mean(exptdata$P)
- msgout("EOSplot: plotting line for P=", P, " bar\n")
+ message("EOSplot: plotting line for P=", P, " bar")
xs <- seq(xlim[1], xlim[2], length.out=200)
calc.X <- EOScalc(coefficients, xs, P, ...)
lines(xs, calc.X, lty=lty)
Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/affinity.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -65,7 +65,7 @@
ibufbasis <- which(!can.be.numeric(mybasis$logact))
if(!is.null(mybasis) & length(ibufbasis) > 0) {
buffer <- TRUE
- msgout('affinity: loading buffer species\n')
+ message('affinity: loading buffer species')
if(!is.null(thermo$species)) is.species <- 1:nrow(thermo$species) else is.species <- numeric()
is.buffer <- buffer(logK=NULL)
thermo <- get("thermo", "CHNOSZ")
Modified: pkg/CHNOSZ/R/buffer.R
===================================================================
--- pkg/CHNOSZ/R/buffer.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/buffer.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -22,8 +22,8 @@
if(state[1]=='') {
thermo$buffers <- thermo$buffers[-imod,]
assign("thermo", thermo, "CHNOSZ")
- msgout(paste('mod.buffer: removed ',c2s(species),' in ',
- c2s(unique(name)),' buffer.\n',sep=''))
+ message(paste('mod.buffer: removed ',c2s(species),' in ',
+ c2s(unique(name)),' buffer.',sep=''))
} else {
if(missing(state)) state <- thermo$buffers$state[imod]
if(missing(logact)) logact <- thermo$buffers$logact[imod]
@@ -35,11 +35,11 @@
thermo$buffers$logact[imod] <- logact
assign("thermo", thermo, "CHNOSZ")
if(identical(state.old,state) & identical(logact.old,logact)) {
- msgout(paste('mod.buffer: nothing changed for ',
- c2s(species),' in ',c2s(unique(name)),' buffer.\n',sep=''))
+ message(paste('mod.buffer: nothing changed for ',
+ c2s(species),' in ',c2s(unique(name)),' buffer.',sep=''))
} else {
- msgout(paste('mod.buffer: changed state and/or logact of ',
- c2s(species),' in ',c2s(unique(name)),' buffer.\n',sep=''))
+ message(paste('mod.buffer: changed state and/or logact of ',
+ c2s(species),' in ',c2s(unique(name)),' buffer.',sep=''))
}
}
} else {
@@ -51,7 +51,7 @@
t <- data.frame(name=name,species=species,state=state,logact=logact)
thermo$buffers <- rbind(thermo$buffers,t)
assign("thermo", thermo, "CHNOSZ")
- msgout(paste('mod.buffer: added ',c2s(unique(name)),'.\n',sep=''))
+ message(paste('mod.buffer: added ',c2s(unique(name)),'.',sep=''))
}
return(invisible(thermo$buffers[thermo$buffers$name %in% name,]))
}
@@ -163,7 +163,7 @@
if(is.null(newbasis)) context <- '' else context <- paste(', ',basisnames[newbasis],' (conserved)',sep='')
reqtext <- paste(c2s(basisnames[ibasisrequested]),' (active)',sep='')
if(length(ibasisadded)==0) addtext <- '' else addtext <- paste(', ',c2s(basisnames[ibasisadded]),sep='')
- msgout(paste('buffer: ( ',bufname,' ) for activity of ',reqtext,addtext,context,'\n',sep=''))
+ message(paste('buffer: ( ',bufname,' ) for activity of ',reqtext,addtext,context,sep=''))
#print(bufbasis)
# there could still be stuff here (over-defined system?)
xx <- bufbasis[,-ibasis,drop=FALSE]
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/diagram.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -72,7 +72,7 @@
plotvar <- eout$property
# we change 'A' to 'A/2.303RT' so the axis label is made correctly
if(plotvar=="A") plotvar <- "A/2.303RT"
- msgout(paste("diagram: plotting", plotvar, "from affinity(), divided by balancing coefficients\n"))
+ message(paste("diagram: plotting", plotvar, "from affinity(), divided by balancing coefficients"))
}
## number of dimensions (T, P or chemical potentials that are varied)
@@ -85,8 +85,8 @@
if(normalize & as.residue) stop("'normalize' and 'as.residue' can not both be TRUE")
if(!eout.is.aout) stop("'normalize' or 'as.residue' can be TRUE only if 'eout' is the output from affinity()")
if(nd!=2) stop("'normalize' or 'as.residue' can be TRUE only for a 2-D (predominance) diagram")
- if(normalize) msgout("diagram: using 'normalize' in calculation of predominant species\n")
- else msgout("diagram: using 'as.residue' in calculation of predominant species\n")
+ if(normalize) message("diagram: using 'normalize' in calculation of predominant species")
+ else message("diagram: using 'as.residue' in calculation of predominant species")
}
## sum activities of species together in groups 20090524
Modified: pkg/CHNOSZ/R/equilibrate.R
===================================================================
--- pkg/CHNOSZ/R/equilibrate.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/equilibrate.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -19,7 +19,7 @@
ispecies <- ispecies[!ina[ispecies]]
if(length(ispecies)==0) stop("all species have NA affinities")
if(!identical(ispecies, 1:nspecies)) {
- msgout(paste("equilibrate: using", length(ispecies), "of", nspecies, "species\n"))
+ message(paste("equilibrate: using", length(ispecies), "of", nspecies, "species"))
aout$species <- aout$species[ispecies, ]
aout$values <- aout$values[ispecies]
n.balance <- n.balance[ispecies]
@@ -27,7 +27,7 @@
## number of species that are left
nspecies <- length(aout$values)
## say what the balancing coefficients are
- if(length(n.balance) < 100) msgout(paste("equilibrate: n.balance is", c2s(n.balance), "\n"))
+ if(length(n.balance) < 100) message(paste("equilibrate: n.balance is", c2s(n.balance)))
## logarithm of total activity of the balance
if(is.null(loga.balance)) {
# sum up the activities, then take absolute value
@@ -35,15 +35,15 @@
sumact <- abs(sum(10^aout$species$logact * n.balance))
loga.balance <- log10(sumact)
}
- msgout(paste0("equilibrate: loga.balance is ", loga.balance, "\n"))
+ message(paste0("equilibrate: loga.balance is ", loga.balance))
## normalize -- normalize the molar formula by the balance coefficients
m.balance <- n.balance
isprotein <- grepl("_", as.character(aout$species$name))
if(normalize | as.residue) {
if(any(n.balance < 0)) stop("one or more negative balancing coefficients prohibit using normalized molar formulas")
n.balance <- rep(1, nspecies)
- if(as.residue) msgout(paste("equilibrate: using 'as.residue' for molar formulas\n"))
- else msgout(paste("equilibrate: using 'normalize' for molar formulas\n"))
+ if(as.residue) message(paste("equilibrate: using 'as.residue' for molar formulas"))
+ else message(paste("equilibrate: using 'normalize' for molar formulas"))
} else m.balance <- rep(1, nspecies)
## Astar: the affinities/2.303RT of formation reactions with
## formed species in their standard-state activities
@@ -57,7 +57,7 @@
if(all(n.balance==1)) method <- method[1]
else method <- method[2]
}
- msgout(paste("equilibrate: using", method[1], "method\n"))
+ message(paste("equilibrate: using", method[1], "method"))
if(method[1]=="boltzmann") loga.equil <- equil.boltzmann(Astar, n.balance, loga.balance)
else if(method[1]=="reaction") loga.equil <- equil.reaction(Astar, n.balance, loga.balance)
## if we normalized the formulas, get back to activities to species
@@ -253,16 +253,16 @@
if(is.numeric(balance[1])) {
# a numeric vector
n.balance <- rep(balance, length.out=length(aout$values))
- msgout("balance: from numeric argument value\n")
+ message("balance: from numeric argument value")
} else {
# "length" for balancing on protein length
if(identical(balance, "length")) {
if(!all(isprotein)) stop("length was the requested balance, but some species are not proteins")
n.balance <- protein.length(aout$species$name)
- msgout("balance: from protein length\n")
+ message("balance: from protein length")
} else if(identical(balance, "volume")) {
n.balance <- info(aout$species$ispecies, check.it=FALSE)$V
- msgout("balance: from volume")
+ message("balance: from volume")
} else {
# is the balance the name of a basis species?
if(length(ibalance)==0) {
@@ -271,7 +271,7 @@
}
# the name of the basis species (need this if we got ibalance which which.balance, above)
balance <- colnames(aout$species)[ibalance[1]]
- msgout(paste("balance: from moles of", balance, "in formation reactions\n"))
+ message(paste("balance: from moles of", balance, "in formation reactions"))
# the balance vector
n.balance <- aout$species[, ibalance[1]]
# we check if that all formation reactions contain this basis species
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/examples.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -36,11 +36,11 @@
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
# say something so the user sees where we are
- msgout("------------\n")
+ message("------------")
if(which[i]=="dehydration" & !to.file) {
- msgout("demos: skipping dehydration demo as to.file is FALSE\n")
+ message("demos: skipping dehydration demo as to.file is FALSE")
next
- } else msgout(paste("demos: running '", which[i], "'\n", sep=""))
+ } else message(paste("demos: running '", which[i], "'", sep=""))
if(to.file & !which[i]=="dehydration") {
if(which[i]=="bugstab") png(paste(which[i], "%d.png", sep=""), width=700, height=500, pointsize=12)
else png(paste(which[i], "%d.png", sep=""), width=500, height=500, pointsize=12)
Modified: pkg/CHNOSZ/R/findit.R
===================================================================
--- pkg/CHNOSZ/R/findit.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/findit.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -51,7 +51,7 @@
else {
# in the ith loop we consider intervals
# of rat^(i-1) of the ranges specified at start
- msgout(paste("optimal:",round(curr,4),"",""))
+ message(paste("optimal:",round(curr,4),"",""), appendLF=FALSE)
range <- range(lim)
int <- abs(diff(range)) * rat^(i-1)
mylims <- c(curr-int/2, curr+int/2)
@@ -61,7 +61,7 @@
# reverse the order if the axis is reversed
if(diff(lim) < 0) mylims <- rev(mylims)
}
- msgout(paste("new limits:",round(mylims[1],4),round(mylims[2],4),"\n"))
+ message(paste("new limits:",round(mylims[1],4),round(mylims[2],4)))
return(mylims)
}
@@ -76,14 +76,14 @@
# loop for the specified number of iterations
# (todo: loop until an error threshhold is reached)
for(i in 1:niter) {
- msgout(paste("\n###### findit: iteration",i,"of",niter,"\n"))
+ message(paste("\n###### findit: iteration",i,"of",niter))
# to generate the argument list for affinity
# with the variables specified in lims
aargs <- list()
for(j in 1:length(lims)) {
if(names(lims)[j] %in% rownames(basis)) {
ibasis <- match(names(lims)[j],rownames(basis))
- msgout(paste("###",rownames(basis)[ibasis],""))
+ message(paste("###",rownames(basis)[ibasis],""), appendLF=FALSE)
# the starting search limits for this species
lim <- lims[[j]]
# center the search interval on the current values
@@ -93,7 +93,7 @@
names(myarg) <- rownames(basis)[ibasis]
aargs <- c(aargs,myarg)
} else if(names(lims[j]) %in% c("T","P")) {
- msgout(paste("###",names(lims[j]),""))
+ message(paste("###",names(lims[j]),""), appendLF=FALSE)
if(names(lims[j])=="T") {
lim <- lims$T
curr <- T
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/info.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -67,8 +67,8 @@
available.states <- thermo$obigt$state[matches.species]
if(length(available.states)==1) a.s.verb <- "is" else a.s.verb <- "are"
a.s.text <- paste("'", available.states, "'", sep="", collapse=" ")
- msgout("info.character: requested state '", state, "' for ", species,
- " but only ", a.s.text, " ", a.s.verb, " available\n")
+ message("info.character: requested state '", state, "' for ", species,
+ " but only ", a.s.text, " ", a.s.verb, " available")
return(NA)
}
matches.species <- matches.state
@@ -83,8 +83,8 @@
if(length(ispecies) > length(ispecies.out)) {
ispecies.other <- ispecies[!ispecies %in% ispecies.out]
othertext <- paste(thermo$obigt$state[ispecies.other], collapse=", ")
- msgout("info.character: found ", species, "(", thermo$obigt$state[ispecies.out],
- "), also available in ", othertext, "\n")
+ message("info.character: found ", species, "(", thermo$obigt$state[ispecies.out],
+ "), also available in ", othertext)
}
return(ispecies.out)
}
@@ -113,8 +113,8 @@
if(length(naGHS)==1) {
# calculate a single missing one of G, H, or S from the others
GHS <- as.numeric(GHS(as.character(this$formula), G=this[,8], H=this[,9], S=this[,10]))
- msgout("info.numeric: ", colnames(this)[8:10][naGHS], " of ",
- this$name, "(", this$state, ") is NA; set to ", round(GHS[naGHS],2), "\n")
+ message("info.numeric: ", colnames(this)[8:10][naGHS], " of ",
+ this$name, "(", this$state, ") is NA; set to ", round(GHS[naGHS],2))
this[, naGHS+7] <- GHS[naGHS]
}
# now perform consistency checks for GHS and EOS parameters if check.it=TRUE
@@ -125,7 +125,7 @@
calcCp <- checkEOS(this, this$state, "Cp")
# fill in NA heat capacity
if(!is.na(calcCp) & is.na(this$Cp)) {
- msgout("info.numeric: Cp of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcCp, 2), "\n")
+ message("info.numeric: Cp of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcCp, 2))
this$Cp <- as.numeric(calcCp)
}
# check tabulated volumes - only for aq (HKF equation)
@@ -133,7 +133,7 @@
calcV <- checkEOS(this, this$state, "V")
# fill in NA volume
if(!is.na(calcV) & is.na(this$V)) {
- msgout("info.numeric: V of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcV, 2), "\n")
+ message("info.numeric: V of ", this$name, "(", this$state, ") is NA; set by EOS parameters to ", round(calcV, 2))
this$V <- as.numeric(calcV)
}
}
@@ -158,20 +158,20 @@
if(!is.na(approx.species[1])) {
# show the names of the species
if(length(approx.species)==1) {
- msgout("info.approx: '", species, "' is similar to ", info.text(approx.species), "\n")
+ message("info.approx: '", species, "' is similar to ", info.text(approx.species))
} else {
napprox.max <- 25
exttext <- ":"
if(length(approx.species) > napprox.max) exttext <- paste(" (showing first ", napprox.max, ")", sep="")
- msgout("info.approx: '", species, "' is ambiguous; has approximate matches to ",
- length(approx.species), " species", exttext, "\n")
+ message("info.approx: '", species, "' is ambiguous; has approximate matches to ",
+ length(approx.species), " species", exttext)
printout <- capture.output(print(thermo$obigt$name[head(approx.species, napprox.max)]))
- msgout(paste(printout, collapse="\n"), "\n")
+ message(paste(printout, collapse="\n"))
}
return(approx.species)
}
# if we got here there were no approximate matches
- msgout("info.approx: '", species, "' has no approximate matches\n")
+ message("info.approx: '", species, "' has no approximate matches")
return(NA)
}
@@ -180,13 +180,13 @@
## if no species are requested, summarize the available data 20101129
thermo <- get("thermo")
if(is.null(species)) {
- msgout("info: 'species' is NULL; summarizing information about thermodynamic data...\n")
- msgout(paste("thermo$obigt has", nrow(thermo$obigt[thermo$obigt$state=="aq", ]), "aqueous,",
- nrow(thermo$obigt), "total species\n"))
- msgout(paste("number of literature sources: ", nrow(thermo$refs), ", elements: ",
- nrow(thermo$element), ", buffers: ", length(unique(thermo$buffers$name)), "\n", sep=""))
- msgout(paste("number of proteins in thermo$protein is", nrow(thermo$protein), "from",
- length(unique(thermo$protein$organism)), "organisms\n"))
+ message("info: 'species' is NULL; summarizing information about thermodynamic data...")
+ message(paste("thermo$obigt has", nrow(thermo$obigt[thermo$obigt$state=="aq", ]), "aqueous,",
+ nrow(thermo$obigt), "total species"))
+ message(paste("number of literature sources: ", nrow(thermo$refs), ", elements: ",
+ nrow(thermo$element), ", buffers: ", length(unique(thermo$buffers$name)), sep=""))
+ message(paste("number of proteins in thermo$protein is", nrow(thermo$protein), "from",
+ length(unique(thermo$protein$organism)), "organisms"))
# print information about SGD.csv, ECO.csv, HUM.csv
more.aa(organism="Sce")
more.aa(organism="Eco")
Modified: pkg/CHNOSZ/R/iprotein.R
===================================================================
--- pkg/CHNOSZ/R/iprotein.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/iprotein.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -31,7 +31,7 @@
if(any(is.na(iprotein))) {
nNA <- sum(is.na(iprotein))
if(nNA==1) ptext <- "" else ptext <- "s"
- msgout("iprotein: ", sum(is.na(iprotein)), " protein", ptext, " not matched\n")
+ message("iprotein: ", sum(is.na(iprotein)), " protein", ptext, " not matched")
}
return(iprotein)
}
@@ -88,9 +88,9 @@
# now the species name
name <- paste(aa$protein, aa$organism, sep="_")
# make some noise for the user
- msgout("aa2eos: found ")
- msgout(name, " (", f, ", ")
- msgout(round(length, 3), " residues)\n")
+ message("aa2eos: found ", appendLF=FALSE)
+ message(name, " (", f, ", ", appendLF=FALSE)
+ message(round(length, 3), " residues)")
ref <- aa$ref
header <- data.frame(name=name, abbrv=NA, formula=f, state=state, ref1=ref, ref2=NA, date=NA, stringsAsFactors=FALSE)
eosout <- cbind(header, eos)
@@ -128,7 +128,7 @@
if(any(ina)) {
aa <- aa[!ina, ]
abundance <- abundance[!ina]
- msgout("aasum: dropped ", sum(ina), " proteins with NA composition and/or abundance\n")
+ message("aasum: dropped ", sum(ina), " proteins with NA composition and/or abundance")
}
# we don't know how to deal with different numbers of polypeptide chains
if(!all(aa$chains==aa$chains[1])) stop("different numbers of polypeptide chains")
@@ -183,7 +183,7 @@
# return the new rownumbers
ip <- iprotein(po)
# make some noise
- if(!all(ipdup)) msgout("add.protein: added ", nrow(aa)-sum(ipdup), " new protein(s) to thermo$protein\n")
- if(any(ipdup)) msgout("add.protein: replaced ", sum(ipdup), " existing protein(s) in thermo$protein\n")
+ if(!all(ipdup)) message("add.protein: added ", nrow(aa)-sum(ipdup), " new protein(s) to thermo$protein")
+ if(any(ipdup)) message("add.protein: replaced ", sum(ipdup), " existing protein(s) in thermo$protein")
return(ip)
}
Modified: pkg/CHNOSZ/R/more.aa.R
===================================================================
--- pkg/CHNOSZ/R/more.aa.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/more.aa.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -12,7 +12,7 @@
mydata <- read.csv(datafile, as.is=TRUE)
# if protein is not supplied, just give some information about the datafile
if(is.null(protein)) {
- msgout("more.aa: ", datapath, " has data for ", nrow(mydata), " proteins\n")
+ message("more.aa: ", datapath, " has data for ", nrow(mydata), " proteins")
return(invisible())
}
# which columns to search for matches
@@ -41,7 +41,7 @@
inotmatch <- which(is.na(imatch))
if(length(inotmatch) > 0) {
if(length(inotmatch)==1) verb <- " was" else verb <- " were"
- msgout("more.aa: ", paste(protein[[i]][inotmatch], collapse=" "), verb, " not matched\n")
+ message("more.aa: ", paste(protein[[i]][inotmatch], collapse=" "), verb, " not matched")
}
aa <- data.frame(mydata[imatch, iaa])
# add the identifying columns
Modified: pkg/CHNOSZ/R/mosaic.R
===================================================================
--- pkg/CHNOSZ/R/mosaic.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/mosaic.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -21,7 +21,7 @@
# a list where we'll keep the affinity calculations
affs <- list()
for(i in seq_along(bases)) {
- msgout(paste("mosaic: current basis species is", bases[i], "\n", sep=" "))
+ message(paste("mosaic: current basis species is", bases[i], sep=" "))
# set up argument list: name of swapped-in basis species
if(!is.na(iswap)) names(myargs)[iswap] <- bases[i]
# calculate affinities
@@ -46,7 +46,7 @@
}
}
# calculate affinities of formation of basis species
- msgout(paste("mosaic: combining diagrams for", paste(bases, collapse=" "), "\n", sep=" "))
+ message(paste("mosaic: combining diagrams for", paste(bases, collapse=" "), sep=" "))
ispecies <- species()$ispecies
species.logact <- species()$logact
species(delete=TRUE)
Deleted: pkg/CHNOSZ/R/msgout.R
===================================================================
--- pkg/CHNOSZ/R/msgout.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/msgout.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -1,57 +0,0 @@
-# CHNOSZ/msgout.R
-# msgout() is a variation on message() from base R
-# 20120117 jmd, adapted from...
-
-# File src/library/base/R/message.R
-# Part of the R package, http://www.R-project.org
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# http://www.r-project.org/Licenses/
-
-
-# a variant of message(), using stdout instead of stderr
-# and with a default setting of appendLF = FALSE
-# this is now used for informative messages in CHNOSZ
-# (in info() and other functions)
-# so that they show up on the console and in Sweave output, but are suppressed
-# when running the 'test_that' testing scripts
-# (messages produced by cat() would mess up the rows of green dots)
-# the appendLF = FALSE is so that the cat("...\n") statements used previously
-# can all be replaced with msgout without further modification
-msgout <-
-function(..., domain = NULL, appendLF = FALSE)
-{
- args <- list(...)
- cond <- if (length(args) == 1L && inherits(args[[1L]], "condition")) {
- if(nargs() > 1L)
- warning("additional arguments ignored in message()")
- args[[1L]]
- } else {
- msg <- .makeMessage(..., domain=domain, appendLF = appendLF)
- call <- sys.call()
- simpleMessage(msg, call)
- }
- defaultHandler <- function(c) {
- ## Maybe use special connection here?
- #cat(conditionMessage(c), file=stderr(), sep="")
- cat(conditionMessage(c), file="", sep="")
- }
- withRestarts({
- signalCondition(cond)
- ## We don't get to the default handler if the signal
- ## is handled with a non-local exit, e.g. by
- ## invoking the muffleMessage restart.
- defaultHandler(cond)
- }, muffleMessage = function() NULL)
- invisible()
-}
Modified: pkg/CHNOSZ/R/nonideal.R
===================================================================
--- pkg/CHNOSZ/R/nonideal.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/nonideal.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -62,7 +62,7 @@
proptable[[i]] <- myprops
if(didit) ndid <- ndid + 1
}
- if(ndid > 0) msgout(paste('nonideal:',ndid,'species were nonideal\n'))
+ if(ndid > 0) message(paste('nonideal:',ndid,'species were nonideal'))
return(proptable)
}
Modified: pkg/CHNOSZ/R/protein.info.R
===================================================================
--- pkg/CHNOSZ/R/protein.info.R 2017-01-22 10:27:31 UTC (rev 122)
+++ pkg/CHNOSZ/R/protein.info.R 2017-01-28 08:29:14 UTC (rev 123)
@@ -163,7 +163,7 @@
protein.equil <- function(protein, T=25, loga.protein=0, digits=4) {
# show the individual steps in calculating metastable equilibrium among proteins
- msgout("protein.equil: temperature from argument is ", T, " degrees C\n")
+ message("protein.equil: temperature from argument is ", T, " degrees C")
TK <- convert(T, "K")
# get the amino acid compositions of the proteins
aa <- ip2aa(protein)
@@ -179,13 +179,13 @@
ionize.it <- TRUE
iword <- "ionized"
pH <- -thermo$basis$logact[match("H+", rownames(bmat))]
- msgout("protein.equil: pH from thermo$basis is ", pH, "\n")
+ message("protein.equil: pH from thermo$basis is ", pH)
}
# tell the user whose [Met] is in thermo$obigt
info.Met <- info(info('[Met]', "aq"))
- msgout("protein.equil: [Met] is from reference ", info.Met$ref1, "\n")
+ message("protein.equil: [Met] is from reference ", info.Met$ref1)
## first set of output: show results of calculations for a single protein
- msgout("protein.equil [1]: first protein is ", pname[1], " with length ", plength[1], "\n")
+ message("protein.equil [1]: first protein is ", pname[1], " with length ", plength[1])
# standard Gibbs energies of basis species
G0basis <- unlist(suppressMessages(subcrt(thermo$basis$ispecies, T=T, property="G")$out))
# coefficients of basis species in formation reactions of proteins
@@ -196,67 +196,67 @@
G0prot <- unlist(suppressMessages(subcrt(pname, T=T, property="G")$out))
# standard Gibbs energy of formation reaction of nonionized protein, cal/mol
G0protform <- G0prot - G0basissum
- msgout("protein.equil [1]: reaction to form nonionized protein from basis species has G0(cal/mol) of ", signif(G0protform[1], digits), "\n")
+ message("protein.equil [1]: reaction to form nonionized protein from basis species has G0(cal/mol) of ", signif(G0protform[1], digits))
if(ionize.it) {
# standard Gibbs energy of ionization of protein, cal/mol
G0ionization <- suppressMessages(ionize.aa(aa, property="G", T=T, pH=pH))[1, ]
- msgout("protein.equil [1]: ionization reaction of protein has G0(cal/mol) of ", signif(G0ionization[1], digits), "\n")
+ message("protein.equil [1]: ionization reaction of protein has G0(cal/mol) of ", signif(G0ionization[1], digits))
# standard Gibbs energy of formation reaction of ionized protein, cal/mol
G0protform <- G0protform + G0ionization
}
# standard Gibbs energy of formation reaction of non/ionized residue equivalents, dimensionless
G0res.RT <- G0protform/thermo$opt$R/TK/plength
- msgout("protein.equil [1]: per residue, reaction to form ", iword, " protein from basis species has G0/RT of ", signif(G0res.RT[1], digits), "\n")
+ message("protein.equil [1]: per residue, reaction to form ", iword, " protein from basis species has G0/RT of ", signif(G0res.RT[1], digits))
# coefficients of basis species in formation reactions of residues
resbasis <- suppressMessages(protein.basis(aa, T=T, normalize=TRUE))
# logQstar and Astar/RT
logQstar <- colSums(t(resbasis) * - thermo$basis$logact)
- msgout("protein.equil [1]: per residue, logQstar is ", signif(logQstar[1], digits), "\n")
+ message("protein.equil [1]: per residue, logQstar is ", signif(logQstar[1], digits))
Astar.RT <- -G0res.RT - log(10)*logQstar
- msgout("protein.equil [1]: per residue, Astar/RT = -G0/RT - 2.303logQstar is ", signif(Astar.RT[1], digits), "\n")
- if(!is.numeric(protein)) msgout("protein.equil [1]: not comparing calculations with affinity() because 'protein' is not numeric\n")
+ message("protein.equil [1]: per residue, Astar/RT = -G0/RT - 2.303logQstar is ", signif(Astar.RT[1], digits))
+ if(!is.numeric(protein)) message("protein.equil [1]: not comparing calculations with affinity() because 'protein' is not numeric")
else {
# for **Astar** we have to set the activities of the proteins to zero, not loga.protein!
a <- suppressMessages(affinity(iprotein=protein, T=T, loga.protein=0))
aAstar.RT <- log(10) * as.numeric(a$values) / plength
- msgout("check it! per residue, Astar/RT calculated using affinity() is ", signif(aAstar.RT[1], digits), "\n")
+ message("check it! per residue, Astar/RT calculated using affinity() is ", signif(aAstar.RT[1], digits))
if(!isTRUE(all.equal(Astar.RT, aAstar.RT, check.attributes=FALSE)))
stop("Bug alert! The same value for Astar/RT cannot be calculated manually as by using affinity()")
}
- if(length(pname)==1) msgout("protein.equil [all]: all done... give me more than one protein for equilibrium calculations\n")
+ if(length(pname)==1) message("protein.equil [all]: all done... give me more than one protein for equilibrium calculations")
else {
## next set of output: equilibrium calculations
- msgout("protein.equil [all]: lengths of all proteins are ", paste(plength, collapse=" "), "\n")
- msgout("protein.equil [all]: Astar/RT of all residue equivalents are ", paste(signif(Astar.RT, digits), collapse=" "), "\n")
+ message("protein.equil [all]: lengths of all proteins are ", paste(plength, collapse=" "))
+ message("protein.equil [all]: Astar/RT of all residue equivalents are ", paste(signif(Astar.RT, digits), collapse=" "))
expAstar.RT <- exp(Astar.RT)
sumexpAstar.RT <- sum(expAstar.RT)
- msgout("protein.equil [all]: sum of exp(Astar/RT) of all residue equivalents is ", signif(sumexpAstar.RT, digits), "\n")
+ message("protein.equil [all]: sum of exp(Astar/RT) of all residue equivalents is ", signif(sumexpAstar.RT, digits))
# boltzmann distribution
alpha <- expAstar.RT / sumexpAstar.RT
- msgout("protein.equil [all]: equilibrium degrees of formation (alphas) of residue equivalents are ", paste(signif(alpha, digits), collapse=" "), "\n")
+ message("protein.equil [all]: equilibrium degrees of formation (alphas) of residue equivalents are ", paste(signif(alpha, digits), collapse=" "))
# check with equilibrate()
if(is.numeric(protein)) {
loga.equil.protein <- unlist(suppressMessages(equilibrate(a, normalize=TRUE))$loga.equil)
# here we do have to convert from logarithms of activities of proteins to degrees of formation of residue equivalents
a.equil.residue <- plength*10^loga.equil.protein
ealpha <- a.equil.residue/sum(a.equil.residue)
- msgout("check it! alphas of residue equivalents from equilibrate() are ", paste(signif(ealpha, digits), collapse=" "), "\n")
+ message("check it! alphas of residue equivalents from equilibrate() are ", paste(signif(ealpha, digits), collapse=" "))
if(!isTRUE(all.equal(alpha, ealpha, check.attributes=FALSE)))
stop("Bug alert! The same value for alpha cannot be calculated manually as by using equilibrate()")
}
# total activity of residues
loga.residue <- log10(sum(plength * 10^loga.protein))
- msgout("protein.equil [all]: for activity of proteins equal to 10^", signif(loga.protein, digits), ", total activity of residues is 10^", signif(loga.residue, digits), "\n")
+ message("protein.equil [all]: for activity of proteins equal to 10^", signif(loga.protein, digits), ", total activity of residues is 10^", signif(loga.residue, digits))
# equilibrium activities of residues
loga.residue.equil <- log10(alpha*10^loga.residue)
- msgout("protein.equil [all]: log10 equilibrium activities of residue equivalents are ", paste(signif(loga.residue.equil, digits), collapse=" "), "\n")
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 123
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