diff MassdbConn.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

--- a/MassdbConn.R	Sat Sep 03 17:02:01 2016 -0400
+++ b/MassdbConn.R	Thu Mar 02 08:55:00 2017 -0500
@@ -1,31 +1,130 @@
-if ( ! exists('MassdbConn')) {
+#####################
+# CLASS DECLARATION #
+#####################
+
+MassdbConn <- methods::setRefClass("MassdbConn", contains = "BiodbConn")
+
+###############################
+# GET CHROMATOGRAPHIC COLUMNS #
+###############################
+
+# Get a list of chromatographic columns contained in this database.
+# compound.ids  A list of compound IDs used to filter results.
+# The returned value is a data.frame with two columns : one for the ID (BIODB.ID) and another one for the title (BIODB.TITLE).
+MassdbConn$methods( getChromCol = function(compound.ids = NULL) {
+	stop("Method getChromCol() is not implemented in concrete class.")
+})
 
-	source('BiodbConn.R')
+#################
+# GET MZ VALUES #
+#################
+
+# Returns a numeric vector of all masses stored inside the database.
+MassdbConn$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
+	stop("Method getMzValues() not implemented in concrete class.")
+})
+
+################
+# GET NB PEAKS #
+################
+
+# Returns the number of peaks contained in the database
+MassdbConn$methods( getNbPeaks = function(mode = NULL, compound.ids = NULL) {
+	stop("Method getNbPeaks() not implemented in concrete class.")
+})
+
+#########################
+# FIND COMPOUND BY NAME #
+#########################
 
-	#####################
-	# CLASS DECLARATION #
-	#####################
-	
-	MassdbConn <- setRefClass("MassdbConn", contains = "BiodbConn")
+# Find a molecule by name
+# name   A vector of molecule names to search for.
+# Return an integer vector of the same size as the name input vector, containing the found molecule IDs, in the same order.
+MassdbConn$methods( findCompoundByName = function(name) {
+	stop("Method findCompoundByName() not implemented in concrete class.")
+})
+
+####################################
+# FIND SPECTRA IN GIVEN MASS RANGE #
+####################################
+# Find spectra in the given mass range.
+# rtype the type of return, objects, dfspecs data.frame of spectra, dfpeaks data.frame of peaks.
+MassdbConn$methods( searchMzRange = function(mzmin, mzmax, rtype = c("objects","dfspecs","dfpeaks")){
+	stop("Method searchMzRange() not implemented in concrete class.")
+})
+
+####################################
+# FIND SPECTRA IN GIVEN MASS RANGE #
+####################################
+MassdbConn$methods( searchMzTol = function(mz, tol, tolunit=BIODB.MZTOLUNIT.PLAIN, rtype = c("objects","dfspecs","dfpeaks")){
+	stop("Method searchMzTol() not implemented in concrete class.")
+})
 
-	###############################
-	# GET CHROMATOGRAPHIC COLUMNS #
-	###############################
+######################################################
+# FIND A MOLECULES WITH PRECURSOR WITHIN A TOLERANCE #
+######################################################
+ MassdbConn$methods( searchSpecPrecTol = function(mz, tol, tolunit=BIODB.MZTOLUNIT.PLAIN, mode = NULL){
+	stop("Method searchSpecPrecTol not implemented in concrete class.")
+ })
+
+#################################
+#perform a database MS-MS search#
+#################################
+
+### spec : the spec to match against the database.
+### precursor : the mass/charge of the precursor to be looked for.
+### mtol : the size of the windows arounf the precursor to be looked for.
+### ppm : the matching ppm tolerance.
+### fun :  
+### dmz : the mass tolerance is taken as the minium between this quantity and the ppm.
+### npmin : the minimum number of peak to detect a match (2 recommended)
+
+MassdbConn$methods( msmsSearch = function(spec, precursor, mztol, tolunit,
+											 ppm, fun = BIODB.MSMS.DIST.WCOSINE,
+											 params = list(), npmin=2, dmz = 0.001,
+											 mode = BIODB.MSMODE.POS, return.ids.only = TRUE){
+
 	
-	# Get a list of chromatographic columns contained in this database.
-	# compound.ids  A list of compound IDs used to filter results.
-	# The returned value is a data.frame with two columns : one for the ID (BIODB.ID) and another one for the title (BIODB.TITLE).
-	MassdbConn$methods( getChromCol = function(compound.ids = NULL) {
-		stop("Method getChromCol() is not implemented in concrete class.")
+	# TODO replace by msms precursor search when available.
+	lspec <- .self$searchSpecPrecTol( precursor, mztol, BIODB.MZTOLUNIT.PLAIN, mode = mode)
+	rspec <- lapply(lspec,function(x){
+        peaks <- x$getFieldValue(BIODB.PEAKS)
+		
+		####Getting the correct fields
+		vcomp <- c(BIODB.PEAK.MZ, BIODB.PEAK.RELATIVE.INTENSITY, BIODB.PEAK.INTENSITY)
+		
+		foundfields <- vcomp %in% colnames(peaks)
+		if(sum(foundfields ) < 2){
+			stop(paste0("fields can't be coerced to mz and intensity : ",colnames(peaks)))
+		}
+		
+		peaks <- peaks[ , vcomp[which( foundfields ) ] ]
+		
+		peaks
 	})
+	
+	# TODO Import compareSpectra into biodb and put it inside massdb-helper.R or hide it as a private method.
+	res <- compareSpectra(spec, rspec, npmin = npmin, fun = fun, params = params)
+	
+	if(is.null(res)) return(NULL) # To decide at MassdbConn level: return empty list (or empty data frame) or NULL.
+	###Adiing the matched peaks and the smimlarity values to spectra.
+	
+	lret <-vector(length(lspec),mode = "list")
+	vsimilarity <- numeric( length( lspec ) )
+	vmatched <- vector( mode = "list", length( lspec ) )
+	
+	if( return.ids.only ){
+	    lret <- sapply( lspec, function( x ) {
+	    	x$getFieldValue( BIODB.ACCESSION )
+	    })
+	}else{
+	    ###TODO implement three types of return.
+	    lret <- lspec
+	}
+	
+	###Reordering the list.
+	lret <- lret[ res$ord ]
+	
 
-	#################
-	# GET MZ VALUES #
-	#################
-	
-	# Returns a numeric vector of all masses stored inside the database.
-	MassdbConn$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
-		stop("Method getMzValues() not implemented in concrete class.")
-	})
-
-}
+	return( list(measure = res$similarity[ res$ord ], matchedpeaks = res$matched [ res$ord ], id = lret))
+})