Done with refactoring of xcmsSet R files

+ Moved all generic method definitions for xcmsSet and xcmsRaw into
  AllGenerics.R.
+ Moved all(?) xcmsSet methods into methods-xcmsSet.R.
+ Moved all xcmsSet functions into functions-xcmsSet.R.
+ Reverted the doRUnit.R file.

DESCRIPTION

@@ -49,6 +49,7 @@ Collate:
     'cwTools.R'
     'databases.R'
     'fastMatch.R'
+    'functions-xcmsSet.R'
     'init.R'
     'matchpeaks.R'
     'methods-netCdfSource.R'
@@ -68,6 +69,5 @@ Collate:
     'xcmsEIC.R'
     'xcmsFragments.R'
     'xcmsRaw.R'
-    'xcmsSet.R'
     'xcmsSource.R'
     'zzz.R'

R/AllGenerics.R

@@ -1,23 +1,115 @@
 ## On the long run it would be nice to have all generics in here.
-if(!isGeneric("getXcmsRaw"))
-    setGeneric("getXcmsRaw", function(object, ...) standardGeneric("getXcmsRaw"))
+## Alphabetically ordered.
 
-if(!isGeneric("mslevel"))
-    setGeneric("mslevel", function(object, ...) standardGeneric("mslevel"))
-if(!isGeneric("mslevel<-"))
-    setGeneric("mslevel<-", function(object, value) standardGeneric("mslevel<-"))
+## C
+setGeneric("calibrate", function(object, ...) standardGeneric("calibrate"))
 
-if(!isGeneric("profinfo"))
-    setGeneric("profinfo", function(object) standardGeneric("profinfo"))
+## D
+setGeneric("deepCopy", function(object) standardGeneric("deepCopy"))
+setGeneric("diffreport", function(object, ...) standardGeneric("diffreport"))
 
-if(!isGeneric("profinfo<-"))
-    setGeneric("profinfo<-", function(object, value) standardGeneric("profinfo<-"))
+## F
+setGeneric("filepaths", function(object) standardGeneric("filepaths"))
+setGeneric("filepaths<-", function(object, value) standardGeneric("filepaths<-"))
+setGeneric("fillPeaks.chrom", function(object, ...) standardGeneric("fillPeaks.chrom"))
+setGeneric("fillPeaks.MSW", function(object, ...) standardGeneric("fillPeaks.MSW"))
+setGeneric("fillPeaks", function(object, ...) standardGeneric("fillPeaks"))
+setGeneric("findmzROI", function(object, ...) standardGeneric("findmzROI"))
+setGeneric("findKalmanROI", function(object, ...) standardGeneric("findKalmanROI"))
+setGeneric("findPeaks", function(object, ...) standardGeneric("findPeaks"))
+setGeneric("findPeaks.centWave", function(object, ...)
+    standardGeneric("findPeaks.centWave"))
+setGeneric("findPeaks.massifquant", function(object, ...)
+    standardGeneric("findPeaks.massifquant"))
+setGeneric("findPeaks.matchedFilter", function(object, ...)
+    standardGeneric("findPeaks.matchedFilter"))
+setGeneric("findPeaks.MSW", function(object, ...) standardGeneric("findPeaks.MSW"))
+setGeneric("findPeaks.MS1", function(object, ...) standardGeneric("findPeaks.MS1"))
 
-if(!isGeneric("scanrange"))
-    setGeneric("scanrange", function(object, ...) standardGeneric("scanrange"))
-if(!isGeneric("scanrange<-"))
-    setGeneric("scanrange<-", function(object, value) standardGeneric("scanrange<-"))
 
+## G
+setGeneric("getEIC", function(object, ...) standardGeneric("getEIC"))
+setGeneric("getEICOld", function(object, ...) standardGeneric("getEICOld"))
+setGeneric("getEICNew", function(object, ...) standardGeneric("getEICNew"))
+setGeneric("getPeaks", function(object, ...) standardGeneric("getPeaks"))
+setGeneric("getScan", function(object, ...) standardGeneric("getScan"))
+setGeneric("getSpec", function(object, ...) standardGeneric("getSpec"))
+setGeneric("getXcmsRaw", function(object, ...) standardGeneric("getXcmsRaw"))
+## There's too many "group" methods here...
+setGeneric("group.density", function(object, ...) standardGeneric("group.density"))
+setGeneric("group.mzClust", function(object, ...) standardGeneric("group.mzClust"))
+setGeneric("group.nearest", function(object, ...) standardGeneric("group.nearest"))
+setGeneric("group", function(object, ...) standardGeneric("group"))
+setGeneric("groupidx", function(object) standardGeneric("groupidx"))
+setGeneric("groupidx<-", function(object, value) standardGeneric("groupidx<-"))
+setGeneric("groupnames", function(object, ...) standardGeneric("groupnames"))
+setGeneric("groups", function(object) standardGeneric("groups"))
+setGeneric("groups<-", function(object, value) standardGeneric("groups<-"))
+setGeneric("groupval", function(object, ...) standardGeneric("groupval"))
+
+## I
+setGeneric("image", function(x, ...) standardGeneric("image"))
+setGeneric("isCentroided", function(object, ...) standardGeneric("isCentroided"))
+
+## L
+setGeneric("levelplot", function(x, data, ...) standardGeneric("levelplot"))
 setGeneric("loadRaw", function(object, ...) standardGeneric("loadRaw"))
+
+## M
+setGeneric("mslevel", function(object, ...) standardGeneric("mslevel"))
+setGeneric("mslevel<-", function(object, value) standardGeneric("mslevel<-"))
+setGeneric("msnparent2ms", function(object, ...) standardGeneric("msnparent2ms"))
+setGeneric("msn2ms", function(object, ...) standardGeneric("msn2ms"))
+setGeneric("mzrange", function(object) standardGeneric("mzrange"))
+
+## P
+setGeneric("peaks<-", function(object, value) standardGeneric("peaks<-"))
+setGeneric("peakTable", function(object, ...) standardGeneric("peakTable"))
+setGeneric("plotChrom", function(object, ...) standardGeneric("plotChrom"))
+setGeneric("plotEIC", function(object, ...) standardGeneric("plotEIC"))
+setGeneric("plotPeaks", function(object, ...) standardGeneric("plotPeaks"))
+setGeneric("plotRaw", function(object, ...) standardGeneric("plotRaw"))
+setGeneric("plotrt", function(object, ...) standardGeneric("plotrt"))
+setGeneric("plotScan", function(object, ...) standardGeneric("plotScan"))
+setGeneric("plotSpec", function(object, ...) standardGeneric("plotSpec"))
+setGeneric("plotSurf", function(object, ...) standardGeneric("plotSurf"))
+setGeneric("plotTIC", function(object, ...) standardGeneric("plotTIC"))
+setGeneric("profinfo", function(object) standardGeneric("profinfo"))
+setGeneric("profinfo<-", function(object, value) standardGeneric("profinfo<-"))
+setGeneric("profMedFilt", function(object, ...) standardGeneric("profMedFilt"))
+setGeneric("profMethod", function(object) standardGeneric("profMethod"))
+setGeneric("profMethod<-", function(object, value) standardGeneric("profMethod<-"))
+setGeneric("profRange", function(object, ...) standardGeneric("profRange"))
+setGeneric("profStep", function(object) standardGeneric("profStep"))
+setGeneric("profStep<-", function(object, value) standardGeneric("profStep<-"))
+setGeneric("profStepPad<-", function(object, value) standardGeneric("profStepPad<-"))
+setGeneric("profMz", function(object) standardGeneric("profMz"))
+setGeneric("progressCallback", function(object) standardGeneric("progressCallback"))
+setGeneric("progressCallback<-", function(object, value) standardGeneric("progressCallback<-"))
+setGeneric("progressInfoUpdate", function(object) standardGeneric("progressInfoUpdate"))
+
+## R
+setGeneric("rawEIC", function(object, ...) standardGeneric("rawEIC"))
+setGeneric("rawMat", function(object, ...) standardGeneric("rawMat"))
+setGeneric("rawMZ", function(object, ...) standardGeneric("rawMZ"))
+setGeneric("retcor", function(object, ...) standardGeneric("retcor"))
+setGeneric("retcor.peakgroups", function(object, ...) standardGeneric("retcor.peakgroups"))
+setGeneric("retcor.obiwarp", function(object, ...) standardGeneric("retcor.obiwarp"))
+setGeneric("revMz", function(object, ...) standardGeneric("revMz"))
+setGeneric("rtrange", function(object) standardGeneric("rtrange"))
+
+## S
+setGeneric("sampclass", function(object) standardGeneric("sampclass"))
+setGeneric("sampclass<-", function(object, value) standardGeneric("sampclass<-"))
+setGeneric("sampnames", function(object) standardGeneric("sampnames"))
+setGeneric("sampnames<-", function(object, value) standardGeneric("sampnames<-"))
+setGeneric("scanrange", function(object, ...) standardGeneric("scanrange"))
+setGeneric("scanrange<-", function(object, value) standardGeneric("scanrange<-"))
+setGeneric("sortMz", function(object, ...) standardGeneric("sortMz"))
+
+## W
+setGeneric("write.cdf", function(object, ...) standardGeneric("write.cdf"))
+
+## X
 setGeneric("xcmsSource", function(object, ...) standardGeneric("xcmsSource"))