@@ -1,7 +1,7 @@

 Package: flowWorkspace

 Type: Package

 Title: Infrastructure for representing and interacting with the gated cytometry

-Version: 3.27.23

+Version: 3.27.24

 Date: 2011-06-10

 Author: Greg Finak, Mike Jiang

 Maintainer: Greg Finak <gfinak@fhcrc.org>,Mike Jiang <wjiang2@fhcrc.org>

@@ -611,6 +611,8 @@ setMethod("GatingSet", c("GatingHierarchy", "character"), function(x, y, path=".

           ##################################

           #transforming and gating

           ##################################

+        gains <- numeric()#gain is no longer relevant

+        names(gains) <- character()

           if(execute)

           {

@@ -643,8 +645,7 @@ setMethod("GatingSet", c("GatingHierarchy", "character"), function(x, y, path=".

             # 

             # names(gains) <- this_pd$name

             # gains <- gains[gains != 1]#only pass the valid gains to save the unnecessary computing

-            gains <- numeric()#gain is no longer relevant

-            names(gains) <- character()

+        

             #update colnames in order for the gating to find right dims

             if(!is.null(prefixColNames)){

               dimnames(mat) <- list(NULL, prefixColNames)

@@ -704,32 +705,32 @@ setMethod("GatingSet", c("GatingHierarchy", "character"), function(x, y, path=".

           #once we have confirmed that ws is a reliable source of keyword

           #EDIT: Acutally we've already found one workspace from PROVIDE study

           #that does not contain the gain keyword for all channels. So the ws is not reliable source of keyword

-

-

-          gains <- rep(1,length(cnd))#init with default 1

-

-          #get gains from keywords

-          kw_gains <- grep("P[0-9]{1,}G", names(kw))

-

-          if(length(kw_gains) > 0){

-            key_names <- unique(names(kw[kw_gains]))

-            kw_gains <- kw[key_names]

-

-            # Sometimes the keywords where the gain is not set, the gain value is NULL.

-            # We replace these instances with the default of 1.

-            kw_gains[sapply(kw_gains, is.null)] <- 1

-

-            #update the default gain values

-            #extract numeric index from channels (Not every channel necessarily has its gain keyword stored in xml)

-            found_gain_chnl_ind <-  as.numeric(gsub('G$', "", gsub('^\\$P', "", key_names)))

-            gains[found_gain_chnl_ind] <- as.numeric(kw_gains)

-          }

-

-

-

-

-          names(gains) <- prefixColNames

-          gains <- gains[gains != 1]#only pass the valid gains to save the unnecessary computing

+          #EDIT: gain is no longer needed #213

+

+          # gains <- rep(1,length(cnd))#init with default 1

+          # 

+          # #get gains from keywords

+          # kw_gains <- grep("P[0-9]{1,}G", names(kw))

+          # 

+          # if(length(kw_gains) > 0){

+          #   key_names <- unique(names(kw[kw_gains]))

+          #   kw_gains <- kw[key_names]

+          # 

+          #   # Sometimes the keywords where the gain is not set, the gain value is NULL.

+          #   # We replace these instances with the default of 1.

+          #   kw_gains[sapply(kw_gains, is.null)] <- 1

+          # 

+          #   #update the default gain values

+          #   #extract numeric index from channels (Not every channel necessarily has its gain keyword stored in xml)

+          #   found_gain_chnl_ind <-  as.numeric(gsub('G$', "", gsub('^\\$P', "", key_names)))

+          #   gains[found_gain_chnl_ind] <- as.numeric(kw_gains)

+          # }

+          # 

+          # 

+          # 

+          # 

+          # names(gains) <- prefixColNames

+          # gains <- gains[gains != 1]#only pass the valid gains to save the unnecessary computing

           #transform and adjust the gates without gating

           if(transform)

             .cpp_computeGates(gs@pointer, guid, gains, extend_val, extend_to)