@@ -1,5 +1,6 @@

 CHANGES IN VERSION 1.1.8

 ------------------------

+ o update get.placement <2015-06-05, Fri>

  o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>

  o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>

  o add mask function <2015-06-02, Tue>

@@ -179,8 +179,10 @@ setMethod("get.fields", signature(object = "jplace"),

 ##' get.placements(jp, by="all")

 setMethod("get.placements", signature(object = "jplace"),

           function(object, by="best", ...) {

+

               placements <- object@placements

               place <- placements[,1]

+              

               ids <- NULL

               if (length(placements) == 2) {

                   ids <- sapply(placements[,2], function(x) x[1])

@@ -189,12 +191,29 @@ setMethod("get.placements", signature(object = "jplace"),

               if (by == "best") { ## best hit

                   place <- lapply(place, function(x) {

                       if (is(x, "data.frame") || is(x, "matrix")) {

-                          return(x[1,])

+                          if (nrow(x) == 1) {

+                              return(x)

+                          }

+                          ## http://astrostatistics.psu.edu/su07/R/html/base/html/all.equal.html

+                          ## due to precision, number are identical maynot be equal, so use all.equal which can test nearly equal number

+                          ## if not equals, the output is a descript string of the differences

+                          idx <- sapply(2:nrow(x), function(i) all.equal(x[1,2], x[i,2]))

+                          if (any(idx == TRUE)) {

+                              return(x[c(1, which(idx==TRUE)),])

+                          } else {

+                              return(x[1,])

+                          }

+                          

                       } else {

+                          ## if only 1 row, it may stored as vector

+                          ## the edge number, for example 523 can be 523.0000 due to R stored number as real number

+                          ## be careful in mapping edge number.

                           return(x)

                       }

                   })

+                  

               }

+              

               place.df <- do.call("rbind", place)

               row.names(place.df) <- NULL

               if (!is.null(ids)) {

@@ -209,8 +228,8 @@ setMethod("get.placements", signature(object = "jplace"),

               } else {

                   colnames(place.df) <- object@fields

               }

-              

               res <- as.data.frame(place.df)

+              

               ## res[] <- lapply(res, as.character)

               ## for (i in 1:ncol(res)) {

               ##     if (all(grepl("^[0-9\\.e]+$", res[,i]))) {