@@ -132,9 +132,6 @@ changeMaxPostCutoff.multivariate <- function(model, maxPost.cutoff, invert=FALSE

     } else if (is(model, class.combined.multivariate.hmm)) {

         ptm <- startTimedMessage("Calculating states from maximum-posterior in each peak ...")

-        mapping.df <- stateBrewer(model$info[,setdiff(names(model$info), 'ID')], mode='full')

-        mapping <- mapping.df$combination

-        names(mapping) <- mapping.df$state

         if (is.null(model$bins$maxPostInPeak)) {

             p <- getMaxPostInPeaks(model$bins$state, model$bins$posteriors)

         } else {

@@ -148,7 +145,12 @@ changeMaxPostCutoff.multivariate <- function(model, maxPost.cutoff, invert=FALSE

                 p.thresholded[,icol] <- p[,icol] < threshold[icol] & p[,icol] > 0

             }

         }

-        states <- factor(bin2dec(p.thresholded), levels=mapping.df$state)

+        decstates <- bin2dec(p.thresholded)

+        binary.matrix <- p.thresholded[!duplicated(decstates),]

+        mapping.df <- stateBrewer(model$info[,setdiff(names(model$info), 'ID')], mode='full')

+        mapping <- mapping.df$combination

+        names(mapping) <- mapping.df$state

+        states <- factor(decstates, levels=mapping.df$state)

         stopTimedMessage(ptm)

         ## Make fake multiHMM to do the segmentation with "combineMultivariates"

         multiHMM <- list()

@@ -379,15 +381,17 @@ changePostCutoff.multivariate <- function(model, post.cutoff) {

         stopTimedMessage(ptm)

     } else if (is(model, class.combined.multivariate.hmm)) {

         ptm <- startTimedMessage("Calculating states from posteriors ...")

-        mapping.df <- stateBrewer(model$info[,setdiff(names(model$info), 'ID')], mode='full')

-        mapping <- mapping.df$combination

-        names(mapping) <- mapping.df$state

         post <- model$bins$posteriors

         post.thresholded <- matrix(FALSE, ncol=ncol(post), nrow=nrow(post))

         for (icol in 1:ncol(post)) {

             post.thresholded[,icol] <- post[,icol] >= threshold[icol]

         }

-        states <- factor(bin2dec(post.thresholded), levels=mapping.df$state)

+        decstates <- bin2dec(post.thresholded)

+        binary.matrix <- post.thresholded[!duplicated(decstates),]

+        mapping.df <- stateBrewer(model$info[,setdiff(names(model$info), 'ID')], mode='full', binary.matrix = binary.matrix)

+        mapping <- mapping.df$combination

+        names(mapping) <- mapping.df$state

+        states <- factor(decstates, levels=mapping.df$state)

         stopTimedMessage(ptm)

         ## Make fake multiHMM

         multiHMM <- list()