@@ -7641,13 +7641,29 @@ reclasify_intern <- function(SG,mievento,pp1,pp2,ppref){

   ppref_2 <- strsplit(unlist(strsplit(ppref,",")),"-")

   pp1_2 <- unlist(lapply(pp1_2, function(X){

-    intersect(grep(X[1],as.vector(SG$Edges$From)),grep(X[2],as.vector(SG$Edges$To)))

+    if(identical(X[1],X[2])){

+      X <- paste0(X,c(".a",".b"))

+    }else{

+      X <- paste0(X,c(".b",".a"))

+    }

+    which(as.vector(SG$Edges$From)==X[1] & as.vector(SG$Edges$To)==X[2])

+    

   }))

   pp2_2 <- unlist(lapply(pp2_2, function(X){

-    intersect(grep(X[1],as.vector(SG$Edges$From)),grep(X[2],as.vector(SG$Edges$To)))

+    if(identical(X[1],X[2])){

+      X <- paste0(X,c(".a",".b"))

+    }else{

+      X <- paste0(X,c(".b",".a"))

+    }

+    which(as.vector(SG$Edges$From)==X[1] & as.vector(SG$Edges$To)==X[2])

   }))

   ppref_2 <- unlist(lapply(ppref_2, function(X){

-    intersect(grep(X[1],as.vector(SG$Edges$From)),grep(X[2],as.vector(SG$Edges$To)))

+    if(identical(X[1],X[2])){

+      X <- paste0(X,c(".a",".b"))

+    }else{

+      X <- paste0(X,c(".b",".a"))

+    }

+    which(as.vector(SG$Edges$From)==X[1] & as.vector(SG$Edges$To)==X[2])

   }))

   Event <- list(P1=SG$Edges[pp1_2,],P2=SG$Edges[pp2_2,],Ref=SG$Edges[ppref_2,])

@@ -7712,41 +7728,32 @@ reclasify_intern <- function(SG,mievento,pp1,pp2,ppref){

     while(TRUE){

-      torm <- which(

-        rowSums(newAdj[-nrow(newAdj),])==0)

+      torm <- which(rowSums(newAdj[-nrow(newAdj),])==0)

       if(length(torm)>0){

         torm_index <- c()

         for(ssx in 1:length(torm)){

           # ssx <- 2

-          subexontoremove <- gsub(

-            "\\..*","",names(torm)[ssx])

-          torm_index <- c(torm_index,

-                          grep(subexontoremove,

-                               rownames(newAdj)))

+          subexontoremove <- names(torm)[ssx]

+          torm_index <- c(torm_index,which(rownames(newAdj)==subexontoremove))

         }

-        newAdj <- newAdj[-torm_index,

-                         -torm_index]     

+        newAdj <- newAdj[-torm_index,-torm_index]     

       }else{

         break

       }

     }

+    

+    

     while(TRUE){

-      torm <- which(

-        colSums(newAdj[,-1])==0)

+      torm <- which(colSums(newAdj[,-1])==0)

       if(length(torm)>0){

         torm_index <- c()

         for(ssx in 1:length(torm)){

           # ssx <- 2

-          subexontoremove <- gsub(

-            "\\..*","",names(torm)[ssx])

-          torm_index <- c(

-            torm_index,

-            grep(subexontoremove,

-                 rownames(newAdj)))

+          subexontoremove <- names(torm)[ssx]

+          torm_index <- c(torm_index,which(rownames(newAdj)==subexontoremove))

         }

-        newAdj <- newAdj[

-          -torm_index,-torm_index]     

+        newAdj <- newAdj[-torm_index,-torm_index]     

       }else{

         break

       }

@@ -7767,6 +7774,12 @@ reclasify_intern <- function(SG,mievento,pp1,pp2,ppref){

     #possible paths:

     numberOfPaths <- solve(

       Diagonal(ncol(newAdj))-newAdj)

+    

+    if(numberOfPaths[

+      ref_junct_ford,ref_junct_revs] > 10){

+      return("Complex Event")

+    }

+    

     distances_list <- vector(

       mode="list",

       length=numberOfPaths[

@@ -22,7 +22,6 @@

 #' @param SplicingGraph A list with the splicing graph of all the genes of

 #'  a reference transcriptome. This data is returned

 #'   by the function EventDetection_transcriptome.

-#' @param cores Number of cores using in the parallel processing (by default = 1)

 #'

 #' @return A data.frame containing a new column with the new classification ('EventType_new'):

 #' 

@@ -39,8 +38,7 @@

 #' #this table has the information of 5 complex events.

 #' 

 #' EventTable_new <- Events_ReClassification(EventTable = EventTable,

-#'                                           SplicingGraph = SG_reclassify,

-#'                                           cores = 1)

+#'                                           SplicingGraph = SG_reclassify)

 #'          

 #'     

 #'

@@ -60,7 +58,7 @@

 #' @importFrom S4Vectors queryHits subjectHits split

 #' @importFrom IRanges relist disjoin %over% reduce

-Events_ReClassification <- function(EventTable,SplicingGraph,cores = 1){

+Events_ReClassification <- function(EventTable,SplicingGraph){

   if (is.null(EventTable)) {

     stop("not EventTable")

@@ -76,11 +74,13 @@ Events_ReClassification <- function(EventTable,SplicingGraph,cores = 1){

   if(length(uux)==0){

     return(EventTable)

   }

-  

-  

-  registerDoParallel(cores = cores)

-  Result <- foreach(jj = seq_len(length(uux))) %dopar%

-    {

+  cat("\nStarting reclassification\n")

+  pb <- txtProgressBar(min = 0, max = length(uux), 

+                       style = 3)

+  misnewtype <- c()

+    for(jj in seq_len(length(uux))){

+      setTxtProgressBar(pb, jj)

+      # cat(jj,"\n")

       mievento <- EventTable$ID[uux][jj]

       # mievento

       ggx <- match(EventTable$GeneName[uux][jj],names(SplicingGraph))

@@ -90,14 +90,17 @@ Events_ReClassification <- function(EventTable,SplicingGraph,cores = 1){

       pp1 <- EventTable$Path.1[uux][jj]

       pp2 <- EventTable$Path.2[uux][jj]

       ppref <- EventTable$Path.Reference[uux][jj]

-      return(reclasify_intern(SG = SG,mievento = mievento,

-                              pp1=pp1,pp2=pp2,ppref=ppref))

+      misnewtype <- c(misnewtype,reclasify_intern(SG = SG,mievento = mievento,

+                                                  pp1=pp1,pp2=pp2,ppref=ppref))

     }

-  Result <- unlist(Result)

+  close(pb)

+  cat("\nReclassification Finished\n")

+  # Result <- unlist(Result)

+  # EventTable$EventType_new[uux] <- Result

-  EventTable$EventType_new[uux] <- Result

+  EventTable$EventType_new[uux] <- misnewtype

   return(EventTable)

@@ -4,7 +4,7 @@

 \alias{Events_ReClassification}

 \title{Events_ReClassification}

 \usage{

-Events_ReClassification(EventTable, SplicingGraph, cores = 1)

+Events_ReClassification(EventTable, SplicingGraph)

 }

 \arguments{

 \item{EventTable}{Table returned by EventDetection_transcriptome. 

@@ -13,8 +13,6 @@ Can be easily loaded using the function read.delim as data.frame.}

 \item{SplicingGraph}{A list with the splicing graph of all the genes of

 a reference transcriptome. This data is returned

  by the function EventDetection_transcriptome.}

-

-\item{cores}{Number of cores using in the parallel processing (by default = 1)}

 }

 \value{

 A data.frame containing a new column with the new classification ('EventType_new'):

@@ -46,8 +44,7 @@ EventTable <- read.delim(file=inputFile)

 #this table has the information of 5 complex events.

 EventTable_new <- Events_ReClassification(EventTable = EventTable,

-                                          SplicingGraph = SG_reclassify,

-                                          cores = 1)

+                                          SplicingGraph = SG_reclassify)

@@ -1033,7 +1033,7 @@ Thus, EventPointer reclassifies the complex events according to how similar the

 The following code shows how this function works for a subset of 5 splicing events:

-```{r reclassify, eval=TRUE}

+```{r reclassification, eval=TRUE}

 #load splicing graph

 data("SG_reclassify")

@@ -1044,54 +1044,12 @@ EventTable <- read.delim(file=inputFile)

 #this table has the information of 5 complex events.

 EventTable_new <- Events_ReClassification(EventTable = EventTable,

-                                          SplicingGraph = SG_reclassify,

-                                          cores = 1)

+                        SplicingGraph = SG_reclassify)

 ```

 The following figures show the structure of these events and their corresponding gene:

 **Example 1** 

-![**Example 1** Complex Event reclassified as alternative 5' splice site and as complex casstte exon  ](example_1_alt5_ce.png)

-```{r example1, eval=TRUE}

-EventTable_new$EventType_new[[1]]

-```

-<br><br><br>

-**Example 2** 

-![**Example 2** Complex Event reclassified as Multiple Exon Skipping  ](example_2_multiple_exon_skipping.png)

-```{r example2, eval=TRUE}

-EventTable_new$EventType_new[[2]]

-```

-

-<br><br><br>

-**Example 3** 

-![**Example 3** Complex Event reclassified as Complex Cassette Exon  ](example3_ce.png)

-```{r example3, eval=TRUE}

-EventTable_new$EventType_new[[3]]

-```

-

-<br><br><br>

-**Example 4** 

-![**Example 4** Complex Event reclassified as Retained Intron and Complex Cassette Exon  ](example_4_ri_ce.png)

-```{r example4, eval=TRUE}

-EventTable_new$EventType_new[[4]]

-```

-

-<br><br><br>

-**Example 5** 

-![**Example 5** Complex Event reclassified as Complex Cassette Exon and complex Alternative 3' Splice Site  ](example_5_ce_alt3.png)

-```{r example5, eval=TRUE}

-EventTable_new$EventType_new[[5]]

-```

-

-

-Further, files needed to load these pictures in IGV are available:

-

-```{r source_pictures,eval=FALSE}

-PathFiles<-system.file("extdata",package="EventPointer")

-paste0(PathFiles,"/example_recla_events.gtf")

-paste0(PathFiles,"/example_recla_genes.gtf")

-```

-

 ## Statistical Tests