--- a
+++ b/scripts/template.R
@@ -0,0 +1,403 @@
+setwd("./templates")
+namefile <- "2.txt"
+namestr <- paste("./../clustall9k/", namefile, sep = "")
+b <- read.csv(namestr, header = F, row.names = NULL, stringsAsFactors = F)
+
+for (i in 1:ncol(b)) { 
+  for (j in 1:nrow(b)) {
+    if (i > 1) {
+      b[j,1] <- paste(b[j,1], b[j, i], sep = "")
+    }
+  }
+}
+
+b <- as.data.frame(b[[1]])
+
+
+b[] <- lapply(b, as.character)
+b[] <- lapply(b, tolower)
+
+
+
+
+cbindPad <- function(...){
+  args <- list(...)
+  n <- sapply(args,nrow)
+  mx <- max(n)
+  pad <- function(x, mx){
+    if (nrow(x) < mx){
+      nms <- colnames(x)
+      padTemp <- matrix(NA, mx - nrow(x), ncol(x))
+      colnames(padTemp) <- nms
+      if (ncol(x)==0) {
+        return(padTemp)
+      } else {
+        return(rbind(x,padTemp))
+      }
+    }
+    else{
+      return(x)
+    }
+  }
+  rs <- lapply(args,pad,mx)
+  return(do.call(cbind,rs))
+}
+
+
+
+##Platelet Change To Rules
+
+b[] <- lapply(b[], function(x) gsub("Platelet","Platelets",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("Plateletss","Platelets",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("Platelet count","Platelets",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("Platelets:","Platelets",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("\\(plts\\)","",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("\\(plt\\)","",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(">",">=",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("greater than or equal to",">=",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(">==",">=",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(" cell/mm\\^3","/mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(" */ *mm\\^3","/mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("/microliters","mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(" *cells/mcL","/mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(" mm\\^3","/mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub(" *x *10\\^9/L","000/mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("100000","100 000",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("ul","mcL",x, ignore.case = T))
+b[] <- lapply(b[], function(x) gsub("mcl","mcL",x, ignore.case = T))
+
+
+
+
+
+
+
+
+l <- as.data.frame(matrix(0, ncol = 1, nrow = (nrow(b))))
+
+
+for (i in 1:nrow(b)) {
+  if (length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))) > ncol(l)) {
+    l <- as.data.frame(matrix(0, ncol = length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))), nrow = (nrow(b))))
+  }
+  
+}
+n <- 1
+for (i in 1:nrow(b)) {
+  
+  n <- as.numeric(as.numeric(ncol(l)) - as.numeric(length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)))))
+  l[i,] <- c( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)), rep("IGNORE", times = as.numeric(n)))
+}
+
+l <- cbind(l, rep(0, times = nrow(l)))
+names(l)[ncol(l)] <- "wc"
+for (i in 1:nrow(l)) {
+  l[i,ncol(l)] <- length(grep("IGNORE", l[i,]))
+}
+
+
+row1 <- unlist(strsplit(unlist(strsplit(b[which.max(l$wc),1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))
+
+wc_df <- as.data.frame(l$wc) 
+for (i in 1:nrow(wc_df)) {
+  wc_df[i,1] <- ncol(l) - wc_df[i,1] - 1
+  wc_df[i,2] <- 0
+}
+
+
+l <- l[1:(ncol(l)-1)]
+
+
+
+
+base_str <- row1
+text_df <- l
+text_df_2 <- text_df
+loc_df <- as.data.frame(matrix(0, ncol = 2*length(base_str), nrow = nrow(text_df)), stringsAsFactors = F)
+rem_df <- as.data.frame(matrix('f', ncol = 1, nrow = nrow(text_df)), stringsAsFactors = F)
+fillins_df <- as.data.frame(matrix(NA, ncol = length(base_str), nrow = nrow(text_df)), stringsAsFactors = F)
+temp_df <- as.data.frame(matrix(NA, ncol = length(base_str) + 1, nrow = 1), stringsAsFactors = F)
+
+i <- 1
+j <- 1
+diff <- 0
+count <- 0
+threshold <- 0.1
+temp_loc <- 1
+fillins_loc <- 1
+loc <- 1
+blank_check <- F
+match_check <- F
+
+while (j <= length(base_str)) {
+  n <- 1
+  k <- 1
+  while (n <= nrow(text_df)) {
+    #print("n:")
+    #print(n)
+    while (k <= (ncol(text_df)-diff)) {
+      #print("k:")
+      #print(k)
+      if ( ((paste(text_df[n, k:(k+diff)], collapse = ' ')) == (paste(base_str[i:j], collapse = ' '))) ) {
+        if (loc == 1) {
+          match_check <- T
+          count <- count + 1
+          loc_df[n,loc] <- k
+          loc_df[n,loc+1] <- k + diff
+          k <- ncol(text_df)-diff+1
+        }
+        
+        else if (diff == 0) {
+          if (k > loc_df[n, loc-1]) {
+          
+            match_check <- T
+            count <- count + 1
+            loc_df[n,loc] <- k
+            loc_df[n,loc+1] <- k + diff
+            k <- ncol(text_df)-diff+1
+          }
+        } else {
+            
+            if (k == (loc_df[n,loc-2])) {
+              match_check <- T
+              count <- count + 1
+              loc_df[n,loc] <- k
+              loc_df[n,loc+1] <- k + diff
+              k <- ncol(text_df)-diff+1
+            }	
+          }
+        }
+      k <- k + 1
+    }
+    if (match_check == F) {
+      rem_df[n,1] <- 't'
+    }else {
+      print("YOU HIT A MATCH")
+    }
+    n <- n + 1
+    k <- 1
+    match_check <- F
+  }
+  if (count >= (nrow(text_df)*threshold)) {
+    if (count < nrow(text_df)) {
+      threshold <- ((threshold)*nrow(text_df_2))/(sum(rem_df$V1 == 'f'))
+    }
+    text_df <- text_df[which(rem_df$V1 == 'f'),]
+    loc_df <- loc_df[which(rem_df$V1 == 'f'),]
+    fillins_df <- fillins_df[which(rem_df$V1 == 'f'),]
+    wc_df <- wc_df[which(rem_df$V1 == 'f'),]
+    rem_df <- subset(rem_df, V1 == 'f')
+    if (loc == 1) {
+      for (n in 1:nrow(loc_df)) {
+        if (loc_df[n, loc] != 1) {
+          temp_df[1,temp_loc]  <- "BLANK"
+          temp_loc <- temp_loc + 1
+          blank_check <- T
+          fillins_loc <- fillins_loc + 1
+          break
+        }
+      }
+    }else {
+        for (n in 1:nrow(loc_df)) {
+          if ((loc_df[n,loc]) - (loc_df[n,loc-1]) > 1) {
+            temp_df[1,temp_loc]  <- "BLANK"
+            temp_loc <- temp_loc + 1
+            blank_check <- T
+            fillins_loc <- fillins_loc + 1
+            break
+          }
+        }
+    }
+    
+    
+    if (diff > 0) {
+      temp_loc <- temp_loc - 1
+      for (x in 1:nrow(loc_df)) {
+        loc_df[x, loc - 2] <- loc_df[x, loc]
+        loc_df[x, loc - 1] <- loc_df[x, loc + 1]
+        loc_df[x, loc] <- 0 
+        loc_df[x, loc + 1] <- 0 
+      }
+      loc <- loc - 2
+    }
+    if (blank_check == T) {
+      print ("BLANK_CHECK")
+      print (loc)
+      print("161")
+      for (x in 1:nrow(fillins_df)) {
+        print("163")
+        if (loc == 1) {
+          print("165")
+          if (loc_df[x, loc] != 1) {
+            print("167")
+            fillins_df[x, fillins_loc] <- paste(text_df[x, 1:(loc_df[x,loc]-1)], collapse = ' ')
+          }
+        }
+        else {
+          print("172")
+          if ((loc_df[x,loc]) - (loc_df[x,loc-1]) > 1) {
+            print("174")
+            fillins_df[x, fillins_loc] <- paste(text_df[x, (loc_df[x,loc-1] + 1):(loc_df[x,loc]-1)], collapse = ' ')
+          }
+        }
+      }
+    }
+    print("180")
+    temp_df[temp_loc] <- paste(base_str[i:j], collapse = ' ')
+    temp_loc <- temp_loc + 1
+    loc <- loc + 2
+    j <- j + 1
+    #threshold <- ((threshold)*nrow(text_df_2))/(sum(rem_df$V1 == 'f'))
+    #text_df <- text_df[which(rem_df$V1 == 'f'),]
+    #loc_df <- loc_df[which(rem_df$V1 == 'f'),]
+    #fillins_df <- fillins_df[which(rem_df$V1 == 'f'),]
+    #wc_df <- wc_df[which(rem_df$V1 == 'f'),]
+    #rem_df <- subset(rem_df, V1 == 'f')
+  }else {
+    #print("YOU HIT ELSE")
+    if (diff > 0) {
+      i <- j
+      j <- i
+    }else {
+      i <- i + 1
+      j <- i
+    }
+    
+    loc_df[loc] <- 0
+    loc_df[loc+1] <- 0
+    rem_df$V1 <- 'f'
+    
+  }
+  
+  print("this is i: ")
+  print (i)
+  count <- 0
+  diff <- j - i
+  print("this is diff:")
+  print(diff)
+}
+
+
+##This part could be cleaner
+loc_df <- loc_df[, colSums(loc_df != 0) > 0]
+
+blank_check_end <- F
+
+for (n in 1:nrow(loc_df)) {
+  if (loc_df[n, ncol(loc_df)] < wc_df[n, 1]) {
+    blank_check_end <- T
+  }
+}
+
+if (blank_check_end == T) {
+  fillins_loc = fillins_loc + 1
+  temp_df[temp_loc] <- "BLANK"
+  for (x in 1:nrow(fillins_df)) {
+    fillins_df[x, fillins_loc] <- paste(text_df[x, (loc_df[x,ncol(loc_df)] + 1):ncol(text_df)], collapse = ' ')
+  }
+}
+
+for (x in 1:nrow(fillins_df)) {
+  fillins_df[x, fillins_loc] <- gsub("IGNORE", "", fillins_df[x, fillins_loc])
+}
+
+
+##Part where we do the counting
+fillins_df <- fillins_df[, colSums(is.na(fillins_df)) != nrow(fillins_df)]
+
+
+for (i in 1:ncol(fillins_df)) {
+  names(fillins_df)[i] <- paste("Blank", as.character(i), collapse = ' ')
+}
+
+fillins_df <- sapply(fillins_df, as.character)
+fillins_df[is.na(fillins_df)] <- ""
+
+
+i <- 1
+while (i <=  ncol(fillins_df)) {
+  fillins_df <- as.data.frame(cbind (fillins_df[,c(1:i)], rep(1, times = nrow(fillins_df)), fillins_df[,-c(1:i)]))
+  i <- i+ 2
+}
+
+for (i in 1:ncol(fillins_df)) {
+  if (i %% 2 == 0) {
+    colnames(fillins_df)[i] <- "Frequency"
+    fillins_df[,i] <- sapply(fillins_df[,i], as.character)
+    fillins_df[,i] <- sapply(fillins_df[,i], as.numeric)
+  }
+}
+
+for (i in 1:ncol(fillins_df)) {
+  if (i %% 2 == 1) {
+    colnames(fillins_df)[i] <- paste("Blank", (i+1)/2, collapse ="")
+    fillins_df[,i] <- sapply(fillins_df[,i], as.character)
+  }
+}
+
+for (j in 1:ncol(fillins_df)) {
+  for (i in 1:nrow(fillins_df)) {
+    if (j %% 2 == 1) {
+      for (k in 1:i) {
+        if (k < i) {
+          if (trimws(fillins_df[i, j], which = "both") == trimws(fillins_df[k,j], which = "both")) {
+            fillins_df[k, j+1] <- fillins_df[k, j+1] + 1
+            fillins_df[i, j] <- paste("IGNORE", i, collapse ="")
+            fillins_df[i, j + 1] <- 0 
+          }
+        }
+      }
+    }
+  }
+}
+
+for (j in 1:ncol(fillins_df)) {
+  for (i in 1:nrow(fillins_df)) {
+    if (j %% 2 == 0) {
+      if (fillins_df[i, j] == 0) {
+        fillins_df[i, j] <- ""  
+      }
+    } else {
+      fillins_df[i, j] <- gsub("IGNORE \\d+", "", fillins_df[i, j])
+    }
+  }
+}
+
+test2 <- as.data.frame(matrix(0, ncol = 0, nrow = (nrow(fillins_df))))
+for (j in 1:ncol(fillins_df)) {
+  if (j %% 2 == 1) {
+    test <- fillins_df[, c(j, j+1)]
+    test[,2] <- as.numeric(test[,2])
+    test <- test[order(-test$Frequency),]
+    test2 <- cbind(test2, test)
+  }
+}
+fillins_df <- test2[rowSums(is.na(test2))!=(ncol(test2)/2),]
+
+
+#for (j in 1:ncol(fillins_df)) {
+#  for (i in 1:nrow(fillins_df)) {
+#    if (j %% 2 == 1) {
+#      while (fillins_df[i, j + 1] == "") {
+#        for (l in i:nrow(fillins_df)) {
+#          if (fillins_df[l, j + 1] != "") {
+#            fillins_df[i, j] <- fillins_df[l, j] 
+#            fillins_df[i, j + 1] <- fillins_df[l, j + 1] 
+#          }
+#        }
+#        break
+#      }
+#      fillins_df[l, j] <- ""
+#      fillins_df[l, j + 1] <- ""
+#    } 
+#  }
+#}
+
+
+#temp_df <- cbindPad(temp_df, b)
+#fillins_df <- cbindPad(fillins_df, b)
+#names(temp_df)[ncol(temp_df)] <- "Cluster Text"
+#names(fillins_df)[ncol(fillins_df)] <- "Cluster Text"
+write.csv(temp_df, file = paste0(namefile, "TEMPLATE.csv"), row.names = F)
+write.csv(fillins_df, file = paste0(namefile, "FILLINS.csv"), col.names = F)
+