Building Fmat and Tmat. Obtaining final alignment from traceback walkback

Schrick-Noah_CS-6643_Lab-9.R

@@ -49,3 +49,41 @@ Fmat[1,]<- seq(from=0,len=y.len+1,by=-abs(gap_penalty))
 Tmat[,1]<- rep(2,x.len+1)  # 2 means align with a gap in the upper seq
 Tmat[1,]<- rep(3,y.len+1)  # 3 means align with a gap in the side seq
 
+
+#### Part C: Building Fmat and Tmat
+## Building Fmat and Tmat
+for (i in 2:nrow(Fmat)){
+  for (j in 2:ncol(Fmat)){    # use F recursive rules 
+    test_three_cases <- c(Fmat[i-1, j-1] + S[rownames(Fmat)[i], colnames(Fmat)[j]],   # 1 mis/match
+                          Fmat[i-1, j] + gap_penalty,    # 2 up-gap
+                          Fmat[i, j-1] + gap_penalty)  # 3 left-gap
+    Fmat[i,j]=max(test_three_cases)
+    Tmat[i,j]=which.max(test_three_cases)
+  }
+}
+final_score <- Fmat[nrow(Fmat),ncol(Fmat)]
+
+## Aligning from Tmat
+n <- nrow(Tmat) 
+m <- ncol(Tmat)
+seq_align <- character()
+while( (n+m)!=2 ){
+  if (Tmat[n,m]==1){
+    curr_align_col <- rbind(x[n-1],y[m-1]) 
+    seq_align <- cbind(curr_align_col,seq_align)
+    n <- n-1
+    m <- m-1
+  }else if(Tmat[n,m]==2){ 
+    curr_align_col <- rbind(x[n-1],"-")
+    seq_align <- cbind(curr_align_col,seq_align)
+    n <- n-1
+  }else{
+    curr_align_col <- rbind("-",y[m-1])
+    seq_align <- cbind(curr_align_col,seq_align)
+    m <- m-1
+  }           
+} # end while
+
+seq_align
+
+