teach diagonal to use the 'diagonal' attribute if a matrix has one

* closes #14
* could help with #8

R/nblast.R

@@ -105,22 +105,27 @@ fc_subscoremat<-function(query, target, scoremat=NULL, distance=FALSE,
 }
 
 # utility function to extract diagonal terms from matrices
+# uses the 'diagonal' attribute when available
 #' @importFrom bigmemory is.big.matrix
 #' @importFrom ff is.ff arrayIndex2vectorIndex
 diagonal<-function(x, indices=NULL){
   if(is.character(indices)) indices=match(indices,rownames(x))
-  if(is.logical(indices)) indices=which(indices)
-  ndiags <- if(is.null(indices)){
-    nrow(x)
-  } else {
-    length(indices)
+  if(!is.null(attr(x,'diagonal'))){
+    return(diagonal[indices])
   }
+
+  if(is.logical(indices)) indices=which(indices)
 
   if(is.ff(x)){
     # convert array indices to vector indices
     vidxs=arrayIndex2vectorIndex(cbind(indices,indices),dim=dim(x))
     x[vidxs]
   } else if(is.big.matrix(x)) {
+    ndiags <- if(is.null(indices)){
+      nrow(x)
+    } else {
+      length(indices)
+    }
     diags=rep(NA,ndiags)
     for(i in seq_len(ndiags)){
       idx=indices[i]

tests/testthat/test-nblast.R

@@ -75,4 +75,13 @@ test_that('fc_subscoremat and fc_nblast agree', {
                fc_subscoremat(nn,nn[1],scoremat=scores,normalisation='mean',distance=FALSE))
 })
 
+test_that('we can use diagonal attribute on a score matrix',{
+  library(ff)
+  scoresff=as.ff(scores)
+  scoresffd=scoresff
+  attr(scoresffd,'diagonal')=diag(scores)
+  expect_equal(fc_nblast(nn[1], nn, scoremat = scoresff),
+               fc_nblast(nn[1], nn, scoremat = scoresffd))
+})
+
 options(op)