Merge pull request #3 from robertfeldt/master

update for Julia 0.4
JuliaCollections · Jan 7, 2016 · b6cc5b8 · b6cc5b8
2 parents 25d11da + 2723e8e
commit b6cc5b8
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Showing 2 changed files with 20 additions and 19 deletions.
diff --git a/src/SuffixArrays.jl b/src/SuffixArrays.jl
@@ -2,7 +2,7 @@ module SuffixArrays
 
 export suffixsort
 
-immutable SuffixArray{S<:String,N<:Signed}
+immutable SuffixArray{S<:AbstractString,N<:Signed}
     string::S
     n::Int
     index::Array{N,1}
@@ -30,7 +30,7 @@ end
 #=contains(haystack, needle)
 
 matchall(substring, s::String)=#
-const MAXCHAR = char(255)
+const MAXCHAR = Char(255)
 
 function lcp2(SA,s)
     inv = similar(SA)

diff --git a/src/sais.jl b/src/sais.jl
@@ -29,6 +29,7 @@ type IntArray
     a::Array{Int,1}
     pos::Int
 end
+import Base: getindex, setindex!
 getindex(a::IntArray,key) = a.a[a.pos + key]
 setindex!(a::IntArray,value,key) = a.a[a.pos + key] = value
 
@@ -44,7 +45,7 @@ function getcounts(T,C,n,k)
         C[i] = 0
     end
     for i = 1:n
-        C[T[i]+1] += 1
+        C[Int(T[i])+1] += 1
     end
 end
 
@@ -115,7 +116,7 @@ function sais(T, SA, fs, n, k, isbwt)
         end
         if 1 <= i
             0 <= b && (SA[b+1] = j)
-            b = (B[c1+1] -= 1)
+            b = (B[Int(c1)+1] -= 1)
             j = i-1
             m += 1
             c1 = c0
@@ -195,7 +196,7 @@ function sais(T, SA, fs, n, k, isbwt)
         c1 = T[p+1]
         while true
             c0 = c1
-            q = B[c0+1]
+            q = B[Int(c0)+1]
             while q < j
                 j -= 1
                 SA[j+1] = 0
@@ -229,16 +230,16 @@ function LMSsort(T, SA, C, B, n, k)
     getbuckets(C,B,k,false)
     j = n - 1
     c1 = T[j+1]
-    b = B[c1+1]
+    b = B[Int(c1)+1]
     j -= 1
     SA[b+1] = T[j+1] < c1 ? ~j : j
     b += 1
     for i = 1:n
         if 0 < (j = SA[i])
             if (c0 = T[j+1]) != c1
-                B[c1+1] = b
+                B[Int(c1)+1] = b
                 c1 = c0
-                b = B[c1+1]
+                b = B[Int(c1)+1]
             end
             j -= 1
             SA[b+1] = T[j+1] < c1 ? ~j : j
@@ -258,7 +259,7 @@ function LMSsort(T, SA, C, B, n, k)
             if c0 != c1
                 B[c1+1] = b
                 c1 = c0
-                b = B[c1+1]
+                b = B[Int(c1)+1]
             end
             j -= 1
             b -= 1
@@ -336,7 +337,7 @@ function induceSA(T,SA,C,B,n,k)
     getbuckets(C,B,k,false)
     j = n - 1
     c1 = T[j+1]
-    b = B[c1+1]
+    b = B[Int(c1)+1]
     SA[b+1] = 0 < j && T[j] < c1 ? ~j : j
     b += 1
     for i = 1:n
@@ -345,9 +346,9 @@ function induceSA(T,SA,C,B,n,k)
         if 0 < j
             j -= 1
             if (c0 = T[j+1]) != c1
-                B[c1+1] = b
+                B[Int(c1)+1] = b
                 c1 = c0
-                b = B[c1+1]
+                b = B[Int(c1)+1]
             end
             SA[b+1] = 0 < j && T[j] < c1 ? ~j : j
             b += 1
@@ -361,9 +362,9 @@ function induceSA(T,SA,C,B,n,k)
         if 0 < (j = SA[i])
             j -= 1
             if (c0 = T[j+1]) != c1
-                B[c1+1] = b
+                B[Int(c1)+1] = b
                 c1 = c0
-                b = B[c1+1]
+                b = B[Int(c1)+1]
             end
             b -= 1
             SA[b+1] = j == 0 || T[j] > c1 ? ~j : j
@@ -379,7 +380,7 @@ function computeBWT(T,SA,C,B,n,k)
     getbuckets(C,B,k,false)
     j = n-1
     c1 = T[j+1]
-    b = B[c1+1]
+    b = B[Int(c1)+1]
     SA[b+1] = 0 < j && T[j] < c1 ? ~j : j
     b += 1
     for i = 1:n   
@@ -388,7 +389,7 @@ function computeBWT(T,SA,C,B,n,k)
             c0 = T[j+1]
             SA[i] = ~c0
             if c0 != c1
-                B[c1+1] = b
+                B[Int(c1)+1] = b
                 c1 = c0
                 b = B[c1+1]
             end
@@ -401,16 +402,16 @@ function computeBWT(T,SA,C,B,n,k)
     C == B && getcounts(T,C,n,k)
     getbuckets(C,B,k,true)
     c1 = 0
-    b = B[c1+1]
+    b = B[Int(c1)+1]
     for i = n:-1:1
         if 0 < (j = SA[i])
             j -= 1
             c0 = T[j+1]
             SA[i] = c0
             if c0 != c1
-                B[c1+1] = b
+                B[Int(c1)+1] = b
                 c1 = c0
-                b = B[c1+1]
+                b = B[Int(c1)+1]
             end
             b -= 1
             SA[b+1] = 0 < j && T[j] > c1 ? ~(T[j]) : j