5cc4a16511d6a2980e27a1225e2f90c72b5ea077
galt
  Wed Apr 26 14:19:28 2017 -0700
-Renaming sha1 to rSha1 etc to avoid silent name collision during linking.

diff --git src/lib/rSha1.c src/lib/rSha1.c
new file mode 100644
index 0000000..7e30ff4
--- /dev/null
+++ src/lib/rSha1.c
@@ -0,0 +1,240 @@
+/* SHA-1 in C
+By Steve Reid <sreid@sea-to-sky.net>
+100% Public Domain
+http://svn.ghostscript.com/jbig2dec/trunk/sha1.c
+*/
+#define RSHA1HANDSOFF    /* Copies data before messing with it. */
+
+#include <stdio.h>
+#include <string.h>
+
+#include "common.h"
+#include "hex.h"
+#include "errAbort.h"
+#include "rSha1.h"
+
+void RSHA1_Transform(bits32 state[5], const bits8 buffer[64]);
+
+#define rol(value, bits) (((value) << (bits)) | ((value) >> (32 - (bits))))
+
+/* blk0() and blk() perform the initial expand. */
+/* I got the idea of expanding during the round function from SSLeay */
+/* FIXME: can we do this in an endian-proof way? */
+#ifdef WORDS_BIGENDIAN
+#define blk0(i) block->l[i]
+#else
+#define blk0(i) (block->l[i] = (rol(block->l[i],24)&0xFF00FF00) \
+    |(rol(block->l[i],8)&0x00FF00FF))
+#endif
+#define blk(i) (block->l[i&15] = rol(block->l[(i+13)&15]^block->l[(i+8)&15] \
+    ^block->l[(i+2)&15]^block->l[i&15],1))
+
+/* (R0+R1), R2, R3, R4 are the different operations used in SHA1 */
+#define R0(v,w,x,y,z,i) z+=((w&(x^y))^y)+blk0(i)+0x5A827999+rol(v,5);w=rol(w,30);
+#define R1(v,w,x,y,z,i) z+=((w&(x^y))^y)+blk(i)+0x5A827999+rol(v,5);w=rol(w,30);
+#define R2(v,w,x,y,z,i) z+=(w^x^y)+blk(i)+0x6ED9EBA1+rol(v,5);w=rol(w,30);
+#define R3(v,w,x,y,z,i) z+=(((w|x)&y)|(w&x))+blk(i)+0x8F1BBCDC+rol(v,5);w=rol(w,30);
+#define R4(v,w,x,y,z,i) z+=(w^x^y)+blk(i)+0xCA62C1D6+rol(v,5);w=rol(w,30);
+
+
+/* Hash a single 512-bit block. This is the core of the algorithm. */
+void RSHA1_Transform(bits32 state[5], const bits8 buffer[64])
+{
+    bits32 a, b, c, d, e;
+    typedef union {
+        bits8 c[64];
+        bits32 l[16];
+    } CHAR64LONG16;
+    CHAR64LONG16* block;
+
+#ifdef RSHA1HANDSOFF
+    static bits8 workspace[64];
+    block = (CHAR64LONG16*)workspace;
+    memcpy(block, buffer, 64);
+#else
+    block = (CHAR64LONG16*)buffer;
+#endif
+
+    /* Copy context->state[] to working vars */
+    a = state[0];
+    b = state[1];
+    c = state[2];
+    d = state[3];
+    e = state[4];
+
+    /* 4 rounds of 20 operations each. Loop unrolled. */
+    R0(a,b,c,d,e, 0); R0(e,a,b,c,d, 1); R0(d,e,a,b,c, 2); R0(c,d,e,a,b, 3);
+    R0(b,c,d,e,a, 4); R0(a,b,c,d,e, 5); R0(e,a,b,c,d, 6); R0(d,e,a,b,c, 7);
+    R0(c,d,e,a,b, 8); R0(b,c,d,e,a, 9); R0(a,b,c,d,e,10); R0(e,a,b,c,d,11);
+    R0(d,e,a,b,c,12); R0(c,d,e,a,b,13); R0(b,c,d,e,a,14); R0(a,b,c,d,e,15);
+    R1(e,a,b,c,d,16); R1(d,e,a,b,c,17); R1(c,d,e,a,b,18); R1(b,c,d,e,a,19);
+    R2(a,b,c,d,e,20); R2(e,a,b,c,d,21); R2(d,e,a,b,c,22); R2(c,d,e,a,b,23);
+    R2(b,c,d,e,a,24); R2(a,b,c,d,e,25); R2(e,a,b,c,d,26); R2(d,e,a,b,c,27);
+    R2(c,d,e,a,b,28); R2(b,c,d,e,a,29); R2(a,b,c,d,e,30); R2(e,a,b,c,d,31);
+    R2(d,e,a,b,c,32); R2(c,d,e,a,b,33); R2(b,c,d,e,a,34); R2(a,b,c,d,e,35);
+    R2(e,a,b,c,d,36); R2(d,e,a,b,c,37); R2(c,d,e,a,b,38); R2(b,c,d,e,a,39);
+    R3(a,b,c,d,e,40); R3(e,a,b,c,d,41); R3(d,e,a,b,c,42); R3(c,d,e,a,b,43);
+    R3(b,c,d,e,a,44); R3(a,b,c,d,e,45); R3(e,a,b,c,d,46); R3(d,e,a,b,c,47);
+    R3(c,d,e,a,b,48); R3(b,c,d,e,a,49); R3(a,b,c,d,e,50); R3(e,a,b,c,d,51);
+    R3(d,e,a,b,c,52); R3(c,d,e,a,b,53); R3(b,c,d,e,a,54); R3(a,b,c,d,e,55);
+    R3(e,a,b,c,d,56); R3(d,e,a,b,c,57); R3(c,d,e,a,b,58); R3(b,c,d,e,a,59);
+    R4(a,b,c,d,e,60); R4(e,a,b,c,d,61); R4(d,e,a,b,c,62); R4(c,d,e,a,b,63);
+    R4(b,c,d,e,a,64); R4(a,b,c,d,e,65); R4(e,a,b,c,d,66); R4(d,e,a,b,c,67);
+    R4(c,d,e,a,b,68); R4(b,c,d,e,a,69); R4(a,b,c,d,e,70); R4(e,a,b,c,d,71);
+    R4(d,e,a,b,c,72); R4(c,d,e,a,b,73); R4(b,c,d,e,a,74); R4(a,b,c,d,e,75);
+    R4(e,a,b,c,d,76); R4(d,e,a,b,c,77); R4(c,d,e,a,b,78); R4(b,c,d,e,a,79);
+
+    /* Add the working vars back into context.state[] */
+    state[0] += a;
+    state[1] += b;
+    state[2] += c;
+    state[3] += d;
+    state[4] += e;
+
+    /* Wipe variables */
+    a = b = c = d = e = 0;
+}
+
+
+/* SHA1Init - Initialize new context */
+void RSHA1_Init(RSHA1_CTX* context)
+{
+    /* SHA1 initialization constants */
+    context->state[0] = 0x67452301;
+    context->state[1] = 0xEFCDAB89;
+    context->state[2] = 0x98BADCFE;
+    context->state[3] = 0x10325476;
+    context->state[4] = 0xC3D2E1F0;
+    context->count[0] = context->count[1] = 0;
+}
+
+
+/* Run your data through this. */
+void RSHA1_Update(RSHA1_CTX* context, const bits8* data, const size_t len)
+{
+    size_t i, j;
+
+    j = (context->count[0] >> 3) & 63;
+    if ((context->count[0] += len << 3) < (len << 3)) context->count[1]++;
+    context->count[1] += (len >> 29);
+    if ((j + len) > 63) {
+        memcpy(&context->buffer[j], data, (i = 64-j));
+        RSHA1_Transform(context->state, context->buffer);
+        for ( ; i + 63 < len; i += 64) {
+            RSHA1_Transform(context->state, data + i);
+        }
+        j = 0;
+    }
+    else i = 0;
+    memcpy(&context->buffer[j], &data[i], len - i);
+
+}
+
+
+/* Add padding and return the message digest. */
+void RSHA1_Final(RSHA1_CTX* context, bits8 digest[RSHA1_DIGEST_SIZE])
+{
+    bits32 i;
+    bits8  finalcount[8];
+
+    for (i = 0; i < 8; i++) {
+        finalcount[i] = (unsigned char)((context->count[(i >= 4 ? 0 : 1)]
+         >> ((3-(i & 3)) * 8) ) & 255);  /* Endian independent */
+    }
+    RSHA1_Update(context, (bits8 *)"\200", 1);
+    while ((context->count[0] & 504) != 448) {
+        RSHA1_Update(context, (bits8 *)"\0", 1);
+    }
+    RSHA1_Update(context, finalcount, 8);  /* Should cause a RSHA1_Transform() */
+    for (i = 0; i < RSHA1_DIGEST_SIZE; i++) {
+        digest[i] = (bits8)
+         ((context->state[i>>2] >> ((3-(i & 3)) * 8) ) & 255);
+    }
+
+    /* Wipe variables */
+    i = 0;
+    memset(context->buffer, 0, 64);
+    memset(context->state, 0, 20);
+    memset(context->count, 0, 8);
+    memset(finalcount, 0, 8);	/* SWR */
+
+#ifdef RSHA1HANDSOFF  /* make RSHA1Transform overwrite its own static vars */
+    RSHA1_Transform(context->state, context->buffer);
+#endif
+}
+
+/* ==================== Routines added by UCSC genome browser ========================= */
+
+
+char *rSha1ToHex(unsigned char hash[20])
+/* Convert binary representation of sha1 to hex string. Do a freeMem on result when done. */
+{
+int hexSize = 20*2;
+char hex[hexSize+1];
+char *h;
+int i;
+for (i = 0, h=hex; i < 20; ++i, h += 2)
+    byteToHex( hash[i], h);  
+hex[hexSize] = 0;
+return cloneString(hex);
+}
+
+
+void rSha1ForFile(char *fileName, unsigned char hash[20])
+/* Make sha1 hash from file */
+{
+FILE *fp = fopen (fileName, "r");
+if (!fp) errAbort("missing file %s", fileName);
+#define BS 4096 /* match coreutils */
+RSHA1_CTX ctx;
+RSHA1_Init(&ctx);
+size_t nr;
+unsigned char buf[BS];
+while ((nr=fread(buf, 1, sizeof(buf), fp)))
+    { 
+    RSHA1_Update(&ctx, buf, nr);
+    };
+RSHA1_Final(&ctx, hash);
+}
+
+char *rSha1HexForFile(char *fileName)
+/* Return Sha1 as Hex string */
+{
+unsigned char hash[20];
+rSha1ForFile(fileName, hash);
+return rSha1ToHex(hash);
+}
+
+void rSha1ForBuf(char *buffer, size_t bufSize, unsigned char hash[20])
+/* Return sha1 hash of buffer. */
+{
+#define BS 4096 /* match coreutils */
+RSHA1_CTX ctx;
+RSHA1_Init(&ctx);
+size_t remaining = bufSize;
+while (remaining > 0)
+    {
+    int bufSize = BS;
+    if (bufSize > remaining)
+	bufSize = remaining;
+    RSHA1_Update(&ctx, (unsigned char*)buffer, bufSize);
+    buffer += bufSize;
+    remaining -= bufSize;
+    }
+RSHA1_Final(&ctx, hash);
+}
+
+char *rSha1HexForBuf(char *buf, size_t bufSize)
+/* Return Sha1 as Hex string */
+{
+unsigned char hash[20];
+rSha1ForBuf(buf, bufSize, hash);
+return rSha1ToHex(hash);
+}
+
+char *rSha1HexForString(char *string)
+/* Return sha sum of zero-terminated string. */
+{
+return rSha1HexForBuf(string, strlen(string));
+}
+