chore: moved string into main libn header

4 files changed, 187 insertions, 64 deletions

diff --git a/include/.include/str.h b/include/.include/str.h
deleted file mode 100644
index 29b5e1e..0000000
--- a/include/.include/str.h
+++ /dev/null
@@ -1,62 +0,0 @@
-#pragma once
-
-typedef byte* string;
-
-typedef struct str·Hdr
-{
-    vlong len;
-    vlong cap;
-    byte  buf[];
-} str·Hdr;
-
-// -------------------------------------------------------------------------
-// UTF-8 functions.
-// Perhaps break into own unit
-// TODO: Add to(upper|lower|title)
-
-typedef uint32 Rune;
-
-enum
-{
-    UTFmax    = 4,
-    RuneSync  = 0x80,
-    RuneSelf  = 0x80,
-    RuneErr   = 0xFFFD,
-    RuneMax   = 0x10FFFF,
-};
-
-int     utf8·fullrune(byte *s, int n);
-byte   *utf8·findrune(byte *s, long i);
-int     utf8·chartorune(Rune *r, byte *s);
-int     utf8·runetochar(byte *s, Rune *r);
-int     utf8·len(byte *s);
-int     utf8·runelen(Rune r);
-int     utf8·isletter(Rune r);
-int     utf8·isdigit(Rune r);
-int     utf8·isspace(Rune r);
-int     utf8·istitle(Rune r);
-
-// -------------------------------------------------------------------------
-// Dynamic string functions
-
-string  str·newcap(const byte *s, vlong len, vlong cap);
-string  str·newlen(const byte *s, vlong len);
-string  str·new(const byte *s);
-string  str·newf(const byte *fmt, ...);
-void    str·free(string s);
-int     str·len(const string s);
-int     str·cap(const string s);
-string  str·clear(string s);
-string  str·grow(string s, vlong delta);
-string  str·fit(string s);
-string  str·appendcount(string s, vlong len, const byte *b);
-string  str·append(string s, const byte* b);
-string  str·appendf(string s, const byte* fmt, ...);
-string  str·appendbyte(string s, const byte b);
-bool    str·equals(const string s, const string t);
-int     str·find(string s, const byte* substr);
-void    str·lower(string s);
-void    str·upper(string s);
-void    str·replace(string s, const byte* from, const byte* to);
-string* str·split(string s, const byte* tok);
-string  str·join(vlong len, byte** fields, const byte* sep);
diff --git a/include/libn.h b/include/libn.h
index 66eabaf..b994159 100644
--- a/include/libn.h
+++ b/include/libn.h
@@ -106,7 +106,65 @@ error   coro·free(Coro *c);
 // Strings
 
 // TODO(nnoll): Move here?
-#include ".include/str.h"
+typedef byte* string;
+
+typedef struct str·Hdr
+{
+    vlong len;
+    vlong cap;
+    byte  buf[];
+} str·Hdr;
+
+// -------------------------------------------------------------------------
+// UTF-8 functions.
+// Perhaps break into own unit
+// TODO: Add to(upper|lower|title)
+
+typedef uint32 Rune;
+
+enum
+{
+    UTFmax    = 4,
+    RuneSync  = 0x80,
+    RuneSelf  = 0x80,
+    RuneErr   = 0xFFFD,
+    RuneMax   = 0x10FFFF,
+};
+
+/* utf8 helpers */
+int     utf8·fullrune(byte *s, int n);
+byte   *utf8·findrune(byte *s, long i);
+int     utf8·chartorune(Rune *r, byte *s);
+int     utf8·runetochar(byte *s, Rune *r);
+int     utf8·len(byte *s);
+int     utf8·runelen(Rune r);
+int     utf8·isletter(Rune r);
+int     utf8·isdigit(Rune r);
+int     utf8·isspace(Rune r);
+int     utf8·istitle(Rune r);
+
+/* string helpers */
+string  str·newcap(const byte *s, vlong len, vlong cap);
+string  str·newlen(const byte *s, vlong len);
+string  str·new(const byte *s);
+string  str·newf(const byte *fmt, ...);
+void    str·free(string s);
+int     str·len(const string s);
+int     str·cap(const string s);
+string  str·clear(string s);
+string  str·grow(string s, vlong delta);
+string  str·fit(string s);
+string  str·appendcount(string s, vlong len, const byte *b);
+string  str·append(string s, const byte* b);
+string  str·appendf(string s, const byte* fmt, ...);
+string  str·appendbyte(string s, const byte b);
+bool    str·equals(const string s, const string t);
+int     str·find(string s, const byte* substr);
+void    str·lower(string s);
+void    str·upper(string s);
+void    str·replace(string s, const byte* from, const byte* to);
+string* str·split(string s, const byte* tok);
+string  str·join(vlong len, byte** fields, const byte* sep);
 
 // -----------------------------------------------------------------------------
 // I/O
diff --git a/sys/libbio/test.c b/sys/libbio/test.c
index e943153..fec0a0c 100644
--- a/sys/libbio/test.c
+++ b/sys/libbio/test.c
@@ -140,10 +140,119 @@ test·fastq()
     return err <= 0 ? 0 : 1;
 }
 
+static byte *SEQ[] = {
+"GGCGGCTTCGGTGCGCTGTGTGCATTGCCGCAAAAATATCGTGAACCCGTGCTGGTTTCCGGCACTGACGGCGTAGGTAC"
+"CAAGCTGCGTCTGGCAATGGACTTAAAACGTCACGACACCATTGGTATTGATCTGGTCGCCATGTGCGTTAATGACCTGG"
+"TGGTGCAAGGTGCGGAACCGCTGTTTTTCCTCGACTATTACGCAACCGGAAAACTGGATGTTGATACCGCTTCAGCGGTG"
+"ATCAGCGGCATTGCGGAAGGTTGTCTGCAATCGGGCTGTTCTCTGGTGGGTGGCGAAACGGCAGAAATGCCGGGGATGTA"
+"TCACGGTGAAGATTACGATGTCGCGGGTTTCTGCGTGGGCGTGGTAGAAAAATCAGAAATCATCGACGGCTCTAAAGTCA"
+"GCGACGGCGATGTGCTGATTGCACTCGGTTCCAGCGGTCCGCACTCGAACGGTTATTCGCTGGTGCGCAAAATTCTTGAA"
+"GTCAGCGGTTGTGATCCGCAAACCACCGAACTTGATGGTAAGCCATTAGCCGATCATCTGCTGGCACCGACCCGCATTTA"
+"CGTGAAGTCAGTGCTGGAGTTGATTGAAAAGGTCGATGTGCATGCCATTGCGCACCTGACCGGCGGCGGCTTCTGGGAAA"
+"ACATTCCGCGCGTATTGCCAGATAATACCCAGGCAGTGATTGATGAATCTTCCTGGCAGTGGCCGGAAGTGTTCAACTGG"
+"CTGCAAACGGCAGGTAACGTTGAGCGCCATGAAATGTATCGCACCTTCAACTGCGGCGTCGGGATGATTATCGCCCTGCC"
+"TGCTCCGGAAGTGGACAAAGCCCTCGCCCTGCTCAATGCCAACGGTGAAAACGCGTGGAAAATCGGTATCATCAAAGCCT"
+"CTGATTCCGAACAACGCGTGGTTATCGAATAATGAATATTGTGGTGCTTATTTCCGGCAACGGAAGTAATTTACAGGCAA"
+"TTATTGACGCCTGTAAAACCAACAAAATTAAAGGCACCGTACGGGCAGTTTTCAGCAATAAGGCCGACGCGTTCGGCCTT"
+"GAACGCGCCCGCCAGGCGGGTATTGCAACGCATACGCTCATCGCCAGCGCGTTTGACAGTCGTGAAGCCTATGACCGGGA"
+"GTTGATTCATGAAATCGACATGTACGCACCCGATGTGGTCGTGCTGGCTGGTTTTATGCGCATTCTCAGCCCGGCGTTTG"
+"TCTCCCACTATGCCGGGCGTTTGCTGAACATTCACCCTTCTCTGCTGCCGAAATATCCCGGATTACACACCCATCGTCAA"
+"GCGCTGGAAAATGGCGATGAAGAGCACGGTACATCGGTGCATTTCGTCACCGATGAACTGGACGGTGGCCCGGTTATTTT"
+"ACAGGCGAAAGTCCCGGTATTTGCTGGTGATACGGAAGATGACGTCACCGCCCGCGTGCAAACCCAGGAACACGCCATTT"
+"ATCCACTGGTGATTAGCTGGTTTGCCGATGGTCGTCTGAAAATGCACGAAAACGCCGCGTGGCTGGATGGTCAACGTCTG"
+"CCGCCGCAGGGCTACGCTGCCGACGAGTAATGCCCCCGTAGTTAAAGCGCCAGCTCTGCCGCTGGCGTTTTTCAATTCAC"
+"CTGTAAATCGCAAGCTCCAGCAGTTTTTTTCCCCCTTTTCTGGCATAGTTGGACATCTGCCAATATTGCTCGCCATAATA"
+"TCCAGGCAGTGTCCCGTGAATAAAACGGAGTAAAAGTGGTAATGGGTCAGGAAAAGCTATACATCGAAAAAGAGCTCAGT"
+"TGGTTATCGTTCAATGAACGCGTGCTTCAGGAAGCGGCGGACAAATCTAACCCGCTGATTGAAAGGATGCGTTTCCTGGG"
+"GATCTATTCCAATAACCTTGATGAGTTCTATAAAGTCCGCTTCGCTGAACTGAAGCGACGCATCATTATTAGCGAAGAAC"
+"AAGGCTCCAACTCTCATTCCCGCCATTTACTGGGCAAAATTCAGTCCCGGGTGCTGAAAGCCGATCAGGAATTCGACGGC"
+"CTCTACAACGAGCTATTGCTGGAGATGGCGCGCAACCAGATCTTCCTGATTAATGAACGCCAGCTCTCCGTCAATCAACA"
+"AAACTGGCTGCGTCATTATTTTAAGCAGTATCTGCGTCAGCACATTACGCCGATTTTAATCAATCCTGACACTGACTTAG"
+"TGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTTCTGGAG"
+"ATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGA"
+"TAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGA"
+"TGACCCGCGATGCCGAATACGATTTAGTGCATGAGATGGAAGCCAGCCTGATGGAGTTGATGTCTTCCAGTCTCAAGCAG"
+"CGTTTAACTGCTGAGCCGGTGCGTTTTGTTTATCAGCGCGATATGCCCAATGCGCTGGTTGAAGTTTTACGCGAAAAACT",
+
+"GGCGGCTTCGGTGCGCTGTGTGCATTGCCGCAAAAATATCGTGAACCCGTGCTGGTTTCCGGCACTGACGGCGTAAATAC"
+"CAAGCTGCGTCTGGCAATGGACTTAAAACGTCACGACACCATTGGTATTGATCTGGTCGCCATGTGCGTTAATGACCTGG"
+"TGGTGCAAGGTGCGGAACCGCTGTTTTTCCTCGACTATTACGCACCGGAAAACTGGATGTTGATACCGCTTCAGCGGTG"
+"ATCAGCGGCATTGCGGAAGGTTGTCTGCAATCGGGCTGTTCTCTGGTGGGTGGCGAAACGGCAGAAATGCCGGGGATGTA"
+"TCACGGTGAAGATTACGATGTCGCGGGTTTCTGCGTGGGCGTGGTAGAAAAATCAGAAATCATCGACGGCAAAGTCA"
+"GCGACGGCGATGTGCTGATTGCACTCGGTTCCAGCGGTCCGCACTCGAACGGTTATTCGCTGGTGCGCAAAATTCTTGAA"
+"GTCAGCGGTTGTGATCCGCAAACCACCGAACTTGATGGTAAGCCATTAGCCGATCATCTGCTGGCACCGACCCGCATTTA"
+"ACATTCCGCGCGTATTGCCAGATAATACCCAGGCAGTGATTGATGAATCTTCCTGGCAGTGGCCGGAAGTGTTCAACTGG"
+"CTGCAAACGGCAGGTAACGTTGAGCGCCATGAAATGTATCGCACCTTCAACTGCGGCGTCGGGATGATTATCCCCTGCC"
+"TGCTCCGGAAGTGGACAAAGCCCTCGCCCTGCTCAATGCCAACGGTGAAAACGCGTGGAAAATCGGTATCATCAAAGCCT"
+"CTGATTCCGAACAACGCGTGGTTATCGAATAATGAATATTGTGTGCTTATTTCCGGCAACGGAAGTAATTTACAGGCAA"
+"TTATTGACGCCTGTAAAACCAACAAAATTAAAGGCACCGTACGGGCAGTTTTCAGCAATAAGGCCGACGCGCGGCCTT"
+"GAACGCGCCCGCCAGGCGGGTATTGCAACGCATACGCTCATCGCCAGCGCGTTTGACAGTCGTGAAGCCTATGACCGGGA"
+"GTTGATTCATGAAATCGACATGTACGCACCCGATGTGGTCGTGCTGGCTGGTTTTATGCGCATTCTCAGCCCGGCGTTTG"
+"TCTCCCACTATGCCGGGCGTTTGCTGAACATTCACCCTTCTCTGCTGCCGAAATATCCCGGATTACACACCCATCGTCAA"
+"GCGCTGGAAAATGGCGATGAAGAGCACGGTACATCGGGCATTTCGTCACCGATGAACTGGACGGTGGCCCGGTTATTTT"
+"ACAGTCGAAAGTCCCGGTATTTGCTGGTGATACGGAAGATGACGTCACCGCCCGCGTGCAAACCCAGGAACACGCCATTT"
+"ATCCTCTGGTGATTAGCTGGTTTGCCGATGGTCGTCTGAAAATGCACGAAAACGCCGCGTGGCTGGATGGTCAACGTCTG"
+"CCGCTGCAGGGCTACGCTGCCGACGAGTAATGCCCCCGTAGTTAAAGCGCCAGCTCTGCCGCTGGCGTTTTTCAATTCAC"
+"CTGTTAATCGCAAGCTCCAGCAGCCCCCCCCCCCCTTTTCTGCATAGTTGGACATCTGCCAATATTGCTCGCCATAATA"
+"TCCATGCAGTGTCCCGTGAATAAAACGGAGTAAAAGTGGTAATGGGTCAGGAAAAGCTATACATAAAAAGAGCTCAGT"
+"TGGTTATCGTTCAATGAACGCGTGCTTCAGGAAGCGGCGGACAAATCTAACCCGCTGATTGAAAGGATGCGTTTCCTGGG"
+"GATCTATTCCAATAACCTTGATGAGTTCTATAAAGTCCGCTTCGCTGAACTGAAGCGACGCATTATTAGCGAAGAAC"
+"AAGGTTCCAACTCTCATTCCCGCCATTTACTGGGAAAATTCAGTCCCGGGTGCTGAAAGCCGATCAGGAATTCGACGGC"
+"CTCTTCAACGAGCTATTGCTGGAGATGGCGCGCAACCAGATCTTCCTGATTAATGAACGCCAGCTCTCCGTCAATCAACA"
+"AAACTGGCTGCGTCATTATTTTAAGCAGTATCTGCGTCAGCACATTACGCCGATTTTAATCAATCCTGACACTGACTTAG"
+"TGCATTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTTCTGGAG"
+"ATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGA"
+"TAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGA"
+"TGACCCGCGATGCCGAATACGATTTAGTGCATGAGATGGAAGCCAGCCTGATGGAGTTGATGTCTTCCAGTCTCAAGCAG"
+"CGTTTAACTGCTGAGCCGGTGCGTTTTGTTTATCGCGCGATATGCCCAATGCGCTGGTTGAAGTTTTACGCGAAAAACT",
+};
+
 error
 main()
 {
-    error err;
+    double  f;
+    error   err;
+    int     i, l, n;
+
+    uint64  mem[aln·N][arrlen(SEQ)][aln·L];
+    uint64 *phi[aln·N];
+    int     loc[aln·N][arrlen(SEQ)][aln·L];
+    int    *pos[aln·N];
+
+    for (i = 0; i < arrlen(SEQ); i++) {
+        for (n = 0; n < aln·N; n++) {
+            phi[n] = mem[n][i];
+            pos[n] = loc[n][i];
+        }
+
+        err = aln·sketch(SEQ[i], aln·L, phi, pos);
+    }
+
+    f = 0;
+    for (n = 0; n < aln·N; n++) {
+        aln·sort(arrlen(SEQ), aln·L, (uint64*)mem[n]);
+
+        if (!memcmp(mem[n][0], mem[n][1], sizeof(uint64)*aln·L)) {
+            f += 1.;
+            printf("True : ");
+        } else {
+            printf("False: ");
+        }
+        for (i = 0; i < arrlen(SEQ); i++) {
+            printf("[");
+            for (l = 0; l < aln·L; l++) {
+                printf("%d,", loc[n][i][l]);
+            }
+            printf("]");
+            if (i == 0) printf(" ~ ");
+        }
+        printf("\n");
+    }
+
+    printf("Fraction hits %f\n", f/aln·N);
+    return err;
+#if 0
+
     if (err = test·newick(), err) {
         errorf("test fail: newick");
     }
@@ -155,5 +264,6 @@ main()
     if (err = test·fastq(), err) {
         errorf("test fail: fastq");
     }
+#endif
 }
 
diff --git a/sys/libn/memory.c b/sys/libn/memory.c
index 8081569..7a0ca30 100644
--- a/sys/libn/memory.c
+++ b/sys/libn/memory.c
@@ -147,3 +147,20 @@ mem·freearena(mem·Arena *a)
 
     a->heap.free(a->impl, a);
 }
+
+// -------------------------------------------------------------------------
+// Generalized memory helpers
+
+void
+memset64(void *dst, uint64 val, uintptr size)
+{
+    intptr i;
+
+    for (i = 0; i < (size & (~7)); i += 8) {
+        memcpy((byte*)dst + i, &val, 8);
+    }
+
+    for (; i < size; i++) {
+        ((byte*)dst)[i] = ((byte*)&val)[i&7];
+    }
+}