sumalibs first commit

liblcs/_lcs.ext.1.c

@@ -0,0 +1,168 @@
+#include "_lcs.h"
+
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+
+#include <stdio.h>
+
+
+
+// Allocate a band allowing to align sequences of length : 'length'
+
+column_t* allocateColumn(int length,column_t *column, bool mode8bits)
+{
+	int size;
+	bool newc = false;
+
+			// The band length should be equal to the length
+			// of the sequence + 7 for taking into account its
+			// shape
+
+	size = (length+1) * ((mode8bits) ? sizeof(int8_t):sizeof(int16_t));
+
+
+			// If the pointer to the old column is NULL we allocate
+			// a new column
+
+	if (column==NULL)
+	{
+
+		column = malloc(sizeof(column_t));
+		if (!column)
+			return NULL;
+
+		column->size = 0;
+		column->data.shrt=NULL;
+		column->score.shrt=NULL;
+		newc = true;
+	}
+
+			// Otherwise we check if its size is sufficient
+			// or if it should be extended
+
+	if (size > column->size)
+	{
+		int16_t *old = column->data.shrt;
+		int16_t *olds= column->score.shrt;
+
+		column->data.shrt = malloc(size);
+		column->score.shrt= malloc(size);
+
+		if (column->data.shrt==NULL || column->score.shrt==NULL)
+		{
+			fprintf(stderr,"Allocation Error on column for a size of %d\n" , size);
+			column->data.shrt = old;
+			column->score.shrt= olds;
+
+			if (newc)
+			{
+				free(column);
+				column=NULL;
+				return NULL;
+			}
+			return NULL;
+		}
+		else
+			column->size = size;
+	}
+
+	return column;
+}
+
+void freeColumn(column_p column)
+{
+	if (column)
+	{
+		if (column->data.shrt)
+			free(column->data.shrt);
+
+		if (column->score.shrt)
+			free(column->score.shrt);
+
+		free(column);
+	}
+}
+
+int fastLCSScore(const char* seq1, const char* seq2,column_pp column,int32_t* lpath)
+{
+	return fastLCSScore16(seq1,seq2,column,lpath);
+}
+
+int simpleLCS(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath)
+{
+	int lseq1,lseq2;		// length of the both sequences
+	int lcs;
+	int itmp;				// tmp variables for swap
+	const char* stmp;		//
+	int32_t *score;
+	int32_t *path;
+	column_t *column;
+	int32_t i,j;
+	int32_t sl,su,sd;
+	int32_t pl,pu,pd;
+
+		// Made seq1 the longest sequences
+	lseq1=strlen(seq1);
+	lseq2=strlen(seq2);
+
+	if (lseq1 < lseq2)
+	{
+		itmp=lseq1;
+		lseq1=lseq2;
+		lseq2=itmp;
+
+		stmp=seq1;
+		seq1=seq2;
+		seq2=stmp;
+	}
+
+	lseq1++;
+	lseq2++;
+
+							// a band sized to the smallest sequence is allocated
+
+	if (ppcolumn)
+		column = *ppcolumn;
+	else
+		column=NULL;
+
+	column = allocateColumn(lseq1*2,column,0);
+	score = (int32_t*) column->score.shrt;
+	path = (int32_t*) column->data.shrt;
+
+	memset(score,0,lseq1 * sizeof(int32_t));
+
+	for (j=0; j < lseq1; j++)
+		path[j]=j;
+
+	for (i=1; i< lseq2; i++)
+	{
+		sl=0;
+		pl=i;
+		for (j=1; j < lseq1; j++)
+		{
+			sd=score[j-1] + (seq2[i-1]==seq1[j-1] ? 1:0);
+			pd=path[j-1]  + 1;
+
+			su=score[j];
+			pu=path[j] + 1;
+
+			score[j-1]=sl;
+
+			if (su > sl) sl=su, pl=pu;
+			if (sd > sl) sl=sd, pl=pd;
+		}
+	}
+
+	lcs = sl;
+	if(lpath) *lpath=pl;
+
+	if (ppcolumn)
+		*ppcolumn=column;
+	else
+		freeColumn(column);
+
+	return lcs;
+}
+