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+/*

+ * dna_astream.h

+ *

+ *  Created on: 07.10.2013

+ *      Author: wolfgang

+ */

+

+#ifndef DNA_ASTREAM_H_

+#define DNA_ASTREAM_H_

+

+#include "dna_fstream.h"

+

+///////////////////////////////////////////////////////////////////////////////////////////////////

+//

+// dna file stream

+//		Keeps two (equal sized) character buffers (raw and processed) and two iterators

+//

+//		Raw buffer can be (re-) filled from dna_fstream.

+//		Client struct can define functions for searching and coypying content into

+//		processed buffer.

+//

+///////////////////////////////////////////////////////////////////////////////////////////////////

+

+

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+//

+// Define buffer size and delimiting characters

+//

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+

+static const char			das_char_eos			='\0';

+

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+//

+// Define status flags

+//

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+

+static const int das_err		=-1;	// Unrecoverable error state

+static const int das_ok			= 0;	// Must be 0 !!!

+static const int das_empty		= 1;	// Future raw size =0

+

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+

+

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+//

+// 	Struct definition

+//

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+

+typedef struct dna_astream

+{

+

+	dfStream *dnaf;

+

+	// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  //

+	// Character array declarations

+

+	unsigned nchar;		// Maximal number of characters in rfc and pos

+						// (array size=nchar+1)

+

+	// Pointers to character arrays (= begin pointers)

+	char * rfc;			// Raw file content				: rfc-array

+	char * pos;			// Processed output sequence	: pos-array

+

+	// Iterators which reside inside arrays

+	char * r_iter;		// iterator for rfc

+	char * p_iter;		// iterator for pos

+

+	//  Point to past-the-end character of arrays ('\0')

+	char * r_end;		// rfc array

+	char * p_end;		// behind last retrievable character

+

+	int npPos;		// Number of character values in pos array (=strlen)

+	//

+	// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  //

+

+	int state;	// Carries stream state flags

+

+	unsigned nFill;

+	unsigned nFillWhole;

+	unsigned nFillWholeIncomp;

+	unsigned nFillPart;

+	unsigned nFillPartIncomp;

+

+} daStream;

+

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+//

+// Check routines

+//

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+

+static inline int dasEmpty(daStream *das) 		{ return das->r_iter == das->r_end; }

+static inline int dasProcEmpty(daStream *das)	{ return das->p_iter == das->p_end; }

+static inline int dasIsError(daStream *das)		{ return das->state & das_err; }

+static inline int dasIsOpen(daStream *das)		{ return dfs_isOpen(das->dnaf); }

+static inline int dasIsEof(daStream *das)		{ return dfs_stream_eof(das->dnaf); }

+

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+//

+// Constructing and and File operations

+//

+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + //

+

+void das_destroy(daStream *das)

+{

+	if(das)

+	{

+		dfs_destroy(das->dnaf);

+		das->dnaf=0;

+		free(das->rfc);

+		das->rfc=0;

+		free(das->pos);

+		das->pos=0;

+		free(das);

+	}

+}

+

+

+int das_fill(daStream *das)

+{

+	//printf("[das_fill] before: '%s'\n",das->rfc);

+	size_t count = 0;

+

+	int rhs= (int)(das->r_end  - das->r_iter);		// Number of unprocessed characters in array

+	int lhs= (int)(das->r_iter - das->rfc);			// Number of   processed characters in array

+

+	if(dfs_isOpen(das->dnaf))

+	{

+		if(rhs>0)

+		{

+			//printf("[das_fill] rhs= %u\n",rhs);

+			if(lhs<rhs)

+			{

+				// Enough space at begin of array?

+				//printf("[das_fill] Partial fill ERROR!\n");

+				das->state = das_err;

+				return das->state;

+			}

+			// Shift unused suffix to begin

+			memcpy(das->rfc, das->r_iter, (size_t) rhs);

+			count = dfs_read(das->dnaf, das->rfc + rhs, (unsigned) lhs);

+

+			/* lhs < 0 should not be possible */

+			if(count < ((size_t) lhs))

+				++das->nFillPartIncomp;

+			++das->nFillPart;

+		}

+		else

+		{	// Refill whole array

+			//printf("[das_fill] rhs== %u\n",rhs);

+			count = dfs_read(das->dnaf, das->rfc, das->nchar);

+			if(count < das->nchar)

+				++das->nFillWholeIncomp;

+			++das->nFillWhole;

+		}

+		das->r_end = das->rfc + count; // past-the-end

+		*das->r_end = das_char_eos;    // '\0'

+		das->r_iter = das->rfc;        // Re-init iter

+		++das->nFill;

+	}

+

+	if(count==0)

+	{

+		//printf("[das_fill] count==0.\n");

+		das->state |= das_empty;

+		return das->state;

+	}

+	// Return success

+	das->state &= (~das_empty);

+	return das_ok;

+}

+

+daStream * das_init(const char* filename, unsigned das_size)

+{

+	daStream *das = calloc(sizeof(daStream), 1);

+	if(!das)

+	{

+		//printf("[das_init] das calloc returned 0!\n");

+		return 0;

+	}

+

+	das->dnaf = dfs_stream_init(filename);

+

+	if(!das->dnaf)

+	{

+		//printf("[das_init] dfs_stream_init returned 0!\n");

+		das->state = das_err;

+		return das;

+	}

+

+	das->nchar = das_size;

+	das->rfc = calloc(das_size + 1, sizeof(char));

+	if(!das->rfc)

+	{

+		//printf("[das_init] rfc calloc returned 0!\n");

+		das->state = das_err;

+		return das;

+	}

+	das->pos = calloc(das_size + 1, sizeof(char));

+	if(!das->pos)

+	{

+		//printf("[das_init] pos calloc returned 0!\n");

+		das->state = das_err;

+		return das;

+	}

+

+	das->r_end = das->rfc + das_size;

+	// Indicates empty buffer

+	// -> first das_fill will

+	// read complete buffer

+	das->r_iter = das->r_end;

+

+	// Returns memory initialized structure

+	// but dfs file is possibly closed

+	// (e.g. file not found).

+	return das;

+}

+

+

+#endif /* DNA_ASTREAM_H_ */