include/qPosList.h File Reference

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Data Structures

struct  queryPosition
struct  codeword

Functions

void qPosList_initialize (int4 maxNumLists)
void qPosList_reset ()
void qPosList_free ()
void qPosList_print ()
void qPosList_addList (int2 *queryPositions, int2 numQueryPositions, int4 codeword)
void qPosList_processLists ()

Variables

memSingleBlock * qPosList_qPosLists
int4 qPosList_numQPosLists
int4 qPosList_maxQPosLists

Function Documentation

void qPosList_addList ( int2 *  queryPositions,
int2  numQueryPositions,
int4  codeword 
)

Definition at line 113 of file qPosList.c.

References initialQPosList::codeword, initialQPosList::numQueryPositions, qPosList_initialQPosLists, qPosList_numInitialQPosLists, and initialQPosList::queryPositions.

Referenced by wordLookupDFA_build().

00114 {
00115         qPosList_initialQPosLists[qPosList_numInitialQPosLists].queryPositions = queryPositions;
00116         qPosList_initialQPosLists[qPosList_numInitialQPosLists].numQueryPositions = numQueryPositions;
00117         qPosList_initialQPosLists[qPosList_numInitialQPosLists].codeword = codeword;
00118 
00119     qPosList_numInitialQPosLists++;
00120 }

Here is the caller graph for this function:

void qPosList_free (  ) 

Definition at line 58 of file qPosList.c.

References memSingleBlock::block, qPosList_initialQPosLists, qPosList_maxQPosLists, and qPosList_qPosLists.

Referenced by wordLookupDFA_build().

00059 {
00060     struct memSingleBlock* list;
00061 
00062     // Free initial lists
00063         free(qPosList_initialQPosLists);
00064 
00065     // Free each final qPos list
00066     while (qPosList_maxQPosLists > 0)
00067     {
00068         qPosList_maxQPosLists--;
00069         list = qPosList_qPosLists + qPosList_maxQPosLists;
00070         free(list->block);
00071     }
00072 
00073     free(qPosList_qPosLists);
00074 }

Here is the caller graph for this function:

void qPosList_initialize ( int4  maxNumLists  ) 

Definition at line 30 of file qPosList.c.

References global_malloc(), memSingleBlock_initializeExisting(), qPosList_initialQPosLists, qPosList_maxQPosLists, qPosList_numInitialQPosLists, qPosList_numQPosLists, and qPosList_qPosLists.

Referenced by wordLookupDFA_build().

00031 {
00032     struct memSingleBlock* list;
00033 
00034     qPosList_qPosLists = (struct memSingleBlock*)global_malloc(sizeof(struct memSingleBlock) * maxNumLists);
00035     qPosList_numQPosLists = 0;
00036     qPosList_maxQPosLists = 0;
00037 
00038     // Initialize lists of query positions
00039     while (qPosList_maxQPosLists < maxNumLists)
00040     {
00041         list = qPosList_qPosLists + qPosList_maxQPosLists;
00042         memSingleBlock_initializeExisting(list, sizeof(struct queryPosition), 10);
00043         qPosList_maxQPosLists++;
00044     }
00045 
00046     qPosList_initialQPosLists = (struct initialQPosList*)global_malloc(sizeof(struct initialQPosList) * maxNumLists);
00047     qPosList_numInitialQPosLists = 0;
00048 }

Here is the call graph for this function:

Here is the caller graph for this function:

void qPosList_print (  ) 

Definition at line 77 of file qPosList.c.

References memSingleBlock::block, int4, memSingleBlock::numEntries, qPosList_numQPosLists, qPosList_qPosLists, and queryPosition::queryPosition.

00078 {
00079         int4 listCount = 0, queryPositionCount;
00080     struct memSingleBlock* list;
00081     struct queryPosition* queryPosition;
00082 
00083     // For each list
00084     while (listCount < qPosList_numQPosLists)
00085     {
00086         list = qPosList_qPosLists + listCount;
00087 
00088         printf("%d) ", listCount); fflush(stdout);
00089 
00090         // Traverse in reverse order and print elements
00091         queryPositionCount = list->numEntries;
00092         while (queryPositionCount > 0)
00093         {
00094                 queryPositionCount--;
00095             queryPosition = (struct queryPosition*)list->block + queryPositionCount;
00096 
00097             if (queryPosition->codewords != NULL)
00098             {
00099                 printf("%d* ", queryPosition->queryPosition); fflush(stdout);
00100             }
00101             else
00102             {
00103                 printf("%d ", queryPosition->queryPosition); fflush(stdout);
00104             }
00105         }
00106         printf("\n");
00107 
00108                 listCount++;
00109     }
00110 }

void qPosList_processLists (  ) 

Definition at line 148 of file qPosList.c.

References initialQPosList::codeword, int2, int4, initialQPosList::numQueryPositions, qPosList_compareInitialList(), qPosList_initialQPosLists, qPosList_numInitialQPosLists, qPosList_processList(), and initialQPosList::queryPositions.

Referenced by wordLookupDFA_build().

00149 {
00150         int2* queryPositions;
00151     int2 numQueryPositions;
00152     int4 codeword;
00153 
00154     // Sort initial query position lists from shortest to longest
00155     qsort(qPosList_initialQPosLists, qPosList_numInitialQPosLists,
00156           sizeof(struct initialQPosList), qPosList_compareInitialList);
00157 
00158     // Add in sorted order
00159         while (qPosList_numInitialQPosLists > 0)
00160     {
00161         qPosList_numInitialQPosLists--;
00162 
00163                 queryPositions = qPosList_initialQPosLists[qPosList_numInitialQPosLists].queryPositions;
00164                 numQueryPositions = qPosList_initialQPosLists[qPosList_numInitialQPosLists].numQueryPositions;
00165                 codeword = qPosList_initialQPosLists[qPosList_numInitialQPosLists].codeword;
00166 
00167         if (numQueryPositions != 0)
00168         {
00169                         qPosList_processList(queryPositions, numQueryPositions, codeword);
00170         }
00171     }
00172 }

Here is the call graph for this function:

Here is the caller graph for this function:

void qPosList_reset (  ) 

Definition at line 51 of file qPosList.c.

References qPosList_numInitialQPosLists, and qPosList_numQPosLists.

Referenced by wordLookupDFA_build().

00052 {
00053     qPosList_numQPosLists = 0;
00054     qPosList_numInitialQPosLists = 0;
00055 }

Here is the caller graph for this function:

Variable Documentation

int4 qPosList_maxQPosLists

Definition at line 21 of file qPosList.c.

Referenced by qPosList_free(), and qPosList_initialize().

int4 qPosList_numQPosLists

Definition at line 20 of file qPosList.c.

Referenced by qPosList_initialize(), qPosList_print(), qPosList_processList(), qPosList_reset(), and wordLookupDFA_build().

struct memSingleBlock* qPosList_qPosLists

Definition at line 19 of file qPosList.c.

Referenced by qPosList_free(), qPosList_initialize(), qPosList_print(), qPosList_processList(), and wordLookupDFA_build().

Generated on Wed Dec 19 20:51:10 2007 for fsa-blast by  doxygen 1.5.2