Hitmap 1.3
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Macros | Functions | Variables
SWpar.c File Reference
#include <hitmap.h>
#include "SWcommon.h"
#include "SWcommon_hit.h"
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Macros

#define aa_hit_t   MPI_SHORT
 
#define h_hit_t   MPI_DOUBLE
 
#define h(i, j)   (hit_tileElemAtNoStride(H,2,i,j))
 
#define xback(i, j)   (hit_tileElemAtNoStride(xTraceback,2,i,j))
 
#define yback(i, j)   (hit_tileElemAtNoStride(yTraceback,2,i,j))
 
#define allTimers(timer)   hit_clockGetMinSeconds(timer),hit_clockGetAvgSeconds(timer),hit_clockGetMaxSeconds(timer)
 
#define MIN(a, b)   (((a)<(b))?(a):(b))
 
#define MAX(a, b)   (((a)>(b))?(a):(b))
 

Functions

 hit_tileNewType (int)
 
void distributeProtein (HitTile_aa_t protein, HitTile_aa_t lprotein, int dim)
 
 hit_tileNewType (double_3int)
 
void recv_Back (int dir, int *pos)
 
void send_Back (int dir, int pos)
 
void composeOutput (HitTile_aa_t out, int *outpos, int *outsize, HitTile_aa_t lout, int loutpos, int loutsize, int *gBegin, int *gEnd)
 
void phase_read_sequences ()
 
void phase_distribute_sequences ()
 
void phase_recv_hmatrix ()
 
void phase_comp_hmatrix ()
 
void phase_send_hmatrix ()
 
void phase_recv_back ()
 
void phase_comp_back ()
 
void phase_send_back ()
 
void phase_compose_sequence ()
 
void debug_show_matrices ()
 
void debug_show_backtracking ()
 
int main (int argc, char *argv[])
 

Variables

int lsize [2]
 
MPI_Op opHMaxLoc
 
HitLayout layout
 
HitShape layshape
 
HitTile_aa_t p1
 
HitTile_aa_t p2
 
HitTile_aa_t out1
 
HitTile_aa_t out2
 
int xMax
 
int yMax
 
int xBegin
 
int yBegin
 
int match_length
 
int match_length1
 
int match_length2
 
int match_pos
 
HitTile_aa_t lp1
 
HitTile_aa_t lp2
 
HitTile_aa_t lout1
 
HitTile_aa_t lout2
 
HitTile_h_t H
 
HitTile_trace_t xTraceback
 
HitTile_trace_t yTraceback
 
h_t lMax
 
int lxMax
 
int lyMax
 
int lxBegin
 
int lyBegin
 
int lmatch_length
 
int lmatch_length1
 
int lmatch_length2
 
int lmatch_pos
 
HitShape lshape
 

Macro Definition Documentation

#define aa_hit_t   MPI_SHORT

Hitmap comm type for the amino acid.

Definition at line 75 of file SWpar.c.

#define h (   i,
 
)    (hit_tileElemAtNoStride(H,2,i,j))

Definition at line 244 of file SWpar.c.

#define h_hit_t   MPI_DOUBLE

Hitmap comm type of the H and PAM matrices

Definition at line 77 of file SWpar.c.

#define MAX (   a,
 
)    (((a)>(b))?(a):(b))

Definition at line 1119 of file SWpar.c.

#define MIN (   a,
 
)    (((a)<(b))?(a):(b))

Definition at line 1118 of file SWpar.c.

#define xback (   i,
 
)    (hit_tileElemAtNoStride(xTraceback,2,i,j))

Definition at line 249 of file SWpar.c.

#define yback (   i,
 
)    (hit_tileElemAtNoStride(yTraceback,2,i,j))

Definition at line 250 of file SWpar.c.

Function Documentation

void composeOutput ( HitTile_aa_t  out,
int *  outpos,
int *  outsize,
HitTile_aa_t  lout,
int  loutpos,
int  loutsize,
int *  gBegin,
int *  gEnd 
)

Function to compose the final output in the root processor.

Definition at line 1123 of file SWpar.c.

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void debug_show_backtracking ( )

Debug to show the backtracking info

Definition at line 1009 of file SWpar.c.

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void debug_show_matrices ( )

Debug function to show the H and backtraking matrices

Definition at line 782 of file SWpar.c.

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void distributeProtein ( HitTile_aa_t  protein,
HitTile_aa_t  lprotein,
int  dim 
)

Function that distributes the protein from the root processor to the remain procs.

Definition at line 1051 of file SWpar.c.

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hit_tileNewType ( int  )
hit_tileNewType ( double_3int  )

Struct used to calculate the processor where the maximum H matrix value is.

int main ( int  argc,
char *  argv[] 
)

Main function.

< Time init

< Time computation

< Accumulate time in read

< Accumulate time in H matrix computation

< Accumulate time in backtracking

< Accumulate time in protein sequence distribution

< Accumulate time in H matrix sync

< Accumulate time in backtracking sync

< Accumulate time in final protein composition

Definition at line 280 of file SWpar.c.

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void phase_comp_back ( )

Compute the traceback

Definition at line 955 of file SWpar.c.

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void phase_comp_hmatrix ( )

Calculate the similarity matrix (H)

Definition at line 708 of file SWpar.c.

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void phase_compose_sequence ( )

Compose the final sequence

Definition at line 1036 of file SWpar.c.

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void phase_distribute_sequences ( )

Distribute the protein sequences

Definition at line 637 of file SWpar.c.

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void phase_read_sequences ( )

Read the protein sequences

Definition at line 619 of file SWpar.c.

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void phase_recv_back ( )

Receive the traceback neighbor values

Definition at line 862 of file SWpar.c.

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void phase_recv_hmatrix ( )

Receive the similarity matrix (H) values from the neighbors.

Definition at line 662 of file SWpar.c.

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void phase_send_back ( )

Receive the traceback values to the appropriate neighbor

Definition at line 927 of file SWpar.c.

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void phase_send_hmatrix ( )

Send the similarity matrix (H) values to the neighbors.

Definition at line 684 of file SWpar.c.

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void recv_Back ( int  dir,
int *  pos 
)

Function to receive the result from the sucessors at the backtracking stage. They will pass the coordinate of the next point of the path or -1 if the alignement do not cross through our portion of H.

Definition at line 1100 of file SWpar.c.

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void send_Back ( int  dir,
int  pos 
)

Function to inform the predecessor processors if they have to rebuild the path using the backtracking algorithm.

Definition at line 1084 of file SWpar.c.

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Variable Documentation

HitTile_h_t H

Definition at line 243 of file SWpar.c.

HitLayout layout

Hitmap layout

Definition at line 194 of file SWpar.c.

HitShape layshape

Shape from the layout

Definition at line 197 of file SWpar.c.

int lmatch_length

Definition at line 265 of file SWpar.c.

int lmatch_length1

Definition at line 266 of file SWpar.c.

int lmatch_length2

Definition at line 267 of file SWpar.c.

int lmatch_pos

Definition at line 270 of file SWpar.c.

h_t lMax

Definition at line 254 of file SWpar.c.

HitTile_aa_t lout1

Definition at line 239 of file SWpar.c.

HitTile_aa_t lout2

Definition at line 240 of file SWpar.c.

HitTile_aa_t lp1

Definition at line 235 of file SWpar.c.

HitTile_aa_t lp2

Definition at line 236 of file SWpar.c.

HitShape lshape

Definition at line 273 of file SWpar.c.

int lsize[2]

Size of the local part of the proteins.

Definition at line 188 of file SWpar.c.

int lxBegin

Definition at line 261 of file SWpar.c.

int lxMax

Definition at line 257 of file SWpar.c.

int lyBegin

Definition at line 262 of file SWpar.c.

int lyMax

Definition at line 258 of file SWpar.c.

int match_length

Definition at line 222 of file SWpar.c.

int match_length1

Definition at line 223 of file SWpar.c.

int match_length2

Definition at line 224 of file SWpar.c.

int match_pos

Definition at line 227 of file SWpar.c.

MPI_Op opHMaxLoc

MPI reduce function for double_3int

Definition at line 191 of file SWpar.c.

HitTile_aa_t out1

Definition at line 210 of file SWpar.c.

HitTile_aa_t out2

Definition at line 211 of file SWpar.c.

HitTile_aa_t p1

Definition at line 206 of file SWpar.c.

HitTile_aa_t p2

Definition at line 207 of file SWpar.c.

int xBegin

Definition at line 218 of file SWpar.c.

int xMax

Definition at line 214 of file SWpar.c.

HitTile_trace_t xTraceback

Definition at line 247 of file SWpar.c.

int yBegin

Definition at line 219 of file SWpar.c.

int yMax

Definition at line 215 of file SWpar.c.

HitTile_trace_t yTraceback

Definition at line 248 of file SWpar.c.