#include <hitmap.h>
#include "SWcommon.h"
#include "SWcommon_hit.h"
Go to the source code of this file.
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#define | aa_hit_t MPI_SHORT |
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#define | h_hit_t MPI_DOUBLE |
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#define | h(i, j) (hit_tileElemAtNoStride(H,2,i,j)) |
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#define | xback(i, j) (hit_tileElemAtNoStride(xTraceback,2,i,j)) |
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#define | yback(i, j) (hit_tileElemAtNoStride(yTraceback,2,i,j)) |
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#define | allTimers(timer) hit_clockGetMinSeconds(timer),hit_clockGetAvgSeconds(timer),hit_clockGetMaxSeconds(timer) |
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#define | MIN(a, b) (((a)<(b))?(a):(b)) |
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#define | MAX(a, b) (((a)>(b))?(a):(b)) |
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| hit_tileNewType (int) |
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void | distributeProtein (HitTile_aa_t protein, HitTile_aa_t lprotein, int dim) |
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| hit_tileNewType (double_3int) |
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void | recv_Back (int dir, int *pos) |
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void | send_Back (int dir, int pos) |
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void | composeOutput (HitTile_aa_t out, int *outpos, int *outsize, HitTile_aa_t lout, int loutpos, int loutsize, int *gBegin, int *gEnd) |
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void | phase_read_sequences () |
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void | phase_distribute_sequences () |
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void | phase_recv_hmatrix () |
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void | phase_comp_hmatrix () |
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void | phase_send_hmatrix () |
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void | phase_recv_back () |
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void | phase_comp_back () |
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void | phase_send_back () |
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void | phase_compose_sequence () |
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void | debug_show_matrices () |
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void | debug_show_backtracking () |
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int | main (int argc, char *argv[]) |
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#define aa_hit_t MPI_SHORT |
Hitmap comm type for the amino acid.
Definition at line 75 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 |
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#define MIN |
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void composeOutput |
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HitTile_aa_t |
out, |
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int * |
outpos, |
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int * |
outsize, |
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HitTile_aa_t |
lout, |
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int |
loutpos, |
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int |
loutsize, |
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int * |
gBegin, |
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int * |
gEnd |
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Function to compose the final output in the root processor.
Definition at line 1123 of file SWpar.c.
void debug_show_backtracking |
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Debug to show the backtracking info
Definition at line 1009 of file SWpar.c.
void debug_show_matrices |
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Debug function to show the H and backtraking matrices
Definition at line 782 of file SWpar.c.
void distributeProtein |
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HitTile_aa_t |
protein, |
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HitTile_aa_t |
lprotein, |
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int |
dim |
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Function that distributes the protein from the root processor to the remain procs.
Definition at line 1051 of file SWpar.c.
hit_tileNewType |
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double_3int |
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Struct used to calculate the processor where the maximum H matrix value is.
int main |
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int |
argc, |
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char * |
argv[] |
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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.
Compute the traceback
Definition at line 955 of file SWpar.c.
void phase_comp_hmatrix |
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Calculate the similarity matrix (H)
Definition at line 708 of file SWpar.c.
void phase_compose_sequence |
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Compose the final sequence
Definition at line 1036 of file SWpar.c.
void phase_distribute_sequences |
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Distribute the protein sequences
Definition at line 637 of file SWpar.c.
void phase_read_sequences |
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Read the protein sequences
Definition at line 619 of file SWpar.c.
Receive the traceback neighbor values
Definition at line 862 of file SWpar.c.
void phase_recv_hmatrix |
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Receive the similarity matrix (H) values from the neighbors.
Definition at line 662 of file SWpar.c.
Receive the traceback values to the appropriate neighbor
Definition at line 927 of file SWpar.c.
void phase_send_hmatrix |
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Send the similarity matrix (H) values to the neighbors.
Definition at line 684 of file SWpar.c.
void recv_Back |
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int |
dir, |
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int * |
pos |
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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.
void send_Back |
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int |
dir, |
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int |
pos |
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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.
Hitmap layout
Definition at line 194 of file SWpar.c.
Shape from the layout
Definition at line 197 of file SWpar.c.
Size of the local part of the proteins.
Definition at line 188 of file SWpar.c.
MPI reduce function for double_3int
Definition at line 191 of file SWpar.c.
HitTile_trace_t xTraceback |
HitTile_trace_t yTraceback |