+++ /dev/null
-
-/* Implementation of the Wozniak "anti-diagonal" vectorization
- strategy for Smith-Waterman comparison, Wozniak (1997) Comp.
- Appl. Biosci. 13:145-150
-
- November, 2004
-*/
-
-/*
- Written by Erik Lindahl, Stockholm Bioinformatics Center, 2004.
- Please send bug reports and/or suggestions to lindahl@sbc.su.se.
-*/
-
-#include <stdio.h>
-
-#include "defs.h"
-#include "param.h"
-#include "dropgsw.h"
-
-#ifdef SW_ALTIVEC
-
-int
-smith_waterman_altivec_word(unsigned char * query_sequence,
- unsigned short * query_profile_word,
- int query_length,
- unsigned char * db_sequence,
- int db_length,
- unsigned short bias,
- unsigned short gap_open,
- unsigned short gap_extend,
- struct f_struct * f_str)
-{
- int i,j,k;
- unsigned short * p;
- unsigned short score;
- unsigned char * p_dbseq;
- int alphabet_size = f_str->alphabet_size;
- unsigned short * workspace = (unsigned short *)f_str->workspace;
-
- vector unsigned short Fup,Hup1,Hup2,E,F,H,tmp;
- vector unsigned char perm;
- vector unsigned short v_maxscore;
- vector unsigned short v_bias,v_gapopen,v_gapextend;
- vector unsigned short v_score;
- vector unsigned short v_score_q1;
- vector unsigned short v_score_q2;
- vector unsigned short v_score_q3;
- vector unsigned short v_score_load;
- vector unsigned char queue1_to_score = (vector unsigned char)(16,17,2,3,4,5,6,7,8,9,10,11,12,13,14,15);
- vector unsigned char queue2_to_queue1 = (vector unsigned char)(0,1,18,19,4,5,6,7,8,9,10,11,12,13,14,15);
- vector unsigned char queue3_to_queue2 = (vector unsigned char)(16,16,16,16,16,21,16,0,16,1,16,2,16,3,16,4);
- vector unsigned char queue3_with_load = (vector unsigned char)(23,5,6,7,8,25,9,10,11,27,12,13,29,14,31,16);
-
- /* Load the bias to all elements of a constant */
- v_bias = vec_lde(0,&bias);
- perm = vec_lvsl(0,&bias);
- v_bias = vec_perm(v_bias,v_bias,perm);
- v_bias = vec_splat(v_bias,0);
-
- /* Load gap opening penalty to all elements of a constant */
- v_gapopen = vec_lde(0,&gap_open);
- perm = vec_lvsl(0,&gap_open);
- v_gapopen = vec_perm(v_gapopen,v_gapopen,perm);
- v_gapopen = vec_splat(v_gapopen,0);
-
- /* Load gap extension penalty to all elements of a constant */
- v_gapextend = vec_lde(0,&gap_extend);
- perm = vec_lvsl(0,&gap_extend);
- v_gapextend = vec_perm(v_gapextend,v_gapextend,perm);
- v_gapextend = vec_splat(v_gapextend,0);
-
- v_maxscore = vec_xor(v_maxscore,v_maxscore);
-
- // Zero out the storage vector
- k = 2*(db_length+7);
-
- for(i=0,j=0;i<k;i++,j+=16)
- {
- // borrow the zero value in v_maxscore to have something to store
- vec_st(v_maxscore,j,workspace);
- }
-
- for(i=0;i<query_length;i+=8)
- {
- // fetch first data asap.
- p_dbseq = db_sequence;
- k = *p_dbseq++;
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // zero lots of stuff.
- // We use both the VPERM and VSIU unit to knock off some cycles.
-
- E = vec_splat_u16(0);
- F = vec_xor(F,F);
- H = vec_splat_u16(0);
- Hup2 = vec_xor(Hup2,Hup2);
- v_score_q1 = vec_splat_u16(0);
- v_score_q2 = vec_xor(v_score_q2,v_score_q2);
- v_score_q3 = vec_splat_u16(0);
-
- // reset pointers to the start of the saved data from the last row
- p = workspace;
-
- // PROLOGUE 1
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 2
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 3
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 4
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 5
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 6
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 7
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 8
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // reset pointers to the start of the saved data from the last row
- p = workspace;
-
- for(j=8;j<db_length;j+=8)
- {
- // STEP 1
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup1 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 2
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup2 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup2 = vec_sld(Hup2,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 3
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup1 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 4
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup2 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup2 = vec_sld(Hup2,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 5
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup1 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 6
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup2 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup2 = vec_sld(Hup2,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 7
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup1 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup1 = vec_sld(Hup1,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // STEP 8
-
- // prefetch next residue
- k = *p_dbseq++;
-
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
-
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // prefetch score for next step
- v_score_load = vec_ld(16*k,query_profile_word);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(256, p);
- Hup2 = vec_ld(272, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,14);
- Hup2 = vec_sld(Hup2,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
- }
-
- v_score_load = vec_splat_u16(0);
-
- for(;j<db_length+7;j++)
- {
- // Create the actual diagonal score vector
- // and update the queue of incomplete score vectors
- //
- // This could of course be done with only vec_perm or vec_sel,
- // but since they use different execution units we have found
- // it to be slightly faster to mix them.
- v_score = vec_perm(v_score_q1, v_score_load, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q3, v_score_load, queue3_with_load);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 16; // move ahead 32 bytes
-
- // v_score_load contains all zeros
- Fup = vec_sld(v_score_load,F,14);
- Hup1 = vec_sld(v_score_load,H,14);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
- }
- vec_st(F, 0, p);
- vec_st(H, 16, p);
-
- query_profile_word += 8*alphabet_size;
- }
-
- // find largest score in the v_maxscore vector
- tmp = vec_sld(v_maxscore,v_maxscore,8);
- v_maxscore = vec_max(v_maxscore,tmp);
- tmp = vec_sld(v_maxscore,v_maxscore,4);
- v_maxscore = vec_max(v_maxscore,tmp);
- tmp = vec_sld(v_maxscore,v_maxscore,2);
- v_maxscore = vec_max(v_maxscore,tmp);
-
- // store in temporary variable
- vec_ste(v_maxscore,0,&score);
-
- // return largest score
- return score;
-}
-
-int
-smith_waterman_altivec_byte(unsigned char * query_sequence,
- unsigned char * query_profile_byte,
- int query_length,
- unsigned char * db_sequence,
- int db_length,
- unsigned char bias,
- unsigned char gap_open,
- unsigned char gap_extend,
- struct f_struct * f_str)
-{
- int i,j,k,k8;
- int overflow;
- unsigned char * p;
- unsigned char score;
- int alphabet_size = f_str->alphabet_size;
- unsigned char * workspace = (unsigned char *)f_str->workspace;
-
- vector unsigned char Fup,Hup1,Hup2,E,F,H,tmp;
- vector unsigned char perm;
- vector unsigned char v_maxscore;
- vector unsigned char v_bias,v_gapopen,v_gapextend;
- vector unsigned char v_score;
- vector unsigned char v_score_q1;
- vector unsigned char v_score_q2;
- vector unsigned char v_score_q3;
- vector unsigned char v_score_q4;
- vector unsigned char v_score_q5;
- vector unsigned char v_score_load1;
- vector unsigned char v_score_load2;
- vector unsigned char v_zero;
-
- vector unsigned char queue1_to_score = (vector unsigned char)(16,1,2,3,4,5,6,7,24,9,10,11,12,13,14,15);
- vector unsigned char queue2_to_queue1 = (vector unsigned char)(16,17,2,3,4,5,6,7,24,25,10,11,12,13,14,15);
- vector unsigned char queue3_to_queue2 = (vector unsigned char)(16,17,18,3,4,5,6,7,24,25,26,11,12,13,14,15);
- vector unsigned char queue4_to_queue3 = (vector unsigned char)(16,17,18,19,4,5,6,7,24,25,26,27,12,13,14,15);
- vector unsigned char queue5_to_queue4 = (vector unsigned char)(16,17,18,19,20,2,3,4,24,25,26,27,28,10,11,12);
- vector unsigned char queue5_with_load = (vector unsigned char)(19,20,21,5,6,22,7,23,27,28,29,13,14,30,15,31);
- vector unsigned char merge_score_load = (vector unsigned char)(0,1,2,3,4,5,6,7,24,25,26,27,28,29,30,31);
-
- v_zero = vec_splat_u8(0);
-
- /* Load the bias to all elements of a constant */
- v_bias = vec_lde(0,&bias);
- perm = vec_lvsl(0,&bias);
- v_bias = vec_perm(v_bias,v_bias,perm);
- v_bias = vec_splat(v_bias,0);
-
- /* Load gap opening penalty to all elements of a constant */
- v_gapopen = vec_lde(0,&gap_open);
- perm = vec_lvsl(0,&gap_open);
- v_gapopen = vec_perm(v_gapopen,v_gapopen,perm);
- v_gapopen = vec_splat(v_gapopen,0);
-
- /* Load gap extension penalty to all elements of a constant */
- v_gapextend = vec_lde(0,&gap_extend);
- perm = vec_lvsl(0,&gap_extend);
- v_gapextend = vec_perm(v_gapextend,v_gapextend,perm);
- v_gapextend = vec_splat(v_gapextend,0);
-
- v_maxscore = vec_xor(v_maxscore,v_maxscore);
-
- // Zero out the storage vector
- k = (db_length+15);
- for(i=0,j=0;i<k;i++,j+=32)
- {
- // borrow the zero value in v_maxscore to have something to store
- vec_st(v_maxscore,j,workspace);
- vec_st(v_maxscore,j+16,workspace);
- }
-
- for(i=0;i<query_length;i+=16)
- {
- // zero lots of stuff.
- // We use both the VPERM and VSIU unit to knock off some cycles.
-
- E = vec_splat_u8(0);
- F = vec_xor(F,F);
- H = vec_splat_u8(0);
- Hup2 = vec_xor(Hup2,Hup2);
- v_score_q1 = vec_splat_u8(0);
- v_score_q2 = vec_xor(v_score_q2,v_score_q2);
- v_score_q3 = vec_splat_u8(0);
- v_score_q4 = vec_xor(v_score_q4,v_score_q4);
- v_score_q5 = vec_splat_u8(0);
-
- // reset pointers to the start of the saved data from the last row
- p = workspace;
-
- // start directly and prefetch score column
- k = db_sequence[0];
- k8 = k;
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = v_score_load1;
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // PROLOGUE 1
- // prefetch next residue
- k = db_sequence[1];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
- // PROLOGUE 2
- // prefetch next residue
- k = db_sequence[2];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 3
- // prefetch next residue
- k = db_sequence[3];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 4
- // prefetch next residue
- k = db_sequence[4];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 5
- // prefetch next residue
- k = db_sequence[5];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
- // PROLOGUE 6
- // prefetch next residue
- k = db_sequence[6];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 7
- // prefetch next residue
- k = db_sequence[7];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_zero,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 8
- // prefetch next residue
- k = db_sequence[8];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
- // PROLOGUE 9
- // prefetch next residue
- k = db_sequence[9];
- k8 = db_sequence[1];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 10
- // prefetch next residue
- k = db_sequence[10];
- k8 = db_sequence[2];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
- // PROLOGUE 11
- // prefetch next residue
- k = db_sequence[11];
- k8 = db_sequence[3];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 12
- // prefetch next residue
- k = db_sequence[12];
- k8 = db_sequence[4];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
- // PROLOGUE 13
- // prefetch next residue
- k = db_sequence[13];
- k8 = db_sequence[5];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 14
- // prefetch next residue
- k = db_sequence[14];
- k8 = db_sequence[6];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 15
- // prefetch next residue
- k = db_sequence[15];
- k8 = db_sequence[7];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup1 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
- // PROLOGUE 16
- // prefetch next residue
- k = db_sequence[16];
- k8 = db_sequence[8];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch score for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(0, p);
- Hup2 = vec_ld(16, p);
- p += 32; // move ahead 32 bytes
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- p = workspace;
-
- for(j=16;j<db_length;j+=16)
- {
- // STEP 1
-
- // prefetch next residue
- k = db_sequence[j+1];
- k8 = db_sequence[j-7];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
- // STEP 2
-
- // prefetch next residue
- k = db_sequence[j+2];
- k8 = db_sequence[j-6];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 3
-
- // prefetch next residue
- k = db_sequence[j+3];
- k8 = db_sequence[j-5];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 4
-
- // prefetch next residue
- k = db_sequence[j+4];
- k8 = db_sequence[j-4];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 5
-
- // prefetch next residue
- k = db_sequence[j+5];
- k8 = db_sequence[j-3];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 6
-
- // prefetch next residue
- k = db_sequence[j+6];
- k8 = db_sequence[j-2];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 7
-
- // prefetch next residue
- k = db_sequence[j+7];
- k8 = db_sequence[j-1];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 8
-
- // prefetch next residue
- k = db_sequence[j+8];
- k8 = db_sequence[j];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
-
-
-
-
-
- // STEP 9
-
- // prefetch next residue
- k = db_sequence[j+9];
- k8 = db_sequence[j+1];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 10
-
- // prefetch next residue
- k = db_sequence[j+10];
- k8 = db_sequence[j+2];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 11
-
- // prefetch next residue
- k = db_sequence[j+11];
- k8 = db_sequence[j+3];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 12
-
- // prefetch next residue
- k = db_sequence[j+12];
- k8 = db_sequence[j+4];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 13
-
- // prefetch next residue
- k = db_sequence[j+13];
- k8 = db_sequence[j+5];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 14
-
- // prefetch next residue
- k = db_sequence[j+14];
- k8 = db_sequence[j+6];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 15
-
- // prefetch next residue
- k = db_sequence[j+15];
- k8 = db_sequence[j+7];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup1 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup1 = vec_sld(Hup1,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- // STEP 16
-
- // prefetch next residue
- k = db_sequence[j+16];
- k8 = db_sequence[j+8];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load1 = vec_ld(16*k,query_profile_byte);
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
-
- // load values of F and H from previous row (one unit up)
- Fup = vec_ld(512, p);
- Hup2 = vec_ld(528, p);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32;
-
- // shift into place so we have complete F and H vectors
- // that refer to the values one unit up from each cell
- // that we are currently working on.
- Fup = vec_sld(Fup,F,15);
- Hup2 = vec_sld(Hup2,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup2,v_gapopen);
- F = vec_max(F,tmp);
-
- v_score_load1 = vec_perm(v_score_load1,v_score_load2,merge_score_load);
-
- // add score to H
- H = vec_adds(Hup1,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
-
- }
-
- for(;j<db_length+15;j++)
- {
- k8 = db_sequence[j-7];
-
- v_score = vec_perm(v_score_q1, v_score_load1, queue1_to_score);
- v_score_q1 = vec_perm(v_score_q2, v_score_load1, queue2_to_queue1);
- v_score_q2 = vec_perm(v_score_q3, v_score_load1, queue3_to_queue2);
- v_score_q3 = vec_perm(v_score_q4, v_score_load1, queue4_to_queue3);
- v_score_q4 = vec_perm(v_score_q5, v_score_load1, queue5_to_queue4);
- v_score_q5 = vec_perm(v_score_q5, v_score_load1, queue5_with_load);
-
-
- // prefetch scores for next step
- v_score_load2 = vec_ld(16*k8,query_profile_byte);
- v_score_load1 = vec_perm(v_zero,v_score_load2,merge_score_load);
-
- // save old values of F and H to use on next row
- vec_st(F, 0, p);
- vec_st(H, 16, p);
- p += 32; // move ahead 32 bytes
-
- Fup = vec_sld(v_zero,F,15);
- Hup1 = vec_sld(v_zero,H,15);
-
- // do the dynamic programming
-
- // update E value
- E = vec_subs(E,v_gapextend);
- tmp = vec_subs(H,v_gapopen);
- E = vec_max(E,tmp);
-
- // update F value
- F = vec_subs(Fup,v_gapextend);
- tmp = vec_subs(Hup1,v_gapopen);
- F = vec_max(F,tmp);
-
- // add score to H
- H = vec_adds(Hup2,v_score);
- H = vec_subs(H,v_bias);
-
- // set H to max of H,E,F
- H = vec_max(H,E);
- H = vec_max(H,F);
-
- // Save value to use for next diagonal H
- Hup2 = Hup1;
-
- // Update highest score encountered this far
- v_maxscore = vec_max(v_maxscore,H);
- }
- vec_st(F, 512, p);
- vec_st(H, 528, p);
-
- query_profile_byte += 16*alphabet_size;
-
- // End of this row (actually 16 rows due to SIMD).
- // Before we continue, check for overflow.
- tmp = vec_subs(vec_splat_u8(-1),v_bias);
- overflow = vec_any_ge(v_maxscore,tmp);
-
-
- }
-
- if(overflow)
- {
- return 255;
- }
- else
- {
- // find largest score in the v_maxscore vector
- tmp = vec_sld(v_maxscore,v_maxscore,8);
- v_maxscore = vec_max(v_maxscore,tmp);
- tmp = vec_sld(v_maxscore,v_maxscore,4);
- v_maxscore = vec_max(v_maxscore,tmp);
- tmp = vec_sld(v_maxscore,v_maxscore,2);
- v_maxscore = vec_max(v_maxscore,tmp);
- tmp = vec_sld(v_maxscore,v_maxscore,1);
- v_maxscore = vec_max(v_maxscore,tmp);
-
- // store in temporary variable
- vec_ste(v_maxscore,0,&score);
-
- // return largest score
- return score;
- }}
-
-
-#else
-
-/* No Altivec support. Avoid compiler complaints about empty object */
-
-int sw_dummy;
-
-#endif
git://source.jalview.org / jabaws.git / blobdiff