598 lines
14 KiB
C
Executable File
598 lines
14 KiB
C
Executable File
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/*
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* Print a SSE register for debug purpose
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*/
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#ifdef __SSE2__
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static void printreg(VTYPE r)
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{
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STYPE a0,a1,a2,a3,a4,a5,a6,a7;
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#if VMODE
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STYPE a8,a9,a10,a11,a12,a13,a14,a15;
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#endif
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a0= EXTRACT_REG(r,0);
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a1= EXTRACT_REG(r,1);
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a2= EXTRACT_REG(r,2);
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a3= EXTRACT_REG(r,3);
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a4= EXTRACT_REG(r,4);
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a5= EXTRACT_REG(r,5);
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a6= EXTRACT_REG(r,6);
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a7= EXTRACT_REG(r,7);
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#if VMODE
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a8= EXTRACT_REG(r,8);
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a9= EXTRACT_REG(r,9);
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a10= EXTRACT_REG(r,10);
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a11= EXTRACT_REG(r,11);
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a12= EXTRACT_REG(r,12);
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a13= EXTRACT_REG(r,13);
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a14= EXTRACT_REG(r,14);
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a15= EXTRACT_REG(r,15);
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#endif
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printf( "a00 :-> %7d %7d %7d %7d "
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" %7d %7d %7d %7d "
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#if VMODE
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"%7d %7d %7d %7d "
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" %7d %7d %7d %7d "
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#endif
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"\n"
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, a0,a1,a2,a3,a4,a5,a6,a7
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#if VMODE
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, a8,a9,a10,a11,a12,a13,a14,a15
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#endif
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);
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}
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/*
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* set position p of a SSE register with the value v
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*/
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static inline VTYPE insert_reg(VTYPE r, STYPE v, int p)
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{
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switch (p) {
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case 0: return INSERT_REG(r,v,0);
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case 1: return INSERT_REG(r,v,1);
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case 2: return INSERT_REG(r,v,2);
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case 3: return INSERT_REG(r,v,3);
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case 4: return INSERT_REG(r,v,4);
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case 5: return INSERT_REG(r,v,5);
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case 6: return INSERT_REG(r,v,6);
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case 7: return INSERT_REG(r,v,7);
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#if VMODE
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case 8: return INSERT_REG(r,v,8);
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case 9: return INSERT_REG(r,v,9);
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case 10: return INSERT_REG(r,v,10);
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case 11: return INSERT_REG(r,v,11);
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case 12: return INSERT_REG(r,v,12);
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case 13: return INSERT_REG(r,v,13);
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case 14: return INSERT_REG(r,v,14);
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case 15: return INSERT_REG(r,v,15);
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#endif
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}
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return _MM_SETZERO_SI128();
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}
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static inline STYPE extract_reg(VTYPE r, int p)
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{
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switch (p) {
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case 0: return EXTRACT_REG(r,0);
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case 1: return EXTRACT_REG(r,1);
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case 2: return EXTRACT_REG(r,2);
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case 3: return EXTRACT_REG(r,3);
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case 4: return EXTRACT_REG(r,4);
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case 5: return EXTRACT_REG(r,5);
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case 6: return EXTRACT_REG(r,6);
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case 7: return EXTRACT_REG(r,7);
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#if VMODE
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case 8: return EXTRACT_REG(r,8);
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case 9: return EXTRACT_REG(r,9);
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case 10: return EXTRACT_REG(r,10);
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case 11: return EXTRACT_REG(r,11);
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case 12: return EXTRACT_REG(r,12);
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case 13: return EXTRACT_REG(r,13);
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case 14: return EXTRACT_REG(r,14);
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case 15: return EXTRACT_REG(r,15);
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#endif
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}
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return 0;
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}
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#define GET_H_SYMBOLE(s,p) ((p && p < lseq1) ? (s)[(p)-1]:255)
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#define GET_V_SYMBOLE(s,p) ((p && p < lseq2) ? (s)[(p)-1]:0)
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#define LSHIFT_SCORE(r) { r = _MM_SLLI_SI128((r),sizeof(STYPE)); }
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#define SET_H_SYMBOLE(r,p,s) { r = insert_reg((r),(STYPE)GET_H_SYMBOLE(seq1,(s)),(p)); }
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#define PUSH_V_SYMBOLE(r,s) { r = insert_reg(_MM_SLLI_SI128((r),sizeof(STYPE)),(STYPE)GET_V_SYMBOLE(seq2,(s)),0); }
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#define EQUAL(f1,f2) _MM_AND_SI128(EQUAL_REG((f1),(f2)),SET_CONST(1))
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int FASTLCSSCORE(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath)
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{
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int lseq1,lseq2; // length of the both sequences
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int itmp; // tmp variables for swap
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const char* stmp; //
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int nbands; // Number of bands of width eight in the score matrix
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int lastband; // width of the last band
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// Register for scanning the score matrix
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VTYPE minus1;
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VTYPE minus2;
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VTYPE current;
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VTYPE left;
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VTYPE top;
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VTYPE diag;
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VTYPE sminus1;
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VTYPE sminus2;
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VTYPE scurrent;
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VTYPE sleft;
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VTYPE stop;
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VTYPE sdiag;
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VTYPE way;
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VTYPE onevect;
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VTYPE maxvect;
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VTYPE fhseq; // The fragment of the horizontal sequence
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// to consider for aligment
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VTYPE fvseq; // The fragment of the horizontal sequence
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// to consider for aligment
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VTYPE match;
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int band;
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int line;
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int limit;
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int lcs;
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int h;
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int i;
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column_t *column;
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// Made seq1 the longest sequences
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lseq1=strlen(seq1);
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lseq2=strlen(seq2);
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if (lseq1 < 10 || lseq2 < 10)
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return simpleLCS(seq1,seq2,ppcolumn,lpath);
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if (lseq1 < lseq2)
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{
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itmp=lseq1;
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lseq1=lseq2;
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lseq2=itmp;
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stmp=seq1;
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seq1=seq2;
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seq2=stmp;
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}
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// we add one to both lengths for taking into
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// account the extra line and column in the score
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// matrix
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lseq1++;
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lseq2++;
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// a band sized to the smallest sequence is allocated
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if (ppcolumn)
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column = *ppcolumn;
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else
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column=NULL;
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column = allocateColumn(lseq2,column,VMODE);
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// Check memory allocation
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if (column == NULL)
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return -1;
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for (i=0; i<lseq2;i++)
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{
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column->data.CMENB[i]=MIN_SCORE;
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column->score.CMENB[i]=-1;
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}
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nbands = lseq1 / VSIZE; // You have VSIZE element in one SSE register
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// Alignment will be realized in nbands
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lastband = lseq1 - (nbands * VSIZE); // plus one of width lastband except if
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// lastband==0
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if (lastband) nbands++;
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else lastband=VSIZE;
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lastband--;
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// printf("seq1 : %s seq2 : %s\n",seq1,seq2);
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minus2 = SET_CONST(MIN_SCORE);
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minus1 = _MM_SETZERO_SI128();
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sminus1= _MM_SETZERO_SI128();
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sminus2= _MM_SETZERO_SI128();
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onevect= SET_CONST(1);
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maxvect= SET_CONST(MAX_SCORE);
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h=0;
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fhseq = _MM_SETZERO_SI128();
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fvseq = _MM_SETZERO_SI128();
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//
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// Beginning of the first band
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//
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for (line = 0; line < VSIZE; line++,h++) // avant VSIZE - 1
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{
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// printf("line= %4d h= %4d\n",line,h);
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SET_H_SYMBOLE(fhseq,line,h)
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PUSH_V_SYMBOLE(fvseq,line)
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minus2 = insert_reg(minus2,0,h);
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minus1 = insert_reg(minus1,MIN_SCORE,line); // 0 avant
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match = EQUAL(fhseq,fvseq);
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if (lpath)
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{
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sminus2 = insert_reg(sminus2,line-1,line); // Je ne suis pas certain de l'initialisation
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sminus1 = insert_reg(sminus1,0,line);
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}
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// printreg(fvseq);
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// printreg(fhseq);
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// printreg(match);
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// printf("================================\n");
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current = minus1; // The best score is the upper one
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// It cannot be the best as set to MIN_SCORE
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left = minus1;
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// printf("Vert = "); printreg(current);
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LSHIFT_SCORE(minus1) // I shift minus1 so now I'll compare with the left position
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minus1=insert_reg(minus1,(column)->data.CMENB[line],0);
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top=minus1;
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if (lpath)
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{
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sleft=sminus1; // I store the path length corresponding to the upper path
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LSHIFT_SCORE(sminus1) // I shift to prepare the score coming from the left side
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sminus1=insert_reg(sminus1,(column)->score.CMENB[line],0);
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stop=sminus1;
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sdiag=sminus2;
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}
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// printf("Horz = "); printreg(minus1);
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current = GET_MAX(current,minus1); // Look for the best between upper and left
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// printf("BstHV= "); printreg(current);
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//
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// printf("Diag = "); printreg(ADD_REG(minus2,match));
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diag=minus2;
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// minus2 = ; // Minus2 contains the diagonal score, so I add the match reward
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// Diag score are setup to 0 so this one will win on the first iteration
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current = GET_MAX(current,ADD_REG(minus2,match));
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if (lpath)
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{
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// printf("\n");
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// printf("current: ");
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// printreg(current);
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// printf("current: ");
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// printreg(SUB_REG(current,match));
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// printf("diag : ");
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// printreg(diag);
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// printf("left : ");
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// printreg(left);
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// printf("top : ");
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// printreg(top);
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way = EQUAL_REG(SUB_REG(current,match),diag);
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scurrent= OR_REG(AND_REG(way,sdiag),
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ANDNOT_REG(way,maxvect));
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// printf("sdiag : ");
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// printreg(scurrent);
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way = EQUAL_REG(current,left);
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scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,sleft),
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ANDNOT_REG(way,maxvect)));
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// printf("sleft : ");
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// printreg(scurrent);
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way = EQUAL_REG(current,top);
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scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,stop),
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ANDNOT_REG(way,maxvect)));
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// printf("stop : ");
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// printreg(scurrent);
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scurrent= ADD_REG(scurrent,onevect);
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sminus2=sminus1;
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sminus1=scurrent;
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}
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// printf("line %d :Best = ",line); printreg(current);
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//
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// printf("================================\n");
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minus2=minus1;
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minus1=current;
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// printf("min2 = "); printreg(minus2);
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// printf("min1 = "); printreg(minus1);
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// printf("================================\n");
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// printf("\n");
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// printf("sdiag : ");
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// printreg(sminus2);
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// printf("scur : ");
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// printreg(scurrent);
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// printf("current: ");
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// printreg(current);
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// printf("%8s\n",seq1);
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// printf("%8s\n",seq2);
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// printf("================================\n");
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} ///// <<<<<<<<------- Fin du debut de la premiere bande
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// printf("================================\n");
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(column)->data.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(current,VSIZE-1);
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if (lpath)
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(column)->score.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(scurrent,VSIZE-1);
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for (band=0; band < nbands; band++)
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{
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// SET_H_SYMBOLE(fhseq,line,h)
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// minus2 = insert_reg(minus2,0,line);
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// minus1 = insert_reg(minus1,MIN_SCORE,line); // 0 avant
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// h++;
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for (; line < lseq2; line++)
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{
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// printf("Je tourne avec line= %d \n",line);
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PUSH_V_SYMBOLE(fvseq,line)
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match = EQUAL(fhseq,fvseq);
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// printreg(fvseq);
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// printreg(fhseq);
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// printreg(match);
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// printf("================================\n");
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current = minus1;
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left = minus1;
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// Store the last current score in extra column
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(column)->data.CMENB[line-VSIZE]=EXTRACT_REG(current,VSIZE-1);
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LSHIFT_SCORE(minus1)
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minus1=insert_reg(minus1,(column)->data.CMENB[line],0);
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top = minus1;
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// printf("Vert = "); printreg(current);
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if (lpath)
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{
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sleft= sminus1;
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(column)->score.CMENB[line-VSIZE]=EXTRACT_REG(scurrent,VSIZE-1);
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LSHIFT_SCORE(sminus1)
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sminus1=insert_reg(sminus1,(column)->score.CMENB[line],0);
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stop=sminus1;
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sdiag=sminus2;
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}
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// printf("line = %d --> get = %d\n",line,(column)->data.CMENB[line]);
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// printf("Horz = "); printreg(minus1);
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current = GET_MAX(current,minus1);
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diag=minus2;
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current = GET_MAX(current,ADD_REG(minus2,match));
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if (lpath)
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{
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// printf("\n");
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// printf("current: ");
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// printreg(current);
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// printf("current: ");
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// printreg(SUB_REG(current,match));
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// printf("diag : ");
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// printreg(diag);
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// printf("left : ");
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// printreg(left);
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// printf("top : ");
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// printreg(top);
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way = EQUAL_REG(SUB_REG(current,match),diag);
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scurrent= OR_REG(AND_REG(way,sdiag),
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ANDNOT_REG(way,maxvect));
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// printf("sdiag : ");
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// printreg(scurrent);
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way = EQUAL_REG(current,left);
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scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,sleft),
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ANDNOT_REG(way,maxvect)));
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// printf("sleft : ");
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// printreg(scurrent);
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way = EQUAL_REG(current,top);
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scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,stop),
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ANDNOT_REG(way,maxvect)));
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// printf("stop : ");
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// printreg(scurrent);
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scurrent= ADD_REG(scurrent,onevect);
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sminus2=sminus1;
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sminus1=scurrent;
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}
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minus2=minus1;
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minus1=current;
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// printf("\n");
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// printf("sdiag : ");
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// printreg(sminus2);
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// printf("scur : ");
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// printreg(scurrent);
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// printf("current: ");
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// printreg(current);
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// printf("%8s\n",seq1);
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// printf("%8s\n",seq2);
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}
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// printf("================================\n");
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// end of the band and beginnig of the next one
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limit=(band==(nbands-1)) ? lastband:VSIZE;
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for (line = 0; line < limit; line++,h++)
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{
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// printf("Je fini avec line= %d \n",line);
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SET_H_SYMBOLE(fhseq,line,h)
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PUSH_V_SYMBOLE(fvseq,line)
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minus2 = insert_reg(minus2,MIN_SCORE,line);
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minus1 = insert_reg(minus1,MIN_SCORE,line);
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current = minus1;
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left=minus1;
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match = EQUAL(fhseq,fvseq);
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if (lpath)
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{
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sminus2 = insert_reg(sminus2,lseq2-VSIZE+line,line);
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sminus1 = insert_reg(sminus1,h,line);
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sleft= sminus1;
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}
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// printf("\n");
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// printf("fhseq = "); printreg(fhseq);
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// printf("fvseq = "); printreg(fvseq);
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// printf("----------------------------------------------------------------\n");
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// printf("match = "); printreg(match);
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(column)->data.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(current,VSIZE-1);
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LSHIFT_SCORE(minus1)
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minus1=insert_reg(minus1,(column)->data.CMENB[line],0);
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top=minus1;
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current = GET_MAX(current,minus1);
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if (lpath)
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{
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(column)->score.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(scurrent,VSIZE-1);
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LSHIFT_SCORE(sminus1)
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sminus1=insert_reg(sminus1,(column)->score.CMENB[line],0);
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stop=sminus1;
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sdiag=sminus2;
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way = EQUAL_REG(current,minus1);
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scurrent= OR_REG(AND_REG(way,sminus1),
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ANDNOT_REG(way,scurrent));
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}
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diag=minus2;
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current = GET_MAX(current,ADD_REG(minus2,match));
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|
if (lpath)
|
|
{
|
|
way = EQUAL_REG(SUB_REG(current,match),diag);
|
|
scurrent= OR_REG(AND_REG(way,sdiag),
|
|
ANDNOT_REG(way,maxvect));
|
|
|
|
way = EQUAL_REG(current,left);
|
|
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,sleft),
|
|
ANDNOT_REG(way,maxvect)));
|
|
|
|
way = EQUAL_REG(current,top);
|
|
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,stop),
|
|
ANDNOT_REG(way,maxvect)));
|
|
|
|
scurrent= ADD_REG(scurrent,onevect);
|
|
|
|
sminus2=sminus1;
|
|
sminus1=scurrent;
|
|
}
|
|
|
|
// printf("currt = "); printreg(current);
|
|
|
|
minus2=minus1;
|
|
minus1=current;
|
|
|
|
// printf("\n");
|
|
// printf("sdiag : ");
|
|
// printreg(sminus2);
|
|
// printf("scur : ");
|
|
// printreg(scurrent);
|
|
// printf("current: ");
|
|
// printreg(current);
|
|
// printf("%8s\n",seq1);
|
|
// printf("%8s\n",seq2);
|
|
|
|
// printf("Je stocke line= %d la valeur %d\n",lseq2-VSIZE+line,(column)->data.CMENB[lseq2-VSIZE+line]);
|
|
}
|
|
|
|
}
|
|
|
|
// printf("\n");
|
|
// printf("line = %d, h= %d, lastband = %d\n",line,h,lastband);
|
|
// printf("currt = "); printreg(current);
|
|
lcs = extract_reg(current,lastband);
|
|
|
|
if(lpath)
|
|
*lpath= extract_reg(scurrent,lastband);
|
|
// printf("lastband = %d (%d) lcs = %d\n",lastband,lseq2,lcs);
|
|
|
|
if (ppcolumn)
|
|
*ppcolumn=column;
|
|
else
|
|
freeColumn(column);
|
|
|
|
return lcs;
|
|
}
|
|
|
|
#else
|
|
int FASTLCSSCORE(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath)
|
|
{
|
|
return simpleLCS(seq1,seq2,ppcolumn,lpath);
|
|
}
|
|
|
|
#endif /* __SSE2__ */
|
|
|