140 			 ajint esub, ajint epos, ajint reverse, ajint gapped);
570     ajint epos;  in embEstPrintAlign()  local
613 	epos = ge->estart;  in embEstPrintAlign()
624 		ecoord[len] = epos;  in embEstPrintAlign()
626 		ebuf[len] = estseq[epos++];  in embEstPrintAlign()
648 		ecoord[len] = epos;  in embEstPrintAlign()
650 		ebuf[len] = estseq[epos++];  in embEstPrintAlign()
657 		ecoord[len] = epos;  in embEstPrintAlign()
688 		    ecoord[j] = epos-1;  in embEstPrintAlign()
705 		    ecoord[j] = epos-1;  in embEstPrintAlign()
718 		    ecoord[j] = epos-1;  in embEstPrintAlign()
845     ajint epos;  in embEstAlignNonRecursive()  local
948 	for(epos=0;epos<elen;epos++)  in embEstAlignNonRecursive()
950 	    t1[epos].left = 0;  in embEstAlignNonRecursive()
951 	    t1[epos].right = epos;  in embEstAlignNonRecursive()
952 	    t2[epos].left = 0;	  /* try initializing t2 explicitly */  in embEstAlignNonRecursive()
953 	    t2[epos].right = epos; /* otherwise it gets missed on first pass */  in embEstAlignNonRecursive()
954 	    best_intron_start[epos] = t1[epos];  in embEstAlignNonRecursive()
959 	for(epos=0;epos<elen;epos++)  in embEstAlignNonRecursive()
961 	    s1[epos] = MINUS_INFINITY;  in embEstAlignNonRecursive()
962 	    best_intron_score[epos] = MINUS_INFINITY;  in embEstAlignNonRecursive()
1003 	for(epos=0;epos<elen;epos++) /* loop thru EST sequence */  in embEstAlignNonRecursive()
1007 	    diagonal = s2[epos-1] + lsimmat[(ajint)g][(ajint)eseq[epos]];  in embEstAlignNonRecursive()
1011 	    delete_est = s1[epos-1] - gap_penalty;  in embEstAlignNonRecursive()
1015 	    delete_genome = s2[epos] - gap_penalty;  in embEstAlignNonRecursive()
1023 	       (splice_sites_str[best_intron_coord[epos]] & DONOR))  in embEstAlignNonRecursive()
1024 		intron = best_intron_score[epos] - splice_penalty;  in embEstAlignNonRecursive()
1026 		intron = best_intron_score[epos] - intron_penalty;  in embEstAlignNonRecursive()
1043 		    s1[epos] = diagonal;  in embEstAlignNonRecursive()
1046 			path[epos/4] =  ajSysCastItouc((ajuint) path[epos/4] |  in embEstAlignNonRecursive()
1047 				      	   (ajuint) diagonal_path[epos%4]);  in embEstAlignNonRecursive()
1050 			if( t2[epos-1].left == -1 ) /* SW start */  in embEstAlignNonRecursive()
1052 			    t1[epos].left = gpos;  in embEstAlignNonRecursive()
1053 			    t1[epos].right = epos;  in embEstAlignNonRecursive()
1054 			    if(debug && t1[epos].left == 10126)  in embEstAlignNonRecursive()
1057 					epos, gpos);  in embEstAlignNonRecursive()
1062 			    t1[epos] = t2[epos-1];  in embEstAlignNonRecursive()
1064 			    if(debug && t1[epos].left == 10126)  in embEstAlignNonRecursive()
1068 					epos, t1[epos].left, t1[epos].right,  in embEstAlignNonRecursive()
1075 		    s1[epos] = delete_est;  in embEstAlignNonRecursive()
1079 			path[epos/4]  =  ajSysCastItouc((ajuint) path[epos/4] |  in embEstAlignNonRecursive()
1080 					    (ajuint) delete_est_path[epos%4]);  in embEstAlignNonRecursive()
1084 			t1[epos] = t1[epos-1];  in embEstAlignNonRecursive()
1086 			if(debug && t1[epos].left == 10126)  in embEstAlignNonRecursive()
1089 				    epos, t1[epos].left);  in embEstAlignNonRecursive()
1095 		    s1[epos] = delete_genome;  in embEstAlignNonRecursive()
1099 			path[epos/4] = ajSysCastItouc((ajuint) path[epos/4] |  in embEstAlignNonRecursive()
1100 					 (ajuint) delete_genome_path[epos%4]);  in embEstAlignNonRecursive()
1104 			t1[epos] = t2[epos];  in embEstAlignNonRecursive()
1106 			if(debug && t1[epos].left == 10126)  in embEstAlignNonRecursive()
1109 				    epos, t1[epos].left);  in embEstAlignNonRecursive()
1115 		    s1[epos] = intron;  in embEstAlignNonRecursive()
1118 			t1[epos] = best_intron_start[epos];  in embEstAlignNonRecursive()
1124 		s1[epos] = 0;  in embEstAlignNonRecursive()
1128 		    t1[epos].left = -1;  in embEstAlignNonRecursive()
1129 		    t1[epos].right = -1;  in embEstAlignNonRecursive()
1134 	    if( best_intron_score[epos] < s1[epos] )  in embEstAlignNonRecursive()
1139 		    if( estDoNotForget(epos,  in embEstAlignNonRecursive()
1140 				       best_intron_coord[epos]) == 0 )  in embEstAlignNonRecursive()
1174 		best_intron_score[epos] = s1[epos];  in embEstAlignNonRecursive()
1175 		best_intron_coord[epos] = gpos;  in embEstAlignNonRecursive()
1178 		    best_intron_start[epos] = t1[epos];  in embEstAlignNonRecursive()
1181 	    if(!needleman && max_score < s1[epos])  in embEstAlignNonRecursive()
1183 		max_score = s1[epos];  in embEstAlignNonRecursive()
1184 		emax = epos;  in embEstAlignNonRecursive()
1189 		    best_start = t1[epos];  in embEstAlignNonRecursive()
1194 				max_score, epos, best_start.left,  in embEstAlignNonRecursive()
1222 	epos = ge->estop;  in embEstAlignNonRecursive()
1242 	while(( needleman || total < max_score) && epos >= 0 && gpos >= 0 )  in embEstAlignNonRecursive()
1244 	    direction = ajSysCastItouc(((ajuint)ppath[gpos][epos/4] &  in embEstAlignNonRecursive()
1245 				    (ajuint)mask[epos%4] ) >> (2*(epos%4)));  in embEstAlignNonRecursive()
1252 		if( gpos-best_intron_coord[epos]  <= 0 )  in embEstAlignNonRecursive()
1256 			       gpos, gpos-best_intron_coord[epos] );  in embEstAlignNonRecursive()
1257 		    gpos1 = estPairRemember(epos, gpos );  in embEstAlignNonRecursive()
1260 		    gpos1 = best_intron_coord[epos];  in embEstAlignNonRecursive()
1277 		total += lsimmat[(ajint)gseq[gpos]][(ajint)eseq[epos]];  in embEstAlignNonRecursive()
1278 		epos--;  in embEstAlignNonRecursive()
1284 		epos--;  in embEstAlignNonRecursive()
1294 	epos++;  in embEstAlignNonRecursive()
1298 	ge->estart = epos;  in embEstAlignNonRecursive()
1794     ajint epos;  in estAlignMidpt()  local
1849     for(epos=0;epos<elen;epos++)  in estAlignMidpt()
1851 	s1[epos] = MINUS_INFINITY;  in estAlignMidpt()
1852 	best_intron_score[epos] = MINUS_INFINITY;  in estAlignMidpt()
1874 	for(epos=0;epos<elen;epos++)  in estAlignMidpt()
1878 	    diagonal = s2[epos-1] + lsimmat[(ajint)g][(ajint)eseq[epos]];  in estAlignMidpt()
1882 	    delete_est = s1[epos-1] - gap_penalty;  in estAlignMidpt()
1886 	    delete_genome = s2[epos] - gap_penalty;  in estAlignMidpt()
1894 	       (splice_sites_str[best_intron_coord[epos]] & DONOR ))  in estAlignMidpt()
1895 		intron = best_intron_score[epos] - splice_penalty;  in estAlignMidpt()
1897 		intron = best_intron_score[epos] - intron_penalty;  in estAlignMidpt()
1912 		s1[epos] = diagonal;  in estAlignMidpt()
1914 		if(epos == middle)  in estAlignMidpt()
1916 		    m1[epos].left = gpos-1;  in estAlignMidpt()
1917 		    m1[epos].right = gpos;  in estAlignMidpt()
1920 		    m1[epos] = m2[epos-1];  in estAlignMidpt()
1924 		s1[epos] = delete_est;  in estAlignMidpt()
1926 		if( epos == middle )  in estAlignMidpt()
1928 		    m1[epos].left = gpos;  in estAlignMidpt()
1929 		    m1[epos].right = gpos;  in estAlignMidpt()
1932 		    m1[epos] = m1[epos-1];  in estAlignMidpt()
1936 		s1[epos] = delete_genome;  in estAlignMidpt()
1937 		m1[epos] = m2[epos];  in estAlignMidpt()
1941 		s1[epos] = intron;  in estAlignMidpt()
1942 		m1[epos] = best_intron_midpt[epos];  in estAlignMidpt()
1945 	    if(best_intron_score[epos] < s1[epos])  in estAlignMidpt()
1947 		best_intron_score[epos] = s1[epos];  in estAlignMidpt()
1948 		best_intron_coord[epos] = gpos;  in estAlignMidpt()
1949 		best_intron_midpt[epos] = m1[epos];  in estAlignMidpt()
2263     ajint epos;  in embEstOutBlastStyle()  local
2284     esub = epos = ge->estart;  in embEstOutBlastStyle()
2299 			    est, esub, epos, reverse, gapped);  in embEstOutBlastStyle()
2334 		esub = epos;  in embEstOutBlastStyle()
2340 		    [(ajint)eststr[(ajint)epos]];  in embEstOutBlastStyle()
2352 		epos++;  in embEstOutBlastStyle()
2359 		    epos++;  in embEstOutBlastStyle()
2366 				gpos, est, esub, epos, reverse, gapped);  in embEstOutBlastStyle()
2367 		    epos++;  in embEstOutBlastStyle()
2368 		    esub = epos;  in embEstOutBlastStyle()
2384 				gpos, est, esub, epos, reverse, gapped);  in embEstOutBlastStyle()
2386 		    esub = epos;  in embEstOutBlastStyle()
2392 		    esub, epos, reverse, gapped);  in embEstOutBlastStyle()
2458 			ajint esub, ajint epos, ajint reverse, ajint gapped)  in estWriteMsp()  argument
2483 			eoff+ajSeqGetLen(est)-epos+1,  in estWriteMsp()
2489 			eoff+esub+1, eoff+epos, ajSeqGetNameS(est),  in estWriteMsp()