16             if (aFrag==WA[iW][iA][WA_iFrag] && WA[iW][iA][WA_sjA]==sjA \  in assignAlignToWindow()
17                 && a1+WA[iW][iA][WA_rStart]==WA[iW][iA][WA_gStart]+aRstart \  in assignAlignToWindow()
18 …     && ( (aRstart>=WA[iW][iA][WA_rStart] && aRstart<WA[iW][iA][WA_rStart]+WA[iW][iA][WA_Length]) \  in assignAlignToWindow()
19 …|| (aRstart+aLength>=WA[iW][iA][WA_rStart] && aRstart+aLength<WA[iW][iA][WA_rStart]+WA[iW][iA][WA_…  in assignAlignToWindow()
24             if (aLength>WA[iW][iA][WA_Length]) {//replace  in assignAlignToWindow()
29                     if (iA0!=iA && aRstart<WA[iW][iA0][WA_rStart])  in assignAlignToWindow()
43                                 WA[iW][iA1][ii]=WA[iW][iA1-1][ii];  in assignAlignToWindow()
49                                 WA[iW][iA1][ii]=WA[iW][iA1+1][ii];  in assignAlignToWindow()
55                 WA[iW][iA0][WA_rStart]=aRstart;  in assignAlignToWindow()
56                 WA[iW][iA0][WA_Length]=aLength;  in assignAlignToWindow()
57                 WA[iW][iA0][WA_gStart]=a1;  in assignAlignToWindow()
58                 WA[iW][iA0][WA_Nrep]=aNrep;  in assignAlignToWindow()
59                 WA[iW][iA0][WA_Anchor]=int(aAnchor);//=0 if not, =1 if yes  in assignAlignToWindow()
60                 WA[iW][iA0][WA_iFrag]=aFrag;  in assignAlignToWindow()
61                 WA[iW][iA0][WA_sjA]=sjA;  in assignAlignToWindow()
72 …if (WA[iW][iA][WA_Anchor]!=1) WALrec[iW]=min(WALrec[iW],WA[iW][iA][WA_Length]); //protect the anch…  in assignAlignToWindow()
87 …if ( WA[iW][iA][WA_Anchor]==1 || WA[iW][iA][WA_Length] > WALrec[iW] ) {//re-record the anchors and…  in assignAlignToWindow()
88 …for (uint ii=0; ii<WA_SIZE; ii++) WA[iW][iA1][ii]=WA[iW][iA][ii]; //re-record the iA-th alignment …  in assignAlignToWindow()
109             if (aRstart<WA[iW][iA][WA_rStart]) break;  in assignAlignToWindow()
113                     WA[iW][iA1][ii]=WA[iW][iA1-1][ii];  in assignAlignToWindow()
118         WA[iW][iA][WA_rStart]=aRstart;  in assignAlignToWindow()
119         WA[iW][iA][WA_Length]=aLength;  in assignAlignToWindow()
120         WA[iW][iA][WA_gStart]=a1;  in assignAlignToWindow()
121         WA[iW][iA][WA_Nrep]=aNrep;  in assignAlignToWindow()
122         WA[iW][iA][WA_Anchor]=int(aAnchor);//=0 if not, =1 if yes  in assignAlignToWindow()
123         WA[iW][iA][WA_iFrag]=aFrag;  in assignAlignToWindow()
124         WA[iW][iA][WA_sjA]=sjA;  in assignAlignToWindow()