+ void makeExactMapping(AlignSeq as, Sequence s1)\r
+ {\r
+ int pdbpos = as.getSeq2Start()-2;\r
+ int alignpos = s1.getStart() + as.getSeq1Start()-3;\r
+\r
+ for(int i=0; i<as.astr1.length(); i++)\r
+ {\r
+ if (as.astr1.charAt(i) != '-')\r
+ {\r
+ alignpos++;\r
+ }\r
+\r
+ if (as.astr2.charAt(i) != '-')\r
+ {\r
+ pdbpos++;\r
+ }\r
+\r
+ if (as.astr1.charAt(i) == as.astr2.charAt(i))\r
+ {\r
+ Residue res = (Residue) residues.elementAt(pdbpos);\r
+ Enumeration en = res.atoms.elements();\r
+ while (en.hasMoreElements())\r
+ {\r
+ Atom atom = (Atom) en.nextElement();\r
+ atom.alignmentMapping = alignpos;\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+\r