+ if(command.position>=tmp.length())\r
+ {\r
+ //This occurs if padding is on, and residues\r
+ //are removed from end of alignment\r
+ int length = command.position-tmp.length();\r
+ while (length > 0)\r
+ {\r
+ tmp.append(command.gapChar);\r
+ length--;\r
+ }\r
+ }\r