Commits for kent

v277_base to v278_preview (2012-12-18 to 2013-01-08) v278

• Starting work on a second pass of processing to put in monomers that did not get omitted by main pass.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 130, context: html, text, full: html, text
• Adding a new check on input.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 29, context: html, text, full: html, text
• More progress towards substituting in missing monomers.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 13, context: html, text, full: html, text
• Fixing end condition in matchExceptCenter. Rearranging debugging code.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 158, context: html, text, full: html, text
• Adding fall back logic to place unused monomers by type if they can't be placed by context.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 61, context: html, text, full: html, text
• Making subCenterInNeighborhood routine work on a wider variety of input and putting in some additional logging/debugging options.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 32, context: html, text, full: html, text