File Changes for cline

v256_preview2 to v256_base (2011-08-23 to 2011-08-29) v256

• src/hg/inc/pbCommon.h
  • lines changed 18, context: html, text, full: html, text
    Adding a central place for #defines common to the proteome browser code
  • lines changed 6, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbCalDist/pbCalDist.c
  • lines changed 10, context: html, text, full: html, text
    Added use of the new pbCommon #define. Added hydrophobicity data for the uncommon amino acids. Got rid of the use of a couple magic numbers in the code
  • lines changed 1, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • lines changed 11, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • lines changed 7, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
  • lines changed 1, context: html, text, full: html, text
    Adding a #define that I forgot to add before...
• src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • lines changed 6, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 2, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 6, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt