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Viewing changes to .pc/fix-path-for-data.patch/Perseus/Perseus.h

  • Committer: Bazaar Package Importer
  • Author(s): Tim Booth, Steffen sponsoring Tim's update
  • Date: 2011-08-21 13:06:37 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20110821130637-a9053ip5b3ryl10r
Tags: 1.25-1
[ Steffen sponsoring Tim's update ]
* Removed Steffen from uploader's list
* Removing emacs-typical backup files from source tree

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.pc/fix-path-for-data.patch/Perseus/Perseus.h
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  int bOutputAlignments;
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  char *szLookUpFile;
 
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  int nSkew;
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} t_Params;
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typedef struct s_Data
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#define SEQ_INPUT_FILE       "-sin"
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#define USE_IMBALANCE        "-d"
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#define OUTPUT_ALIGNMENTS    "-a"
 
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#define SKEW                 "-s"
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#define GAP_PENALTY     1.5
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#define GAP             '-'
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#define T_GAP           '.'
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#define COMMA           ","
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#define DEFAULT_SKEW          1
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#define GAP_PENALTY_N         15.0
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#define HOMOPOLYMER_PENALTY   4.0
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void destroyData(t_Data *ptData);
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int alignAll(int nI, int nLenI, int *pnBest, int *pnBestJ, int *anRestrict, int nK, t_Data *ptSeqData, t_Data *ptRefData, t_Align* atAlign);
 
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int alignAll(int nI, int nLenI, int *pnBest, int *pnBestJ, int *anRestrict, int nK, t_Data *ptSeqData, t_Data *ptRefData, t_Align* atAlign, t_Params *ptParams);
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int getBestChimera(int nK, t_Data *ptRefData, int* pnP1, int* pnP2, int *pnSplit, int* anRestrict, int nLenI, t_Align* atAlign, int* anD, int* anR, int* anBestD, int* anBestR);
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