/*****************************************************************************
#   Copyright (C) 1994-2008 by David Gordon.
#   All rights reserved.                           
#                                                                           
#   This software is part of a beta-test version of the Consed/Autofinish
#   package.  It should not be redistributed or
#   used for any commercial purpose, including commercially funded
#   sequencing, without written permission from the author and the
#   University of Washington.
#   
#   This software is provided ``AS IS'' and any express or implied
#   warranties, including, but not limited to, the implied warranties of
#   merchantability and fitness for a particular purpose, are disclaimed.
#   In no event shall the authors or the University of Washington be
#   liable for any direct, indirect, incidental, special, exemplary, or
#   consequential damages (including, but not limited to, procurement of
#   substitute goods or services; loss of use, data, or profits; or
#   business interruption) however caused and on any theory of liability,
#   whether in contract, strict liability, or tort (including negligence
#   or otherwise) arising in any way out of the use of this software, even
#   if advised of the possibility of such damage.
#
#   Building Consed from source is error prone and not simple which is
#   why I provide executables.  Due to time limitations I cannot
#   provide any assistance in building Consed.  Even if you do not
#   modify the source, you may introduce errors due to using a
#   different version of the compiler, a different version of motif,
#   different versions of other libraries than I used, etc.  For this
#   reason, if you discover Consed bugs, I can only offer help with
#   those bugs if you first reproduce those bugs with an executable
#   provided by me--not an executable you have built.
# 
#   Modifying Consed is also difficult.  Although Consed is modular,
#   some modules are used by many other modules.  Thus making a change
#   in one place can have unforeseen effects on many other features.
#   It may takes months for you to notice these other side-effects
#   which may not seen connected at all.  It is not feasable for me to
#   provide help with modifying Consed sources because of the
#   potentially huge amount of time involved.
#
#*****************************************************************************/
#include    <cmath>
using namespace std;
#include    "library.h"
#include    "consedParameters.h"
#include    "fileDefines.h"


void library :: finalProcessingOfInsertSize() {

   if ( nNumberOfForwardReversePairsForCalculation_ > 0 ) {
     double dMeanInsertSize = 
       dSumOfInsertSizes_ / nNumberOfForwardReversePairsForCalculation_;

     nMeanInsertSize_ = (int) dMeanInsertSize;

      nStandardDeviationOfInsertSize_ =
         (int) sqrt( 
                    dSumOfSquaresOfInsertSizes_ / nNumberOfForwardReversePairsForCalculation_ 
                    -
                    dMeanInsertSize * dMeanInsertSize 
                    );

   }
   else
      nStandardDeviationOfInsertSize_ = 200;


   if ( nNumberOfForwardReversePairsForCalculation_ >=
        pCP->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ) {
      bAverageInsertSizeFromForwardReversePairs_ = true;
      nAverageInsertSizeToUse_ = nMeanInsertSize_;
      nALittleLessThanAverageInsertSizeToUse_ = nMeanInsertSize_ -
         pCP->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ 
         * nStandardDeviationOfInsertSize_;

      nMaxInsertSize_ = nMeanInsertSize_ + 
         2.5 * nStandardDeviationOfInsertSize_;


      if ( nMaxInsertSizeFromFile_ != 0 ) {

         float fRatio = (float) nMaxInsertSize_ / 
            (float) nMaxInsertSizeFromFile_;

         if ( fRatio < 0.55 || fRatio > 1.3 ) {
            fprintf( pAO, "warning: librariesInfo.txt says library %s has max insert size %d but for/rev pair calculations show it to be %d which we will use.  Could some be misnamed or not from this library?\n",
                     soName_.data(),
                     nMaxInsertSizeFromFile_,
                     nMaxInsertSize_ );
         }
      }
      else {
            fprintf( pAO, "library %s has maximum insert size %d\n",
                     soName_.data(),
                     nMaxInsertSize_ );
      }
   }
   else {
      bAverageInsertSizeFromForwardReversePairs_ = false;
      nAverageInsertSizeToUse_ = nDefaultInsertSize_;
      nALittleLessThanAverageInsertSizeToUse_ = 
         nDefaultInsertSize_ * 
         pCP->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ 
         / 100;
   }

}



void library :: increasePrimersMaxInsertSizeOfASubcloneIfNecessary() {


   if ( nMaxInsertSize_ > 
        pCP->nPrimersMaxInsertSizeOfASubclone_ ) {

      int nOldPrimersMaxInsertSizeOfASubclone = 
         pCP->nPrimersMaxInsertSizeOfASubclone_;
      pCP->nPrimersMaxInsertSizeOfASubclone_ = nMaxInsertSize_;

      fprintf( pAO, "increasing pCP->nPrimersMaxInsertSizeOfASubclone_ (used for finding templates for primers) from %d to %d due to library %s\n",
               nOldPrimersMaxInsertSizeOfASubclone,
               pCP->nPrimersMaxInsertSizeOfASubclone_,
               soName_.data() );
   }
}