/*****************************************************************************
#   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    "rwctokenizer.h"
#include    <iostream.h>
#include    <stdio.h>
#include    "nSystemReadALine.h"
#include    "someOtherProgramSentACommandToConsed.h"
#include    "contig.h"
#include    "assembly.h"
#include    "contigwin.h"
#include    "consed.h"
#include    "bIsNumericMaybeWithWhitespace.h"
#include    "locatedFragment.h"
#include    "popupErrorMessage.h"
#include    <unistd.h>
#include    "socketConnection.h"




void someOtherProgramSentACommandToConsed( XtPointer p,
                                                    int* pFID,
                                                    XtInputId* pID ) {

   socketConnection* pSocket = (socketConnection*) p;

   int nSocketFD = pSocket->nFileDescriptor_;

   cout << "some other program sent command to consed" << endl;


   #define nMaxLine 500
   char szLine[nMaxLine];


   int n = nSystemReadALine( nSocketFD, szLine, nMaxLine );
   if (n == 0 ) {
      XtRemoveInput( pSocket->xtinputid_ );
      close( nSocketFD );

      return;  /* connection terminated */
   }
   else if (n < 0 ) {
      cout << "problem from readline since n = " << n << endl;
   }

   szLine[n] = '\0';


   char szLine2[ nMaxLine ];

   sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine );

   cout << szLine2 << endl;

   
   
   RWCString soCommandToConsed( szLine );

   RWCTokenizer tok( soCommandToConsed );

   RWCString soCommandName = tok();
   if ( soCommandName.isNull() ) {
      GuiApp::popupErrorMessage( "Some other program sent a null command to consed:  " + soCommandToConsed );
      return;
   }

   if (soCommandName == "Scroll" ) {
      RWCString soContigName = tok();
      if (soContigName.isNull() ) {
         GuiApp::popupErrorMessage( "Some other program sent an incomplete scroll command to consed.  Should be of form:\nScroll (contig) (base position)" );
         return;
      }


      Assembly* pAssembly = ConsEd::pGetAssembly();
      Contig* pContig = pAssembly->pGetContigByName( soContigName );

      if (!pContig ) {
         GuiApp::popupErrorMessage( "Some other program sent following command but contig not found by consed:\n" 
                                    + soCommandToConsed  );
         return;
      }

      RWCString soUnpaddedConsPos = tok();
      if (soUnpaddedConsPos.isNull() ) {
         GuiApp::popupErrorMessage( "Some other program sent an incomplete scrol command to consed (missing base position).  Should be of form:\nScroll (contig) (base position)" );

         return;
      }

      int nUnpaddedPos;
      if (! bIsNumericMaybeWithWhitespace( soUnpaddedConsPos, nUnpaddedPos ) ) {
         GuiApp::popupErrorMessage( "Some other program sent a message with a non-numeric consensus position:\n" +
                                    soCommandToConsed );
         return;
      }


      if (! pContig->bUnpaddedConsPosInRange( nUnpaddedPos ) ) {
         RWCString soMessage = "Some other program told consed to scroll to a location that is out of range.  Command to consed is\n" + soCommandToConsed +
            " but range is %d to %d";
         GuiApp::popupErrorMessage( soMessage, 
                                    pContig->nGetUnpaddedStartIndex(),
                                    pContig->nGetUnpaddedEndIndex() );
         return;
      }


      int nConsPos = pContig->nPaddedIndex(  nUnpaddedPos );

      ContigWin* pContigWin = 
         ConsEd::pGetConsEd()->pScrollExistingContigWinOrMakeNewContigWin( pContig, 
                    nConsPos );
      pContigWin->moveCursorToConsPos( nConsPos );

      // raise the window--Bill Gilliland wanted 02/06/27
      pContigWin->raiseWindow();
   } // if (soCommandName == "Scroll" )
   else if ( soCommandName == "PopupTraces" ) {
      RWCString soReadName = tok();
      RWCString soReadPosition = tok();

      if ( soReadName.isNull() ) {
         popupErrorMessage( "Some other program sent incomplete PopupTraces command to consed.  Should be of the form:\nPopupTraces (read name) (read position)" );
         return;
      }

      Assembly* pAssembly = ConsEd::pGetAssembly();

      LocatedFragment* pLocFrag = pAssembly->pGetLocatedFragmentByName( soReadName );

      if ( !pLocFrag ) {
         popupErrorMessage( "Some other program sent command " +
                             soCommandName + " but couldn't find read " +
                             soReadName );
         return;
      }

      int nReadPosInDirectionOfSequencing;

      if ( !bIsNumericMaybeWithWhitespace( soReadPosition,
                                           nReadPosInDirectionOfSequencing ) ) {
         popupErrorMessage( "Some other program sent command " +
                            soCommandName + " but read position " +
                            soReadPosition + " wasn't numeric" );

         return;
      }

      if ( !  (
               ( pLocFrag->nGetUnpaddedStartIndex() <= 
                 nReadPosInDirectionOfSequencing ) &&
               ( nReadPosInDirectionOfSequencing <=
                 pLocFrag->nGetUnpaddedEndIndex() ) ) ) {
         popupErrorMessage( "Some other program sent command %s but position must be between %d and %d",
                            (char*) soCommandName.data(),
                            pLocFrag->nGetUnpaddedStartIndex(),
                            pLocFrag->nGetUnpaddedEndIndex() );
         return;
      }


      int nPaddedConsPos = pLocFrag->nConsPosFromOrientedUnpaddedFragPos(
                                       nReadPosInDirectionOfSequencing );

      
      ContigWin* pContigWin =
         ConsEd::pGetConsEd()->pScrollExistingContigWinOrMakeNewContigWin(
                 pLocFrag->pGetContig(),
                 nPaddedConsPos );
      
      cout << "popupTracesByConsensusPosition " << pLocFrag->soGetName() <<
         " padded consensus position " << nPaddedConsPos << endl;

      pContigWin->popupTracesByConsensusPosition( pLocFrag,
                                                  nPaddedConsPos );
   }
   else {
      popupErrorMessage( "unrecognized command: " + soCommandName + 
                         " acceptable commands are Scroll and PopupTraces" );
   }
}