int DoBdiff( const char *srcPath, const char *tgtPath, const char *name )
{
long savings;
foff buffsize;
int i;
// if( !MsgInit() ) exit( EXIT_FAILURE );
/* initialize static variables each time */
SimilarRegions = NULL;
DiffRegions = NULL;
HoleRegions = NULL;
SimilarSize = 0;
NumHoles = 0;
NumDiffs = 0;
DiffSize = 0;
HolesInRegion = 0;
HoleHeaders = 0;
for( i = 0; i < 3; i += 1 ) {
HoleCount[i] = 0;
}
init_diff();
newName = name;
EndOld = FileSize( srcPath, &OldCorrection );
EndNew = FileSize( tgtPath, &NewCorrection );
buffsize = ( EndOld > EndNew ) ? ( EndOld ) : ( EndNew );
buffsize += sizeof( PATCH_LEVEL );
OldFile = ReadIn( srcPath, buffsize, EndOld );
NewFile = ReadIn( tgtPath, buffsize, EndNew );
ScanSyncString( SyncString );
FindRegions();
if( NumHoles == 0 && DiffSize == 0 && EndOld == EndNew ) {
printf( "Patch file not created - files are identical\n" );
MsgFini();
exit( EXIT_SUCCESS );
}
MakeHoleArray();
SortHoleArray();
ProcessHoleArray( 0 );
savings = HolesToDiffs();
WritePatchFile( "", newName );
FreeHoleArray();
VerifyCorrect( tgtPath );
print_stats( savings );
MsgFini();
return ( EXIT_SUCCESS );
}
void main( int argc, char **argv )
{
long savings;
foff buffsize;
algorithm alg;
if( !MsgInit() )
exit( EXIT_FAILURE );
alg = ParseArgs( argc, argv );
EndOld = FileSize( argv[1], &OldCorrection );
EndNew = FileSize( argv[2], &NewCorrection );
buffsize = ( EndOld > EndNew ) ? ( EndOld ) : ( EndNew );
buffsize += sizeof( PATCH_LEVEL );
OldFile = ReadIn( argv[1], buffsize, EndOld );
NewFile = ReadIn( argv[2], buffsize, EndNew );
ScanSyncString( SyncString );
switch( alg ) {
case ALG_NOTHING:
FindRegions();
break;
#ifdef USE_DBGINFO
case ALG_ONLY_NEW:
case ALG_BOTH:
SymbolicDiff( alg, argv[1], argv[2] );
break;
#endif
}
if( NumHoles == 0 && DiffSize == 0 && EndOld == EndNew ) {
printf( "Patch file not created - files are identical\n" );
MsgFini();
exit( EXIT_SUCCESS );
}
MakeHoleArray();
SortHoleArray();
ProcessHoleArray( 0 );
savings = HolesToDiffs();
WritePatchFile( argv[3], newName );
FreeHoleArray();
VerifyCorrect( argv[2] );
print_stats( savings );
MsgFini();
exit( EXIT_SUCCESS );
}
MultipleAlignment* AlignAlignments(MultipleAlignment *originalSrcMA1, MultipleAlignment *originalSrcMA2, int index1, int index2, int selfAlignDistance) {
int i,j,k;
/* New multiple alignment */
MultipleAlignment *ma = (MultipleAlignment *)calloc(1, sizeof(MultipleAlignment));
/* Duplicate source alignments. Moves the index1 chain to the front.
* Also realigns and extends the aligned blocks. */
MultipleAlignment *srcMA1 = DuplicateAlignment(originalSrcMA1, index1);
MultipleAlignment *srcMA2 = DuplicateAlignment(originalSrcMA2, index2);
MatchedBlockPair *regions;
int numRegions;
ma->order = CombineAssemblyOrders(srcMA1->order, srcMA2->order);
ma->numChains = srcMA1->numChains + srcMA2->numChains;
ma->chains = (ResiduePositions **)malloc(ma->numChains * sizeof(ResiduePositions *));
memcpy(ma->chains, srcMA1->chains, srcMA1->numChains * sizeof(ResiduePositions *));
memcpy(ma->chains + srcMA1->numChains, srcMA2->chains, srcMA2->numChains * sizeof(ResiduePositions *));
FindRegions(®ions, &numRegions, srcMA1, srcMA2, selfAlignDistance);
for (i=0; i < numRegions; i++) {
ma->numResidues += regions[i].len;
}
ma->score = -5000;
/* Alignment found (If no alignment, will return what we already have). */
if (numRegions) {
int pos = 0;
ma->score = regions[numRegions-1].bestAssembledScore;
ma->numBlocks = numRegions;
ma->blocks = (AlignedBlock *) malloc(numRegions * sizeof(AlignedBlock));
ma->residues = (WeightedResiduePositions*) malloc(ma->numChains*sizeof(WeightedResiduePositions));
for (i=0; i<ma->numChains; i++) {
ma->residues[i].res = (ResiduePosition*) malloc(ma->numResidues*sizeof(ResiduePosition));
ma->residues[i].weight = 0;
}
for (i=0; i < numRegions; i++) {
ma->blocks[i].first = pos;
ma->blocks[i].last = pos + regions[i].len-1;
pos += regions[i].len;
for (j=0; j<regions[i].len; j++) {
for (k=0; k<srcMA1->numChains; k++) {
ma->residues[k].res[ma->blocks[i].first+j] = srcMA1->residues[k].res[regions[i].p1 + j];
}
for (; k<ma->numChains; k++) {
ma->residues[k].res[ma->blocks[i].first+j] = srcMA2->residues[k-srcMA1->numChains].res[regions[i].p2 + j];
transformVect(&ma->residues[k].res[ma->blocks[i].first+j].coords, ®ions[i].m, &srcMA2->residues[k-srcMA1->numChains].res[regions[i].p2 + j].coords);
}
}
}
free(regions);
}
CleanupAlignment(srcMA1);
CleanupAlignment(srcMA2);
return ma;
}
