int checkNewPoint(int *match, int *xs, int *ys, int len) {
for (int i = -20; i < 20; i++) {
for (int j = -20; j < 20; j++) {
if (inArray((match[0]+i),xs,len) && inArray((match[1]+j),ys,len)) {
return 0;
}
}
}
return 1;
}
/* 2.1 Write code to remove duplicates from an unsorted linked list*/
Node *RemoveDup(Node *list){
Node *c = list;
Node *head, *temp;
head = NULL;
int buffer[50];
int index = 0, size = 50;
for (int i = 0; i < size; ++i){
//initialize array
buffer[i] = -1;
}
while(c->next != NULL){
if (inArray(buffer, c->val, size) < 1){
temp = (Node *)malloc(sizeof(Node));
temp->val = c->val;
temp->next = head;
head = temp;
}
buffer[index] = c->val;
c = c->next;
index++;
}
return head;
}
/* Refers to RFC 1945 5. Request (page 22)
* Method + URI + HTTP-Version
*/
static int checkHttpRequest(char * requestLine, char ** url, char ** method, status * st)
{
char * pch;
pch = strtok (requestLine,sp);
char *res[3];
bzero(res,sizeof(res));
int i=0;
// We split the request using a space as delimiter
while ((pch != NULL)&&(i<3))
{
res[i]= pch;
// printf("%s%s\n","RES", res[i] );
pch = strtok (NULL, sp);
i++;
}
if(i<3) // If the request has less than the mandatory arguments
{
st->code = 400;
st->reason = "Bad Request";
return 0;
}
// We check that the method and the version are correct
if((inArray(res[0])) && (versionHTTP(res[2])))
{
// We save the method and the url in a variable
*method = res[0];
*url = res[1];
return 1;
}
st->code = 400;
st->reason = "Bad Request";
return 0;
}
void addElement(char *el, char ***array, unsigned *count)
/* Add a new element to a array of elements */
{
char *arrayCurr, arrayNew[MAX_ID_LIST];
int sizeOne, size;
char **cArray, **rArray=NULL, ***dArray;
/* Check if already present in array */
if (!inArray(el, *array, *count))
{
size = *count;
arrayCurr = sqlStringArrayToString(*array, *count);
safef(arrayNew, ArraySize(arrayNew), "%s%s,", arrayCurr, el);
size++;
dArray = array;
/* if (*dArray)
freeMem(dArray); */
sqlStringDynamicArray(arrayNew, &cArray, &sizeOne);
assert(sizeOne == size);
*count = size;
AllocArray(rArray, size);
CopyArray(cArray, rArray, size);
*array = rArray;
}
}
/**
* renvoie l'élément qui a pour clé key
**/
function getItem(key, dict) {
for (var item in dict) {
if (inArray(item, key)) {
return item[1];
}
}
return null;
}
/**
* supprime l'élément qui a la clé key
**/
function deleteItem(key, dict) {
for (var i = 0; i < count(dict); i++) {
if (inArray(dict[i], key)) {
remove(dict, i);
return 1;
}
}
return -1;
}
void ScriptFontImportOptions::internal_SetFontSizes(ScriptFontImportOptions* thisPtr, MonoArray* value)
{
ScriptArray inArray(value);
Vector<UINT32> fontSizes(inArray.size());
for (UINT32 i = 0; i < inArray.size(); i++)
fontSizes[i] = inArray.get<UINT32>(i);
thisPtr->getFontImportOptions()->setFontSizes(fontSizes);
}
Status HashIndexCursor::seek(const BSONObj& position) {
//Use FieldRangeSet to parse the query into a vector of intervals
//These should be point-intervals if this cursor is ever used
//So the FieldInterval vector will be, e.g. <[1,1], [3,3], [6,6]>
FieldRangeSet frs( "" , position, true, true );
const vector<FieldInterval>& intervals = frs.range( _hashedField.c_str() ).intervals();
//Construct a new query based on the hashes of the previous point-intervals
//e.g. {a : {$in : [ hash(1) , hash(3) , hash(6) ]}}
BSONObjBuilder newQueryBuilder;
BSONObjBuilder inObj( newQueryBuilder.subobjStart( _hashedField ) );
BSONArrayBuilder inArray( inObj.subarrayStart("$in") );
vector<FieldInterval>::const_iterator i;
for( i = intervals.begin(); i != intervals.end(); ++i ){
if ( ! i->equality() ){
_oldCursor.reset(
BtreeCursor::make( nsdetails( _descriptor->parentNS()),
_descriptor->getOnDisk(),
BSON( "" << MINKEY ) ,
BSON( "" << MAXKEY ) ,
true ,
1 ) );
return Status::OK();
}
inArray.append(HashAccessMethod::makeSingleKey(i->_lower._bound, _seed, _hashVersion));
}
inArray.done();
inObj.done();
BSONObj newQuery = newQueryBuilder.obj();
// FieldRangeVector needs an IndexSpec so we make it one.
BSONObjBuilder specBuilder;
BSONObjIterator it(_descriptor->keyPattern());
while (it.more()) {
BSONElement e = it.next();
specBuilder.append(e.fieldName(), 1);
}
BSONObj spec = specBuilder.obj();
IndexSpec specForFRV(spec);
//Use the point-intervals of the new query to create a Btree cursor
FieldRangeSet newfrs( "" , newQuery , true, true );
shared_ptr<FieldRangeVector> newVector(
new FieldRangeVector( newfrs , specForFRV, 1 ) );
_oldCursor.reset(
BtreeCursor::make(nsdetails(_descriptor->parentNS()),
_descriptor->getOnDisk(),
newVector,
0,
1));
return Status::OK();
}
void ScriptFontImportOptions::internal_SetCharRanges(ScriptFontImportOptions* thisPtr, MonoArray* value)
{
ScriptArray inArray(value);
thisPtr->getFontImportOptions()->clearCharIndexRanges();
for (UINT32 i = 0; i < inArray.size(); i++)
{
CharRange range = inArray.get<CharRange>(i);
thisPtr->getFontImportOptions()->addCharIndexRange(range.start, range.end);
}
}
void ScriptAnimationCurve::internal_Create(MonoObject* instance, MonoArray* keyFrames)
{
ScriptArray inArray(keyFrames);
UINT32 numKeyframes = inArray.size();
Vector<TKeyframe<float>> nativeKeyframes(numKeyframes);
memcpy(nativeKeyframes.data(), (UINT8*)inArray.getRawPtr<TKeyframe<float>>(),
numKeyframes * sizeof(TKeyframe<float>));
SPtr<TAnimationCurve<float>> curve = bs_shared_ptr_new<TAnimationCurve<float>>(nativeKeyframes);
new (bs_alloc<ScriptAnimationCurve>()) ScriptAnimationCurve(instance, curve);
}
///////////////////////////////////////////////////////////////////////////
// result[n] will be initialized with a set of random numbers, no duplicates
// Values between 0 and max.
//
void UniqRandInt(int max, int n, int result[]) {
int cntr = 0, r;
while(cntr < n) {
r = rand(); //Get random number
r = r % (max + 1);
if (!inArray(result, cntr, r)) {
result[cntr] = r;
cntr++;
}
}
return;
}
shared_ptr<Cursor> HashedIndexType::newCursor( const BSONObj& query ,
const BSONObj& order , int numWanted ) const {
//Use FieldRangeSet to parse the query into a vector of intervals
//These should be point-intervals if this cursor is ever used
//So the FieldInterval vector will be, e.g. <[1,1], [3,3], [6,6]>
FieldRangeSet frs( "" , query , true, true );
const vector<FieldInterval>& intervals = frs.range( _hashedField.c_str() ).intervals();
//Force a match of the query against the actual document by giving
//the cursor a matcher with an empty indexKeyPattern. This insures the
//index is not used as a covered index.
//NOTE: this forcing is necessary due to potential hash collisions
const shared_ptr< CoveredIndexMatcher > forceDocMatcher(
new CoveredIndexMatcher( query , BSONObj() ) );
//Construct a new query based on the hashes of the previous point-intervals
//e.g. {a : {$in : [ hash(1) , hash(3) , hash(6) ]}}
BSONObjBuilder newQueryBuilder;
BSONObjBuilder inObj( newQueryBuilder.subobjStart( _hashedField ) );
BSONArrayBuilder inArray( inObj.subarrayStart("$in") );
vector<FieldInterval>::const_iterator i;
for( i = intervals.begin(); i != intervals.end(); ++i ){
if ( ! i->equality() ){
const shared_ptr< BtreeCursor > exhaustiveCursor(
BtreeCursor::make( nsdetails( _spec->getDetails()->parentNS().c_str()),
*( _spec->getDetails() ),
BSON( "" << MINKEY ) ,
BSON( "" << MAXKEY ) ,
true ,
1 ) );
exhaustiveCursor->setMatcher( forceDocMatcher );
return exhaustiveCursor;
}
inArray.append( makeSingleKey( i->_lower._bound , _seed , _hashVersion ) );
}
inArray.done();
inObj.done();
BSONObj newQuery = newQueryBuilder.obj();
//Use the point-intervals of the new query to create a Btree cursor
FieldRangeSet newfrs( "" , newQuery , true, true );
shared_ptr<FieldRangeVector> newVector(
new FieldRangeVector( newfrs , *_spec , 1 ) );
const shared_ptr< BtreeCursor > cursor(
BtreeCursor::make( nsdetails( _spec->getDetails()->parentNS().c_str()),
*( _spec->getDetails() ), newVector , 1 ) );
cursor->setMatcher( forceDocMatcher );
return cursor;
}
/**
* Evaluates each command stored in the parser struct and exeutes either the runShellCommand
* function or the runCommand function.
* @param parser A constructed LashParser struct with fully populated commands
* @return 0 if a command was "exit", 1 otherwise
*/
int executeCommand(struct LashParser *parser){
int i;
int nextinput = -1;
for(i = 0; i < parser->commandNum; i++){
struct Command *command = parser->commands[i];
int shellCommand = inArray(command->args[0], inbuiltCommands, NUMINBUILTCOMMANDS);
if(shellCommand){
return runShellCommand(parser, command);
}
else if(strcmp(command->args[0], "") != 0){
nextinput = runCommand(command, nextinput);
}
}
return 1;
}
void listOthers(char uname[USERNAME_SIZE], char **followees, int clientSock, int size){
//Sends all usernames that uname is not following (excluding his own uname) to the clientSock
FILE * fp;
if ((fp = fopen(CREDENTIALS_FILE, "r")) == NULL)
{
perror("Couldn't open file");
exit(FOPEN_FAILED);
}
char oneLine[CREDENTIALS_ENTRY_SIZE];
bzero(oneLine, CREDENTIALS_ENTRY_SIZE);
while(fgets(oneLine, CREDENTIALS_ENTRY_SIZE, fp))
{
char* credentialsEntryTok[NUM_FIELDS_CREDENTIALS+1];
tokenize(credentialsEntryTok, oneLine, SEPARATOR);
//puts(credentialsEntryTok[0]);
//if credentialsEntryTok[0] exists, and is not in uname's followees and is not uname
if(credentialsEntryTok[0] && !inArray(credentialsEntryTok[0], followees, size) && !(strncmp(uname, credentialsEntryTok[0], strlen(uname)) == 0 && (strlen(uname) == strlen(credentialsEntryTok[0]))))
{
char temp[USERNAME_SIZE+1];
bzero(temp, USERNAME_SIZE+1);
if(snprintf(temp, USERNAME_SIZE+1, "%s\n", credentialsEntryTok[0]) < 0)
{
perror("Snprintf failed.");
exit(SNPRINTF_FAILED);
}
if(send(clientSock, temp, strlen(temp), 0) == -1)
{
perror("Send Failed.");
exit(SEND_FAILED);
}
}
for(int i = 0; credentialsEntryTok[i]; i++)
{
free(credentialsEntryTok[i]);
}
bzero(oneLine, CREDENTIALS_ENTRY_SIZE);
}
if(fclose(fp) == EOF)
{
perror("Close failed.");
exit(FCLOSE_FAILED);
}
}
void ScriptAnimationCurve::internal_SetKeyFrames(ScriptAnimationCurve* thisPtr, MonoArray* keyFrames)
{
ScriptArray inArray(keyFrames);
UINT32 numKeyframes = inArray.size();
Vector<TKeyframe<float>> nativeKeyframes(numKeyframes);
memcpy(nativeKeyframes.data(), (UINT8*)inArray.getRawPtr<TKeyframe<float>>(),
numKeyframes * sizeof(TKeyframe<float>));
std::sort(nativeKeyframes.begin(), nativeKeyframes.end(),
[](const TKeyframe<float>& x, const TKeyframe<float>& y)
{
return x.time < y.time;
});
thisPtr->mCurve = bs_shared_ptr_new<TAnimationCurve<float>>(nativeKeyframes);
}
void listTweets(char uname[USERNAME_SIZE], char **followees, int clientSock, int size){
//sends all of uname's tweets as well as all tweets of followees to the clientSock
FILE * fp;
if ((fp = fopen(TWEETS_FILE, "r")) == NULL)
{
perror("Couldn't open file");
exit(FOPEN_FAILED);
}
char oneLine[TWEET_ENTRY_SIZE];
bzero(oneLine, TWEET_ENTRY_SIZE);
while(fgets(oneLine, TWEET_ENTRY_SIZE, fp))
{
char* tweetsEntryTok[NUM_FIELDS_TWEETS+1];
tokenize(tweetsEntryTok, oneLine, SEPARATOR);
//if author of a tweet is in uname's followees array OR author is uname
if(tweetsEntryTok[0] && (inArray(tweetsEntryTok[0], followees, size) ||
(strncmp(uname, tweetsEntryTok[0], strlen(uname)) == 0 && strlen(uname) == strlen(tweetsEntryTok[0]))))
{
char temp[TWEET_ENTRY_SIZE];
bzero(temp, TWEET_ENTRY_SIZE);
if(snprintf(temp, TWEET_SIZE+3, "%s\t%s\t%s\n", tweetsEntryTok[0], tweetsEntryTok[1], tweetsEntryTok[2]) < 0)
{
perror("Snprintf failed.");
exit(SNPRINTF_FAILED);
}
if(send(clientSock, temp, strlen(temp), 0) == -1)
{
perror("Send Failed.");
exit(SEND_FAILED);
}
}
for(int i = 0; tweetsEntryTok[i]; i++)
{
free(tweetsEntryTok[i]);
}
bzero(oneLine, TWEET_ENTRY_SIZE);
}
if(fclose(fp) == EOF)
{
perror("Close failed.");
exit(FCLOSE_FAILED);
}
}
int main(){
std::ifstream infile ( "input.txt" );
if ( !infile.bad ( ) ) {
int residentsCount; // Число дачников
int coordinates[10];
infile >> residentsCount;
int accuracyResidents = 0 ; // Число точно приземлившихся
for ( int i = 1; i <= residentsCount; i++ ) {
for ( int j = 0 ; j < 10 ; ++j ) {
infile >> coordinates [ j ] ;
}
if ( inArray ( coordinates ) )
++accuracyResidents ;
}
infile.close();
std::ofstream outfile("output.txt");
if (!outfile.bad()) {
outfile << accuracyResidents ;
outfile.close();
}
std::cout << "Accuracy: " <<
accuracyResidents << std::endl ;
}
/**
Builds the logger configuration by parsing the default configuration file.
@return The parsed logger configuration.
**/
LoggerConfig buildLoggerConfig(FILE *configFile)
{
char buff[CONFIG_BUFF_SIZE] = "";
char *buffPointer = NULL;
const char *instr[CONFIG_INSTR_ARRAY_SIZE] = {"logLevel", "logFile"};
LoggerConfig config;
while(!feof(configFile))
{
fgets(buff, CONFIG_BUFF_SIZE, configFile);
if((buffPointer = strchr(buff, '=')) != NULL)
{
*buffPointer = '\0';
buffPointer++;
LoggerConfigRoutingProc(&config, buffPointer, inArray(buffPointer, instr, CONFIG_INSTR_ARRAY_SIZE));
}
else
{
fprintf(stderr, "Warning : \"%s\" line could not be parsed !", buff);
}
}
return config;
}
void eval( Node *node )
{
int i, j;
Number n1, n2, n3, n4;
char *string1;
Symbol *s;
Node *n;
Array *a;
/* debugging */
#ifdef __DEBUG_TRACE__
SourceCode *sc;
#endif
/* init vars */
n1=0;
n2=0;
n3=0;
n4=0;
if (node == NULL) {
return;
}
/* test node */
eMemTest( "eval: node is corrupt", node );
eMemTest( "eval: node->left is corrupt", node->left );
eMemTest( "eval: node->right is corrupt", node->right );
/* tracing */
if (node->trace != -1) {
runLineId = node->trace;
#ifdef __DEBUG_TRACE__
sc = eFindSource( runLineId );
eConsole("%d: %s\n", sc->lineNum, sc->text );
#endif
/* sdlBasic_debugging */
if (debug==1){
screendebug(); ////////////////////////////////////
}
}
/* debugging */
#ifdef __DEBUG_TRACE__
eConsole( "Op:%s\n", opcodeName[node->op] );
#endif
switch( node->op ) {
//case NULL:
// break;
case OpAdd:
eval( node->left );
eval( node->right );
/* add or concat? */
if (getStackType( tos ) == DATA_STRING) {
basConcat();
} else {
n2 = popNumber();
n1 = popNumber();
pushNumber( n1 + n2 );
}
break;
case OpAnd:
/* short circuit */
eval( node->left );
if (!popNumber()) {
pushNumber( (Number)0 );
} else {
eval( node->right );
if (popNumber()) {
pushNumber( (Number)1 );
} else {
pushNumber( (Number)0 );
}
}
break;
case OpArgList:
eval( node->left );
eval( node->right );
break;
case OpArrayGet:
eval( node->left ); /* indices and index */
getArrayElement( node->value.symbol );
break;
case OpArrayPtr:
pushArray( node->value.symbol );
break;
case OpArraySet:
eval( node->right ); /* value to store */
eval( node->left ); /* indices and index */
setArrayElement( node->value.symbol );
break;
case OpAssign:
/* value to be assigned. note the *right* node is used */
eval( node->right );
/* variable to assign to */
setVar( node->value.symbol );
break;
case OpBuiltin:
case OpBuiltinCall:
/* for argcount */
n1 = tos;
/* mark start of created objects */
pushCreateStack( 0 );
/* the args */
eval( node->left );
/* builtin symbol */
s = node->value.symbol;
if (s == NULL) {
ePrintf( Runtime, "builtin pointer is null");
}
/* set args */
argCount = (int)(tos - n1);
/* call the c function */
(*s->builtin)();
/* destroy created objects */
clearCreateStack();
/* drop result? */
if (node->op == OpBuiltinCall) {
dropTos();
}
break;
case OpCaseSelect:
/* top level of a case statement */
/* value to compare */
eval( node->left );
/* resolve into real data */
switch (getStackType( tos )) {
case DATA_NUMBER:
pushNumber( popNumber() );
break;
case DATA_STRING:
pushString( popString() );
break;
default:
ePrintf( Runtime, "OpCaseSelect: can't resolve type %s",
datumName[getStackType( tos )] );
}
/* get first test */
if (node == NULL) {
/* no tests */
break;
} else {
node = node->right;
}
/* walk the chain of cases */
while (1) {
/* get a test/action pair */
n = node->left;
/* perform the tests */
eval( n->left );
/* true? */
if (popNumber()) {
/* perform action and leave loop */
eval( n->right );
break;
}
/* move to next test */
node = node->right;
if (node == NULL) {
break;
}
}
/* drop the test value from the stack */
dropTos();
break;
case OpCaseCmp:
case OpCaseRange:
case OpCaseElse:
/* perform chain of tests until true or end */
while (1) {
switch (node->op) {
case OpCaseCmp:
/* value to compare */
eval(node->left);
/* what type of test? */
switch (getStackType( tos-1 )) {
case DATA_NUMBER:
numberCompare( node->value.iValue, 0 );
break;
case DATA_STRING:
stringCompare( node->value.iValue, 0 );
break;
default:
ePrintf( Runtime, "OpCaseCmp: bad data type" );
}
break;
case OpCaseRange:
/* values to compare */
n = node->left;
eval( n->left );
eval( n->right );
/* what type of comparison? */
switch (getStackType( tos-2 )) {
case DATA_NUMBER:
numberRangeCompare();
break;
case DATA_STRING:
stringRangeCompare();
break;
default:
ePrintf( Runtime, "OpCaseRange: bad data type" );
break;
}
break;
case OpCaseElse:
/* put true on stack */
pushNumber( 1 );
break;
default:
ePrintf( Runtime, "opcode %s found in Case test chain",
opcodeName[node->op] );
}
/* was result true? */
if (stack[tos].value.number) {
/* leave true flag on stack and exit */
break;
}
/* move to next test */
node = node->right;
if (node == NULL) {
/* exit with false flag */
break;
}
/* drop test result flag */
dropTos();
}
break;
case OpClassMethod:
case OpClassMethodCall:
/* the args */
n1 = tos;
/* mark start of created objects */
pushCreateStack( 0 );
/* the args */
eval( node->right );
argCount = (int)(tos - n1);
me = 0;
runMethod( node->left->value.symbol->klass, node->value.string );
/* destroy created objects */
clearCreateStack();
/* drop result? */
if (node->op == OpClassMethodCall) {
dropTos();
}
break;
case OpClose:
if (node->left == NULL) {
fileCloseAll();
} else {
eval( node->left );
i = (int)popNumber();
fileClose( i );
}
break;
case OpCmp:
eval( node->left );
eval( node->right );
switch(getStackType(tos)) {
case DATA_NUMBER:
numberCompare( node->value.iValue, 1 );
break;
case DATA_STRING:
stringCompare( node->value.iValue, 1 );
break;
default:
ePrintf( Runtime, "opCmp: can't handle datatype" );
}
break;
case OpComma:
/* optimized for linked lists */
while (1) {
/* exit flag set? */
if (exitForFlag != 0 ||
exitRoutineFlag != 0 ||
exitDoFlag != 0 ||
exitWhileFlag != 0 ||
continueFlag ) {
break;
}
if (node->left != NULL ) {
eval( node->left );
}
/* end of list? */
if (node->right == NULL ) {
break;
/* linked list? */
} else if (node->right->op == OpComma) {
node = node->right;
/* not a list */
} else {
eval( node->right );
break;
}
}
break;
case OpConcat:
eval( node->left );
eval( node->right );
basConcat();
break;
case OpConstGet:
s = node->value.symbol;
i = s->stackPos;
/* this better not be indirected! */
switch (stack[i].datatype) {
case DATA_STRING:
pushString( stack[i].value.string );
break;
case DATA_NUMBER:
pushNumber( stack[i].value.number );
break;
default:
ePrintf( Runtime, "Can't fetch Const type %s",
datumName[stack[i].datatype] );
break;
}
break;
case OpConstSet:
s = node->value.symbol;
eval( node->left );
switch (stack[tos].datatype) {
case DATA_STRING:
stack[s->stackPos].datatype = DATA_STRING;
stack[s->stackPos].value.string = stack[tos].value.string;
stack[tos].datatype = DATA_NUMBER;
tos--;
break;
case DATA_NUMBER:
stack[s->stackPos].datatype = DATA_NUMBER;
stack[s->stackPos].value.number = stack[tos].value.number;
tos--;
break;
default:
ePrintf( Runtime, "Can't set Const to %s", datumName[stack[tos].datatype] );
break;
}
break;
case OpDelete:
eval( node->left );
runDestructor( (int)popNumber(), OpDelete );
break;
case OpDestroy:
eval( node->left );
runDestructor( (int)popNumber(), OpDestroy );
break;
case OpContinue:
continueFlag = 1;
break;
case OpDiv:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
if (n2 == 0.0) {
ePrintf( Runtime, "Division by zero" );
}
pushNumber( n1 / n2 );
break;
case OpDo:
while (1) {
/* test */
eval( node->left );
/*if (!popNumber()){
break;
}*/
/* code */
eval( node->right );
//printf("exitDoFlag:%d\n",exitDoFlag);
if (exitDoFlag != 0) {
exitDoFlag = 0;
break;
}
else if (continueFlag) {
continueFlag = 0;
}
}
break;
case OpEnd:
eShutdown(0);
break;
case OpErase:
if (node->left == NULL) {
/* erase entire array */
eraseArray( node->value.symbol );
} else {
/* evaluate the indexes */
eval( node->left );
/* erase single element from array */
eraseArrayElement( node->value.symbol );
}
break;
case OpExitDo:
exitDoFlag = 1;
break;
case OpExitFor:
exitForFlag = 1;
break;
case OpExitRoutine:
currentScope=oldScope[oldScopeP--];
exitRoutineFlag = 1;
break;
case OpExitWhile:
exitWhileFlag = 1;
break;
case OpFloat:
pushNumber( node->value.fValue );
break;
case OpFor:
s = node->value.symbol;
eval( node->left );
n2 = popNumber();
n1 = popNumber();
/* initial value */
pushNumber( n3 );
setVar( s );
for( n3=n1; n3 <= n2; n3++ ) {
/* set loop variable */
pushNumber( n3 );
setVar( s );
/* run code */
eval( node->right );
/* special exit condition? */
if (exitForFlag) {
exitForFlag = 0;
break;
} else if (continueFlag) {
continueFlag = 0;
}
/* get loop value (in case it changed) */
getVar( s );
n3 = popNumber();
}
break;
case OpForEach:
/* variable to assign */
s = node->value.symbol;
/* array to read from */
a = getArray( node->left->value.symbol );
/* iterate through keys */
i = 0;
/* put key on stack, or exit */
while (getDynamicKey( a, i )) {
/* assign to variable */
setVar( s );
/* run block */
eval( node->right );
/* next */
i += 1;
}
break;
case OpForStep:
s = node->value.symbol;
eval( node->left );
n3 = popNumber(); /* step */
n2 = popNumber(); /* end */
n1 = popNumber(); /* start */
/* which direction? */
if (n3 > 0) {
n2 += ALLOWABLE_ERROR;
for( n4=n1; n2 >= n4; n4 += n3 ) {
/* set loop variable */
pushNumber( n4 );
setVar( s );
/* run code */
eval( node->right );
/* special exit condition? */
if (exitForFlag) {
exitForFlag = 0;
break;
} else if (continueFlag) {
continueFlag = 0;
}
/* get loop value (in case it changed) */
getVar( s );
n4 = popNumber();
}
} else {
n2 -= ALLOWABLE_ERROR;
for( n4=n1; n2 <= n4; n4 += n3 ) {
/* set loop variable */
pushNumber( n4 );
setVar( s );
/* run code */
eval( node->right );
/* special exit condition? */
if (exitForFlag) {
exitForFlag = 0;
break;
} else if (continueFlag) {
continueFlag = 0;
}
/* get loop value (in case it changed) */
getVar( s );
n4 = popNumber();
}
}
break;
case OpFunction:
case OpFunctionCall:
callFunction( node );
break;
case OpInitArray:
if (node->left == NULL) {
createDynamicArray( node->value.symbol );
} else {
eval( node->left );
createStaticArray( node->value.symbol );
}
break;
case OpInput:
if (node->value.iValue == 1) {
eval( node->left );
i = (int)popNumber();
string1 = fileLineInput( i );
pushString( string1 );
} else {
/* command line */
ePrintf( Runtime, "Input statement is not currently supported" );
}
break;
case OpInt:
pushNumber( node->value.iValue );
break;
case OpMethod:
case OpMethodCall:
/* the index */
eval( node->left );
n1 = popNumber();
/* method name */
string1 = node->value.string;
/* mark start of created objects */
pushCreateStack( 0 );
/* args */
n2 = tos;
eval( node->right );
argCount = (int)(tos - n2);
/* resolve and run method */
resolveMethod( (int)n1, string1 );
/* drop result? */
if (node->op == OpMethodCall) {
dropTos();
}
/* destroy created objects */
clearCreateStack();
break;
case OpMod:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
//pushNumber( (long)n1 % (long)n2 );
pushNumber( fmod(n1,n2) );
break;
case OpMul:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
pushNumber( n1 * n2 );
break;
case OpOpen:
/* file name */
eval( node->left );
string1 = popString();
/* mode */
i = node->value.iValue;
/* file number */
eval( node->right );
n1 = popNumber();
fileOpen( string1, i, (int)n1 );
free( string1 );
break;
case OpOr:
/* short circuit */
eval( node->left );
if (popNumber()) {
pushNumber( (Number)1 );
} else {
eval( node->right );
if (popNumber()) {
pushNumber( (Number)1 );
} else {
pushNumber( (Number)0 );
}
}
break;
case OpOrBits:
eval( node->left );
eval( node->right);
i = popNumber();
j = popNumber();
pushNumber( i | j );
break;
case OpIDiv:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
/* check for division by zero */
if (n2 == 0.0) {
ePrintf( Runtime, "Division by zero" );
}
pushNumber( floor(n1 / n2) );
break;
case OpIf:
n = node->left;
/* test */
eval( n->left );
n1 = popNumber();
if (n1 != 0) {
/* true portion */
eval( n->right );
} else {
/* false portion */
eval( node->right );
}
break;
case OpIfTrue:
ePrintf( Runtime, "OpIfTrue: internal error" );
break;
case OpIn:
/* evaluate key */
eval( node->left );
/* look for it in array */
pushNumber( inArray( node->value.symbol ) );
break;
case OpInv:
ePrintf( Runtime, "Inv is not implemented yet" );
break;
case OpNegate:
eval( node->left );
n1 = popNumber();
pushNumber( -n1 );
break;
case OpNew:
case OpNewTmp:
/* mark start of created objects */
pushCreateStack( 0 );
/* the args */
n1 = tos;
eval( node->left );
argCount = (int)(tos - n1);
runMethod( node->value.symbol->klass, "new" );
/* destroy created objects *before* adding new object to stack */
clearCreateStack();
/* add new object to create stack? */
if (node->op == OpNewTmp) {
/* track on stack */
copyStackItem( tos );
pushCreateStack( (int)popNumber() );
}
break;
case OpNoOp:
break;
case OpNot:
eval( node->left );
n1 = popNumber();
pushNumber( !n1 );
break;
case OpPower:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
pushNumber( pow( n1, n2 ) );
break;
case OpPrint:
if (node->left == NULL) {
i = 0;
} else {
eval( node->left );
i = (int)popNumber();
}
node = node->right;
/* empty print statement */
if (node == NULL) {
if (i==0) {
eConsole("\n");
} else {
filePrintString( i, "\n" );
}
}
/* process nodes */
while(node != NULL) {
/* data value */
if (node->left != NULL) {
eval( node->left );
string1 = popString();
if (i==0) {
eConsole("%s", string1 );
} else {
filePrintString( i, string1 );
}
eFree( string1 );
}
/* field delimiter */
switch (node->value.iValue) {
case PRINT_TAB:
if (i==0) {
eConsole("\t");
} else {
filePrintString( i, "\t" );
}
break;
case PRINT_NEWLINE:
if (i==0) {
eConsole("\n");
} else {
filePrintString( i, "\n" );
}
break;
default:
/* no action */
break;
}
/* link */
node = node->right;
}
break;
case OpReturnValue:
eval( node->left );
setReturn();
exitRoutineFlag = 1;
break;
case OpReturnSetValue:
eval( node->left );
setReturn();
break;
case OpShl:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
pushNumber( (long)n1 << (long)n2 );
break;
case OpShr:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
pushNumber( (long)n1 >> (long)n2 );
break;
case OpString:
pushStringCopy( node->value.string );
break;
case OpSub:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
pushNumber( n1 - n2 );
break;
case OpUndefined:
ePrintf( Runtime, "Opcode is undefined" );
break;
case OpVar:
/* check type */
getVar( node->value.symbol );
if (getStackType(tos) == DATA_UNDEFINED) {
ePrintf( Runtime, "the value of %s is undefined",
node->value.symbol->name );
}
break;
case OpWhile:
while (1) {
/* test */
eval( node->left );
if (!popNumber()){
break;
}
/* code */
eval( node->right );
if (exitWhileFlag != 0) {
exitWhileFlag = 0;
break;
} else if (continueFlag) {
continueFlag = 0;
}
}
break;
case OpXor:
eval( node->left );
eval( node->right );
n2 = popNumber();
n1 = popNumber();
pushNumber( (long)n1 ^ (long)n2 );
break;
default:
ePrintf( Runtime, "Unknown Opcode: %d", node->op );
}
}
bool ZCMGen::isArrayDimType(const string& t) { return inArray(arrayDimTypes, t); }
bool ZCMGen::isLegalConstType(const string& t) { return inArray(constTypes, t); }
bool ZCMGen::isPrimitiveType(const string& t) { return inArray(primitiveTypes, t); }
int main (int argc, char **argv)
{
puts("Program starts");
/* Checking command line,
throw exception if not complete */
//printf("%s %s %s %s %s %s %s\n", argv[0], argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]);
if (argc != 12)
{
printf("\nUsage: %s <input file 1.pdb> <input file 2.pdb> <output file> <chain1> <chain2> <start1> <end1> <start2> <end2> <file name for score> <is on server>", argv[0]);
printf("\nExample: %s 3hdd.pdb 1puf.pdb superpos_3hdd_1puf.pdb A B 5 60 zero inf max_score.txt 0\n\n", argv[0]);
exit (1);
} /* end if */
/* Done checking command line */
/* Reading command line arguments */
char *infile1, *infile2, *outfile, *max_score_filename;
char *start1, *end1, *start2, *end2;
char chain1, chain2;
unsigned int SERVER;
infile1 = (char *)malloc( sizeof(char)*(strlen(argv[1])+1) );
sscanf(argv[1],"%s", infile1);
infile2 = (char *)malloc( sizeof(char)*(strlen(argv[2])+1) );
sscanf(argv[2],"%s", infile2);
outfile = (char *)malloc( sizeof(char)*(strlen(argv[3])+1) );
sscanf(argv[3], "%s", outfile);
sscanf(argv[4], "%c", &chain1);
sscanf(argv[5], "%c", &chain2);
start1 = (char *)malloc( sizeof(char)*(strlen(argv[6])+1) );
end1 = (char *)malloc( sizeof(char)*(strlen(argv[7])+1) );
start2 = (char *)malloc( sizeof(char)*(strlen(argv[8])+1) );
end2 = (char *)malloc( sizeof(char)*(strlen(argv[9])+1) );
sscanf(argv[6], "%s", start1);
sscanf(argv[7], "%s", end1);
sscanf(argv[8], "%s", start2);
sscanf(argv[9], "%s", end2);
max_score_filename = (char *)malloc( sizeof(char)*(strlen(argv[10])+1) );
sscanf(argv[10], "%s", max_score_filename);
sscanf(argv[11], "%u", &SERVER);
/* Done reading arguments */
/* DECLARATION AND ASSIGNMENT
OF SOME VARIABLES */
struct atom *atoms_prot1 = NULL, *atoms_prot2 = NULL;
struct atom *all_atoms_dna1 = NULL, *all_atoms_dna2 = NULL;
struct atom *atoms_wat1 = NULL, *atoms_wat2 = NULL;
struct atom *atoms_prot_CA1 = NULL, *atoms_prot_CA2 = NULL;
struct atom *atoms_prot_C1 = NULL, *atoms_prot_C2 = NULL;
struct atom *atoms_prot_i1 = NULL, *atoms_prot_i2 = NULL;
struct atom *atoms_prot_j1 = NULL, *atoms_prot_j2 = NULL;
struct atom *C_atoms_prot_i1 = NULL, *C_atoms_prot_j2 = NULL;
struct atomname *list1, *list2;
unsigned int maxnumber = 256; //primary number of atoms in each groups (DNA, protein, water)
FILE *flow_out;
unsigned int all_m1=0, n1=0, w1=0, i, j, all_m2=0, n2=0, w2=0;
/* m - number of DNA atoms
* n - number of protein atoms
* w - number of water atoms */
char *dna_chains1 = (char *)malloc( sizeof(char)*(2+1) );
char *prot_chains1 = (char *)malloc( sizeof(char)*(2+1) );
char *dna_chains2 = (char *)malloc( sizeof(char)*(2+1) );
char *prot_chains2 = (char *)malloc( sizeof(char)*(2+1) );
/*** For server ***/
FILE *max_score;
//printf("%s", max_score_filename);
max_score = fopen(max_score_filename, "w");
if (max_score == NULL) {
perror(max_score_filename);
exit(1);
}
/* Reading PDB file */
puts("Reading 1st PDB file...");
readerPDB(infile1, &all_m1, &n1, &w1, maxnumber, &all_atoms_dna1, &dna_chains1, &atoms_prot1, &prot_chains1, &atoms_wat1, &list1);
// pdb.c function, read PDB and put protein, DNA and water atoms in three different arrays
printf("...done; %d atoms of dna, %d atoms of protein, %d atoms of water\n", all_m1, n1, w1);
if (all_m1 == 0)
{fprintf(max_score, "Error\nFirst structure has no DNA!");
exit(1); }
if (chain1=='@')
chain1 = prot_chains1[1];
else
if ( inArray(chain1, prot_chains1)==0 )
{ fprintf(max_score, "Error\nChain %c is not a protein chain in first structure", chain1);
exit(1); }
SelectChain(atoms_prot1, n1, &atoms_prot1, &n1, chain1);
SelectRange(atoms_prot1, n1, &atoms_prot1, &n1, start1, end1);
// pdb.c function
printf("Atoms in selected chain: %u\n\n", n1);
// print to stdout number of protein atoms in selected chain
puts("Reading 2nd PDB file...");
readerPDB(infile2, &all_m2, &n2, &w2, maxnumber, &all_atoms_dna2, &dna_chains2, &atoms_prot2, &prot_chains2, &atoms_wat2, &list2);
printf("...done; %d atoms of dna, %d atoms of protein, %d atoms of water\n", all_m2, n2, w2);
if (all_m2 == 0)
{fprintf(max_score, "Error\nSecond structure has no DNA!");
exit(1); }
if (chain2=='@')
chain2 = prot_chains2[1];
else
if ( inArray(chain2, prot_chains2)==0 )
{ fprintf(max_score, "Error\nChain %c is not a protein chain in second structure!", chain2);
exit(1); }
SelectChain(atoms_prot2, n2, &atoms_prot2, &n2, chain2);
SelectRange(atoms_prot2, n2, &atoms_prot2, &n2, start2, end2);
printf("Atoms in selected chain: %u\n\n", n2);
dna_chains1[0] = ' '; dna_chains2[0] = ' ';
/*** For server ***/
char dna_chain1, dna_chain2;
//dna_chain2 = dna_chains2[1];
printf("DNA1 chains: %s; DNA2 chains: %s\n", dna_chains1, dna_chains2);
/* Done reading */
/*** 3DNA block ***/
unsigned int *compl_list1, *compl_list2, n_pairs1, n_pairs2, pair1, pair2;
int **compl_pairs1, **compl_pairs2;
char **pairs1, **pairs2;
run_3dna(infile1, &compl_list1, &compl_pairs1, &pairs1, &n_pairs1, SERVER, max_score_filename);
run_3dna(infile2, &compl_list2, &compl_pairs2, &pairs2, &n_pairs2, SERVER, max_score_filename);
/*** 3DNA block end ***/
/*** MAIN FOR CYCLE ***/
struct atom *best_atoms_dna1 = NULL, *best_atoms_dna2 = NULL;
struct atom *best_dna1_chain1, *best_dna1_chain2, *best_dna2_chain1, *best_dna2_chain2;
unsigned int *best_list_P1, *best_list_C11, *best_list_OP11, *best_list_OP21, *best_list_P2, *best_list_C12, *best_list_OP12, *best_list_OP22;
unsigned int best_n_P1, best_n_P2;
unsigned int best_dna1_chain1_n, best_dna1_chain2_n, best_dna2_chain1_n, best_dna2_chain2_n;
unsigned int best_i_max_measure, best_j_max_measure;
unsigned int best_compl1, best_compl2;
unsigned int best_n_first_chain, best_m_first_chain;
unsigned int best_pair1, best_pair2;
double best_S_max = -1;
for (pair1=1; pair1<=n_pairs1; pair1++)
{
struct atom *atoms_dna1 = NULL, *dna1_chain1 = NULL, *dna1_chain2 = NULL;
unsigned int m1, dna1_chain1_n=0, dna1_chain2_n=0;
SelectChain(all_atoms_dna1, all_m1, &dna1_chain1, &dna1_chain1_n, pairs1[pair1][1]);
SelectChain(all_atoms_dna1, all_m1, &dna1_chain2, &dna1_chain2_n, pairs1[pair1][2]);
atomlistmerge(&atoms_dna1, &m1, dna1_chain1, dna1_chain1_n, dna1_chain2, dna1_chain2_n);
//printf("%u/%u\n", pair1, n_pairs1);
/* Make lists of P, C1', OP1 atoms
of dna and CA atoms of protein */
unsigned int *list_P1, *list_C11, *list_OP11, *list_OP21, *list_CA1, *list_C1;
unsigned int n_P1, n_C11, n_OP11, n_OP21, n_CA1, n_C1;
getAtomsNumbers(atoms_dna1, m1, &list_P1, &n_P1, "P");
// pdb.c function, get only indexes of atoms
getAtomsNumbers(atoms_dna1, m1, &list_C11, &n_C11, "C1'");
getAtomsNumbers(atoms_dna1, m1, &list_OP11, &n_OP11, "OP1");
getAtomsNumbers(atoms_dna1, m1, &list_OP21, &n_OP21, "OP2");
getAtomsNumbers(atoms_prot1, n1, &list_CA1, &n_CA1, "CA");
getAtomsNumbers(atoms_prot1, n1, &list_C1, &n_C1, "C");
correctC1_P(atoms_dna1, &list_C11, &n_C11, list_P1, &n_P1);
//for (i=1; i<=n_C11; i++) printf("%s.%c\n", atoms_dna1[list_C11[i]].ResNumber, atoms_dna1[list_C11[i]].Chain);
//corrects list_C1 to use rule list_P[i] and list_C1[i+1] are in the same nucleotide
atoms_prot_CA1 = (struct atom *)malloc( sizeof(struct atom)*(n_CA1+1) );
for (i=1; i<=n_CA1; i++) {
atomcpy(&atoms_prot_CA1[i], atoms_prot1[list_CA1[i]]);
//pdb.c function. Copy all properties of atom
}
atoms_prot_C1 = (struct atom *)malloc( sizeof(struct atom)*(n_C1+1) );
for (i=1; i<=n_C1; i++) {
atomcpy(&atoms_prot_C1[i], atoms_prot1[list_C1[i]]);
}
printf("Done atoms:\tP %u\tC1 %u\tOP1 %u\tOP2 %u\tCA %u\tC %u\n",n_P1, n_C11, n_OP11, n_OP21, n_CA1, n_C1);
for (pair2=1; pair2<=n_pairs2; pair2++)
{
//printf("%u/%u\n", pair2, n_pairs2);
printf("\nCYCLE %c:%c vs %c:%c\n", pairs1[pair1][1], pairs1[pair1][2], pairs2[pair2][1], pairs2[pair2][2]);
struct atom *atoms_dna2 = NULL, *dna2_chain1, *dna2_chain2;
unsigned int m2, dna2_chain1_n=0, dna2_chain2_n=0;
SelectChain(all_atoms_dna2, all_m2, &dna2_chain1, &dna2_chain1_n, pairs2[pair2][1]);
SelectChain(all_atoms_dna2, all_m2, &dna2_chain2, &dna2_chain2_n, pairs2[pair2][2]);
atomlistmerge(&atoms_dna2, &m2, dna2_chain1, dna2_chain1_n, dna2_chain2, dna2_chain2_n);
unsigned int *list_P2, *list_C12, *list_OP12, *list_OP22, *list_CA2, *list_C2;
unsigned int n_P2, n_C12, n_OP12, n_OP22, n_CA2, n_C2;
getAtomsNumbers(atoms_dna2, m2, &list_P2, &n_P2, "P");
getAtomsNumbers(atoms_dna2, m2, &list_C12, &n_C12, "C1'");
getAtomsNumbers(atoms_dna2, m2, &list_OP12, &n_OP12, "OP1");
getAtomsNumbers(atoms_dna2, m2, &list_OP22, &n_OP22, "OP2");
getAtomsNumbers(atoms_prot2, n2, &list_CA2, &n_CA2, "CA");
getAtomsNumbers(atoms_prot2, n2, &list_C2, &n_C2, "C");
correctC1_P(atoms_dna2, &list_C12, &n_C12, list_P2, &n_P2);
atoms_prot_CA2 = (struct atom *)malloc( sizeof(struct atom)*(n_CA2+1) );
for (i=1; i<=n_CA2; i++) {
atomcpy(&atoms_prot_CA2[i], atoms_prot2[list_CA2[i]]);
}
atoms_prot_C2 = (struct atom *)malloc( sizeof(struct atom)*(n_C2+1) );
for (i=1; i<=n_C2; i++) {
atomcpy(&atoms_prot_C2[i], atoms_prot2[list_C2[i]]);
}
printf("Done atoms:\tP %u\tC1 %u\tOP1 %u\tOP2 %u\tCA %u\tC %u\n",n_P2, n_C12, n_OP12, n_OP22, n_CA2, n_C2);
/* Done making lists */
/* Create array of measures for
all pairs of dna P atoms (list_measure).
dim(list_measure) = n_P2 x n_P1 */
double **list_measure;
unsigned int n_hit;
unsigned int **list_hit;
list_measure = (double **)malloc( (n_P2+1)*sizeof(double *)*(n_P1+1) );
for (i=1; i<=n_P1; i++) list_measure[i] = (double *)malloc( sizeof(double)*(n_P2+1) );
//for (i=1; i<=n_P1; i++) for (j=1; j<=n_P2;j++) list_measure[i][j] = (unsigned int *)malloc( sizeof(unsigned int) );
// Enable if measure function returns unsigned int
for (i=1; i<=n_P1; i++){
for (j=1; j<=n_P2; j++){
ChangeSystem(atoms_prot_CA1, n_CA1, &atoms_prot_i1, atoms_dna1[list_P1[i]], atoms_dna1[list_C11[i+1]], atoms_dna1[list_OP11[i]], atoms_dna1[list_OP21[i]], 'E');
// pdb.c function. Change the coordinate system of protein with given nucleotide
ChangeSystem(atoms_prot_C1, n_C1, &C_atoms_prot_i1, atoms_dna1[list_P1[i]], atoms_dna1[list_C11[i+1]], atoms_dna1[list_OP11[i]], atoms_dna1[list_OP21[i]], 'E');
ChangeSystem(atoms_prot_CA2, n_CA2, &atoms_prot_j2, atoms_dna2[list_P2[j]], atoms_dna2[list_C12[j+1]], atoms_dna2[list_OP12[j]], atoms_dna2[list_OP22[j]], 'F');
ChangeSystem(atoms_prot_C2, n_C2, &C_atoms_prot_j2, atoms_dna2[list_P2[j]], atoms_dna2[list_C12[j+1]], atoms_dna2[list_OP12[j]], atoms_dna2[list_OP22[j]], 'F');
BidirectionalHit(atoms_prot_i1, C_atoms_prot_i1, n_CA1, atoms_prot_j2, C_atoms_prot_j2, n_CA2, &list_hit, &n_hit);
// pdb.c function.
Measure2_p(&(list_measure[i][j]), list_hit, n_hit, atoms_prot_i1, atoms_prot_j2);
// pdb.c function.
// printf("Measure: %f i: %u j: %u n_P1: %u n_P2: %u \n",(list_measure[i][j]), i,j, n_P1, n_P2);
// Enable in test mode
}
}
/* Done creation of array of measures */
/* Start working with diagonals */
unsigned int i_max, j_max, i_start, j_start, i_max_measure, j_max_measure;
unsigned int n_first_chain, m_first_chain;
unsigned int compl1, compl2;
double S_max;
struct atom *atoms_dna_P1 = NULL;
struct atom *atoms_dna_P2 = NULL;
// print measure-table
/*printf(" ");
for (j=1; j<=n_P2; j++) printf("%4d", j);
puts("");
for (i=n_P1; i>=1; i--){
printf("%2d", i);
for (j=1; j<=n_P2; j++){
printf("%4.0f", list_measure[i][j]>0 ? list_measure[i][j] : 0);
}
puts("");
}
printf(" ");
for (j=1; j<=n_P2; j++) printf("%4d", j);
puts(""); */
i_max_measure=0;
j_max_measure=0;
atoms_dna_P1 = (struct atom *)malloc( sizeof(struct atom)*(n_P1+1) );
for (i=1; i<=n_P1; i++) {
atomcpy(&atoms_dna_P1[i], atoms_dna1[list_P1[i]]);
}
atoms_dna_P2 = (struct atom *)malloc( sizeof(struct atom)*(n_P2+1) );
for (i=1; i<=n_P2; i++) {
atomcpy(&atoms_dna_P2[i], atoms_dna2[list_P2[i]]);
}
//find_compl(atoms_dna1, list_P1, list_C11, list_OP11, list_OP21, atoms_dna_P1, n_P1, &compl1, &n_first_chain, max_score);
run_find_compl(atoms_dna_P1, n_P1, &compl1, &n_first_chain, compl_pairs1[pair1]);
//find_compl(atoms_dna2, list_P2, list_C12, list_OP12, list_OP22, atoms_dna_P2, n_P2, &compl2, &m_first_chain, max_score);
run_find_compl(atoms_dna_P2, n_P2, &compl2, &m_first_chain, compl_pairs2[pair2]);
BestDiag(list_measure, n_P1, n_P2, &S_max, &i_max, &j_max, &i_start, &j_start, &i_max_measure, &j_max_measure,
atoms_dna1, list_P1, atoms_dna2, list_P2, compl1, compl2, n_first_chain, m_first_chain);
// pdb.c function
/* Done diagonal search */
if (S_max > best_S_max)
{
best_S_max = S_max;
atomlistcpy(&best_dna1_chain1, dna1_chain1, dna1_chain1_n);
best_dna1_chain1_n = dna1_chain1_n;
atomlistcpy(&best_dna1_chain2, dna1_chain2, dna1_chain2_n);
best_dna1_chain2_n = dna1_chain2_n;
atomlistcpy(&best_dna2_chain1, dna2_chain1, dna2_chain1_n);
best_dna2_chain1_n = dna2_chain1_n;
atomlistcpy(&best_dna2_chain2, dna2_chain2, dna2_chain2_n);
best_dna2_chain2_n = dna2_chain2_n;
best_n_P1 = n_P1;
best_n_P2 = n_P2;
atomlistcpy(&best_atoms_dna1, atoms_dna1, m1);
best_list_P1 = (unsigned int *)malloc(sizeof(unsigned int)*(n_P1+1));
best_list_C11 = (unsigned int *)malloc(sizeof(unsigned int)*(n_C11+1));
best_list_OP11 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP11+1));
best_list_OP21 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP21+1));
memcpy(best_list_P1, list_P1, sizeof(unsigned int)*(n_P1+1));
memcpy(best_list_C11, list_C11, sizeof(unsigned int)*(n_C11+1));
memcpy(best_list_OP11, list_OP11, sizeof(unsigned int)*(n_OP11+1));
memcpy(best_list_OP21, list_OP21, sizeof(unsigned int)*(n_OP21+1));
atomlistcpy(&best_atoms_dna2, atoms_dna2, m2);
best_list_P2 = (unsigned int *)malloc(sizeof(unsigned int)*(n_P2+1));
best_list_C12 = (unsigned int *)malloc(sizeof(unsigned int)*(n_C12+1));
best_list_OP12 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP12+1));
best_list_OP22 = (unsigned int *)malloc(sizeof(unsigned int)*(n_OP22+1));
memcpy(best_list_P2, list_P2, sizeof(unsigned int)*(n_P2+1));
memcpy(best_list_C12, list_C12, sizeof(unsigned int)*(n_C12+1));
memcpy(best_list_OP12, list_OP12, sizeof(unsigned int)*(n_OP12+1));
memcpy(best_list_OP22, list_OP22, sizeof(unsigned int)*(n_OP22+1));
best_i_max_measure = i_max_measure;
best_j_max_measure = j_max_measure;
best_compl1 = compl1;
best_compl2 = compl2;
best_n_first_chain = n_first_chain;
best_m_first_chain = m_first_chain;
best_pair1 = pair1;
best_pair2 = pair2;
}
//free array's memory after cycle
/*free(list_P2);
free(list_C12);
free(list_OP12);
free(list_OP22);
free(list_CA2);
free(list_C2);
free(atoms_prot_CA2);
free(atoms_prot_C2);
for (i=1; i<=n_P1; i++) free(list_measure[i]);
free(list_measure);
free(atoms_dna_P1);
free(atoms_dna_P2);
free(atoms_dna2);
free(dna2_chain1);
free(dna2_chain2);
free(atoms_prot_i1);
free(C_atoms_prot_i1);
free(atoms_prot_j2);
free(C_atoms_prot_j2);*/
}
/*free(list_P1);
free(list_C11);
free(list_OP11);
free(list_OP21);
free(list_CA1);
free(list_C1);
free(atoms_prot_CA1);
free(atoms_prot_C1);
free(atoms_dna1);
free(dna1_chain1);
free(dna1_chain2);*/
}
/*** END OF MAIN CYCLE ***/
/****reading DNA sequences ***/
unsigned int dna_n11, dna_n12, dna_n21, dna_n22; //sequence length
char *dna_seq11, *dna_seq12, *dna_seq21, *dna_seq22;
char *dna_num_seq11, *dna_num_seq12, *dna_num_seq21, *dna_num_seq22;
int dna1_chain1_start, dna1_chain2_start, dna2_chain1_start, dna2_chain2_start;
//SelectChain(atoms_dna1, m1, &dna1_chain1, &dna1_chain1_n, dna_chains1[1]);
Seq(best_dna1_chain1, best_dna1_chain1_n, &dna_seq11, &dna_num_seq11, &dna_n11, max_score);
sscanf(best_dna1_chain1[1].ResNumber, "%d", &dna1_chain1_start);
Seq(best_dna1_chain2, best_dna1_chain2_n, &dna_seq12, &dna_num_seq12, &dna_n12, max_score);
sscanf(best_dna1_chain2[1].ResNumber, "%d", &dna1_chain2_start);
Seq(best_dna2_chain1, best_dna2_chain1_n, &dna_seq21, &dna_num_seq21, &dna_n21, max_score);
sscanf(best_dna2_chain1[1].ResNumber, "%d", &dna2_chain1_start);
Seq(best_dna2_chain2, best_dna2_chain2_n, &dna_seq22, &dna_num_seq22, &dna_n22, max_score);
sscanf(best_dna2_chain2[1].ResNumber, "%d", &dna2_chain2_start);
//printf("%c %c %c %c %c %c\n%lg\n%s\n%s", chain1, chain2, dna_chains1[1], dna_chains1[2], dna_chains2[1], dna_chains2[2], S_max, dna_string1, dna_string2);
/*** For server work - DNA alignment making ***/
if (best_S_max == 0)
fprintf(max_score, "Warning! The score is zero! It seems you have specified wrong parameters.\n");
unsigned int i_max_measure_compl, j_max_measure_compl;
unsigned int is_reverse1, is_reverse2;
//printf("n_first_chain=%u i_max_measure=%u best_compl1=%u\n", best_n_first_chain, best_i_max_measure, best_compl1);
is_reverse1 = ((best_i_max_measure > best_n_first_chain) ? 1 : 0);
is_reverse2 = ((best_j_max_measure > best_m_first_chain) ? 1 : 0);
i_max_measure_compl = ((best_i_max_measure > best_n_first_chain) ? best_compl1-best_i_max_measure+1 : best_compl1-best_i_max_measure+1);
j_max_measure_compl = ((best_j_max_measure > best_m_first_chain) ? best_compl2-best_j_max_measure+1 : best_compl2-best_j_max_measure+1);
//printf("i_max_measure=%u i_max_measure_compl=%u\n", best_i_max_measure, i_max_measure_compl);
//printf("i_max_measure=%s\n", best_atoms_dna1[best_list_P1[best_i_max_measure]].ResNumber);
//printf("i_max_measure_compl=%s\n", best_atoms_dna1[best_list_P1[i_max_measure_compl]].ResNumber);
//puts("OK1");
if (i_max_measure_compl > best_n_P1)
{
//printf("i_compl=%u n11=%u n12=%u\n", i_max_measure_compl, dna_n11, dna_n12);
j_max_measure_compl = j_max_measure_compl-(i_max_measure_compl-best_n_P1);
i_max_measure_compl = best_n_P1;
//printf("i_compl=%u n11=%u n12=%u\n", i_max_measure_compl, dna_n11, dna_n12);
}
if (j_max_measure_compl > best_n_P2)
{
//printf("j_compl=%u n21=%u n22=%u\n", j_max_measure_compl, dna_n21, dna_n22);
i_max_measure_compl = i_max_measure_compl-(j_max_measure_compl-best_n_P2);
j_max_measure_compl = best_n_P2;
//printf("j_compl=%u n21=%u n22=%u\n", j_max_measure_compl, dna_n21, dna_n22);
}
//puts("OK2");
//if max_compl = 0 or less
if (i_max_measure_compl < 1)
{
i_max_measure_compl = 1;
j_max_measure_compl = j_max_measure_compl + 1 - i_max_measure_compl;
}
if (j_max_measure_compl < 1)
{
j_max_measure_compl = 1;
i_max_measure_compl = i_max_measure_compl + 1 - j_max_measure_compl;
}
//puts("OK3");
int i_max_measure_compl_num, j_max_measure_compl_num;
char *i_max_measure_compl_str, *j_max_measure_compl_str;
i_max_measure_compl_str = (char *)malloc( sizeof(char)*7 );
j_max_measure_compl_str = (char *)malloc( sizeof(char)*7 );
sscanf(best_atoms_dna1[best_list_P1[i_max_measure_compl]].ResNumber, "%d", &i_max_measure_compl_num);
sscanf(best_atoms_dna2[best_list_P2[j_max_measure_compl]].ResNumber, "%d", &j_max_measure_compl_num);
if (i_max_measure_compl==best_i_max_measure)
{
sscanf(best_atoms_dna1[best_list_P1[i_max_measure_compl+1]].ResNumber, "%d", &i_max_measure_compl_num);
i_max_measure_compl_num = i_max_measure_compl_num - 1;
//puts("Here1");
}
if (j_max_measure_compl==best_j_max_measure)
{
sscanf(best_atoms_dna2[best_list_P2[j_max_measure_compl+1]].ResNumber, "%d", &j_max_measure_compl_num);
j_max_measure_compl_num = j_max_measure_compl_num - 1;
//puts("Here2");
}
//printf("%d\n", j_max_measure_compl_num);
//puts("OK4");
int start, i_start;
start = (is_reverse1 == 1) ? dna1_chain1_start : dna1_chain2_start;
i_start = (is_reverse1 == 1) ? 1 : dna_n11+1;
if (i_max_measure_compl_num < start && i_max_measure_compl < i_start)
{
//printf("ires_compl=%d start=%d\n", i_max_measure_compl_num, start);
j_max_measure_compl_num = j_max_measure_compl_num + start - i_max_measure_compl_num;
i_max_measure_compl_num = start;
//printf("ires_compl=%d start=%d\n", i_max_measure_compl_num, start);
}
start = (is_reverse2 == 1) ? dna2_chain1_start : dna2_chain2_start;
i_start = (is_reverse2 == 1) ? 1 : dna_n21+1;
if (j_max_measure_compl_num < start && j_max_measure_compl < i_start)
{
//printf("jres_compl=%d start=%d\n", j_max_measure_compl_num, start);
i_max_measure_compl = i_max_measure_compl_num + start - j_max_measure_compl_num;
j_max_measure_compl = start;
//printf("jres_compl=%d start=%d\n", j_max_measure_compl_num, start);
}
//printf("%d\n", j_max_measure_compl_num);
sprintf(i_max_measure_compl_str, "%d", i_max_measure_compl_num);
sprintf(j_max_measure_compl_str, "%d", j_max_measure_compl_num);
//printf("%d\n", j_max_measure_compl_num);
//puts("OK5");
fprintf(max_score, "%c %c %c %c %c %c %s %s %s %s %u %u\n%lg\n%s %s\n%s %s\n%s %s\n%s %s", chain1, chain2, pairs1[best_pair1][1], pairs1[best_pair1][2], pairs2[best_pair2][1], pairs2[best_pair2][2], best_atoms_dna1[best_list_P1[best_i_max_measure]].ResNumber, best_atoms_dna2[best_list_P2[best_j_max_measure]].ResNumber, i_max_measure_compl_str, j_max_measure_compl_str, is_reverse1, is_reverse2, best_S_max, dna_seq11, dna_num_seq11, dna_seq12, dna_num_seq12, dna_seq21, dna_num_seq21, dna_seq22, dna_num_seq22);
fclose(max_score);
struct atom *atoms_dna_i1 = NULL;
struct atom *atoms_dna_i2 = NULL;
struct atom *atoms_dna_j1 = NULL;
struct atom *atoms_dna_j2 = NULL;
/* Change the system to i and j coordinates, write the alignment to file */
ChangeSystem(atoms_prot1, n1, &atoms_prot_i1, best_atoms_dna1[best_list_P1[best_i_max_measure]], best_atoms_dna1[best_list_C11[best_i_max_measure+1]], best_atoms_dna1[best_list_OP11[best_i_max_measure]], best_atoms_dna1[best_list_OP21[best_i_max_measure]], 'E');
// Note that names of chains will be changed to 'E' and 'F' by default! Modify if required.
ChangeSystem(atoms_prot2, n2, &atoms_prot_j2, best_atoms_dna2[best_list_P2[best_j_max_measure]], best_atoms_dna2[best_list_C12[best_j_max_measure+1]], best_atoms_dna2[best_list_OP12[best_j_max_measure]], best_atoms_dna2[best_list_OP22[best_j_max_measure]], 'F');
ChangeSystem(best_dna1_chain1, best_dna1_chain1_n, &atoms_dna_i1, best_atoms_dna1[best_list_P1[best_i_max_measure]], best_atoms_dna1[best_list_C11[best_i_max_measure+1]], best_atoms_dna1[best_list_OP11[best_i_max_measure]], best_atoms_dna1[best_list_OP21[best_i_max_measure]], 'A');
ChangeSystem(best_dna1_chain2, best_dna1_chain2_n, &atoms_dna_i2, best_atoms_dna1[best_list_P1[best_i_max_measure]], best_atoms_dna1[best_list_C11[best_i_max_measure+1]], best_atoms_dna1[best_list_OP11[best_i_max_measure]], best_atoms_dna1[best_list_OP21[best_i_max_measure]], 'B');
ChangeSystem(best_dna2_chain1, best_dna2_chain1_n, &atoms_dna_j1, best_atoms_dna2[best_list_P2[best_j_max_measure]], best_atoms_dna2[best_list_C12[best_j_max_measure+1]], best_atoms_dna2[best_list_OP12[best_j_max_measure]], best_atoms_dna2[best_list_OP22[best_j_max_measure]], 'C');
ChangeSystem(best_dna2_chain2, best_dna2_chain2_n, &atoms_dna_j2, best_atoms_dna2[best_list_P2[best_j_max_measure]], best_atoms_dna2[best_list_C12[best_j_max_measure+1]], best_atoms_dna2[best_list_OP12[best_j_max_measure]], best_atoms_dna2[best_list_OP22[best_j_max_measure]], 'D');
//puts("\nFix 'nan' in pdb with this data:");
createPDB(outfile, outfile);
// pdb.c function
writetoPDB(outfile, atoms_dna_i1, best_dna1_chain1_n);
writetoPDB(outfile, atoms_dna_i2, best_dna1_chain2_n);
writetoPDB(outfile,
atoms_prot_i1, n1);
// pdb.c function. Write protein atoms to outfile
writetoPDB(outfile,
atoms_prot_j2, n2);
writetoPDB(outfile, atoms_dna_j1, best_dna2_chain1_n);
writetoPDB(outfile, atoms_dna_j2, best_dna2_chain2_n);
endPDB(outfile);
return 0;
}