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fixed most of the clang warnings
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@anishp
anishp committed Apr 8, 2016
1 parent d56a5d6 commit 77bc311
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Showing 37 changed files with 1,159 additions and 1,162 deletions.
43 changes: 21 additions & 22 deletions include/inchi/aux2atom.h
View file
Expand Up @@ -405,7 +405,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
if ( *p ) {
/* has label name */
/*p ++;*/
if ( q = strchr( p, '=' ) ) {
if ( (q = strchr( p, '=' )) ) {
/* '=' separates label name from the value */
len = inchi_min( q-p+1, MAX_SDF_HEADER-1);
if ( pSdfLabel ) {
Expand All @@ -423,7 +423,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
}

} else
if ( q = strstr( p, sStructHdrPlnNoLblVal ) ) {
if ( (q = strstr( p, sStructHdrPlnNoLblVal )) ) {
len = inchi_min( q-p+1, MAX_SDF_HEADER-1);
if ( pSdfLabel ) {
mystrncpy( pSdfLabel, p, len );
Expand Down Expand Up @@ -626,7 +626,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
}
i ++;
}
if ( !bItemIsOver || i != num_atoms || s && p != s ) {
if ( !bItemIsOver || i != num_atoms || (s && p != s) ) {
num_atoms = INCHI_INP_ERROR_RET; /* error */
*err = INCHI_INP_ERROR_ERR;
MOLFILE_ERR_SET (*err, 0, "Wrong number of atoms");
Expand Down Expand Up @@ -658,7 +658,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
while ( i < num_atoms ) {
p = LoadLine( inp_molfile, &bTooLongLine, &bItemIsOver, &s,
szLine, sizeof(szLine), INCHI_LINE_ADD, p, &res );
if ( i >= num_atoms || s && p >= s ) {
if ( i >= num_atoms || (s && p >= s) ) {
break; /* end of bonds (plain) */
}
/* bond, first char */
Expand Down Expand Up @@ -831,7 +831,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
len_stereo0D ++;
}
}
if ( !bItemIsOver || i != num_atoms || s && p != s ) {
if ( !bItemIsOver || i != num_atoms || (s && p != s) ) {
num_atoms = INCHI_INP_ERROR_RET; /* error */
*err = INCHI_INP_ERROR_ERR;
MOLFILE_ERR_SET (*err, 0, "Wrong number of bonds");
Expand All @@ -852,7 +852,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
goto bypass_end_of_INChI_plain;
} else {
/* coordinates block started */
if ( pszCoord = (MOL_COORD*) inchi_malloc(inchi_max(num_atoms,1) * sizeof(MOL_COORD)) ) {
if ( (pszCoord = (MOL_COORD*) inchi_malloc(inchi_max(num_atoms,1) * sizeof(MOL_COORD))) ) {
memset( pszCoord, ' ', inchi_max(num_atoms,1) * sizeof(MOL_COORD));
} else {
num_atoms = INCHI_INP_FATAL_RET; /* allocation error */
Expand All @@ -866,7 +866,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
while ( i < num_atoms ) {
p = LoadLine( inp_molfile, &bTooLongLine, &bItemIsOver, &s,
szLine, sizeof(szLine), INCHI_LINE_ADD, p, &res );
if ( i >= num_atoms || s && p >= s ) {
if ( i >= num_atoms || (s && p >= s) ) {
break; /* end of bonds (plain) */
}

Expand Down Expand Up @@ -928,7 +928,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
goto bypass_end_of_INChI_plain;
}
}
if ( !bItemIsOver || s && p != s || i != num_atoms ) {
if ( !bItemIsOver || (s && p != s) || i != num_atoms ) {
num_atoms = INCHI_INP_ERROR_RET; /* error */
*err = INCHI_INP_ERROR_ERR;
MOLFILE_ERR_SET (*err, 0, "Wrong number of coordinates");
Expand Down Expand Up @@ -1357,7 +1357,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
longID = 0;
num_atoms = 0;
/* structure number */
if ( q = strstr( p, sStructHdrXmlNumber ) ) {
if ( (q = strstr( p, sStructHdrXmlNumber )) ) {
p = q + sizeof(sStructHdrXmlNumber)-1;
longID = strtol( p, &q, 10);
if ( q && *q == '\"' )
Expand All @@ -1370,7 +1370,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
pSdfValue[0] = '\0';
}
/* pSdfLabel */
if ( q = strstr( p, sStructHdrXmlIdName ) ) {
if ( (q = strstr( p, sStructHdrXmlIdName )) ) {
p = q + sizeof(sStructHdrXmlIdName)-1;
q = strchr( p, '\"' );
if ( q ) {
Expand All @@ -1382,7 +1382,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
}
}
/* pSdfValue */
if ( q = strstr( p, sStructHdrXmlIdValue ) ) {
if ( (q = strstr( p, sStructHdrXmlIdValue )) ) {
p = q + sizeof(sStructHdrXmlIdValue)-1;
q = strchr( p, '\"' );
if ( q ) {
Expand All @@ -1398,8 +1398,8 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
bHeaderRead = 1;
bErrorMsg = bRestoreInfo = 0;
} else
if ( bHeaderRead && (bFatal=0, len=sizeof(sStructMsgXmlErr)-1, !memcmp(szLine, sStructMsgXmlErr, len)) ||
bHeaderRead && (len=sizeof(sStructMsgXmlErrFatal)-1, !memcmp(szLine, sStructMsgXmlErrFatal, len))&&(bFatal=1)) {
if ( (bHeaderRead && (bFatal=0, len=sizeof(sStructMsgXmlErr)-1, !memcmp(szLine, sStructMsgXmlErr, len))) ||
(bHeaderRead && (len=sizeof(sStructMsgXmlErrFatal)-1, !memcmp(szLine, sStructMsgXmlErrFatal, len))&&(bFatal=1))) {
p = szLine+len;
q = strchr( p, '\"' );
if ( q && !bFindNext ) {
Expand Down Expand Up @@ -1854,7 +1854,7 @@ int INChITo_Atom(INCHI_IOSTREAM *inp_molfile, MOL_COORD **szCoord,
goto bypass_end_of_INChI;
}
/********************** coordinates xml ****************************/
if ( pszCoord = (MOL_COORD*) inchi_malloc(inchi_max(num_atoms,1) * sizeof(MOL_COORD)) ) {
if ( (pszCoord = (MOL_COORD*) inchi_malloc(inchi_max(num_atoms,1) * sizeof(MOL_COORD))) ) {
memset( pszCoord, ' ', inchi_max(num_atoms,1) * sizeof(MOL_COORD));
res = inchi_ios_gets( szLine, sizeof(szLine)-1, inp_molfile, &bTooLongLine );
if ( res <= 0 ||
Expand Down Expand Up @@ -2552,8 +2552,8 @@ int Extract0DParities( inp_ATOM *at, int nNumAtoms, inchi_Stereo0D *stereo0D,
parity = (stereo0D[i0D].parity & SB_PARITY_MASK);
parityNM = (stereo0D[i0D].parity & SB_PARITY_FLAG) >> SB_PARITY_SHFT;
if ( parity == INCHI_PARITY_NONE ||
parity != INCHI_PARITY_ODD && parity != INCHI_PARITY_EVEN &&
parity != INCHI_PARITY_UNKNOWN && parity != INCHI_PARITY_UNDEFINED ) {
(parity != INCHI_PARITY_ODD && parity != INCHI_PARITY_EVEN &&
parity != INCHI_PARITY_UNKNOWN && parity != INCHI_PARITY_UNDEFINED) ) {
char szTemp[16];
sprintf( szTemp, "#%d", i0D+1 );
MOLFILE_ERR_SET (*err, 0, "Wrong 0D stereo descriptor(s):");
Expand All @@ -2567,11 +2567,11 @@ int Extract0DParities( inp_ATOM *at, int nNumAtoms, inchi_Stereo0D *stereo0D,
sb_ord_from_i1 = sb_ord_from_i2 = sn_ord_from_i1 = sn_ord_from_i2 = -1;
i1n = i2n = i1 = i2 = MAX_ATOMS+1;

if ( (type == INCHI_StereoType_Tetrahedral ||
if ( ((type == INCHI_StereoType_Tetrahedral ||
type == INCHI_StereoType_Allene ) &&
0 <= a2 && a2 < nNumAtoms ||
type == INCHI_StereoType_DoubleBond &&
a2 == NO_ATOM) {
0 <= a2 && a2 < nNumAtoms) ||
(type == INCHI_StereoType_DoubleBond &&
a2 == NO_ATOM)) {
/* test the quadruplet */
for ( j = 0, k_prev = -1; j < 4; j ++, k_prev = k ) {
k = stereo0D[i0D].neighbor[j];
Expand Down Expand Up @@ -2774,7 +2774,7 @@ int Extract0DParities( inp_ATOM *at, int nNumAtoms, inchi_Stereo0D *stereo0D,

#ifdef TARGET_API_LIB

if ( k = ReconcileAllCmlBondParities( at, nNumAtoms, 0 ) ) {
if ( (k = ReconcileAllCmlBondParities( at, nNumAtoms, 0 )) ) {
char szErrCode[16];
sprintf( szErrCode, "%d", k);
AddMOLfileError( pStrErr, "0D Parities Reconciliation failed:" );
Expand All @@ -2788,4 +2788,3 @@ int Extract0DParities( inp_ATOM *at, int nNumAtoms, inchi_Stereo0D *stereo0D,
}

#endif

6 changes: 3 additions & 3 deletions include/inchi/ichiparm.h
View file
Expand Up @@ -736,7 +736,7 @@ int ReadCommandLineParms(int argc, const char *argv[], INPUT_PARMS *ip,
k ++;
}
t = strtod( pArg+k+1, (char**)&q ); /* cast deliberately discards 'const' qualifier */
if ( q > pArg+k+1 && errno == ERANGE || t < 0.0 || t*1000.0 > (double)ULONG_MAX)
if ( (q > pArg+k+1 && errno == ERANGE) || t < 0.0 || t*1000.0 > (double)ULONG_MAX)
{
ul = 0;
}
Expand Down Expand Up @@ -1410,7 +1410,7 @@ int ReadCommandLineParms(int argc, const char *argv[], INPUT_PARMS *ip,
char *sz;
if ( argv[i] && argv[i][0] )
{
if ( sz = (char*) inchi_malloc( (strlen(argv[i]) + 1)*sizeof(sz[0])) )
if ( (sz = (char*) inchi_malloc( (strlen(argv[i]) + 1)*sizeof(sz[0]))) )
{
strcpy( sz, argv[i] );
}
Expand Down Expand Up @@ -1500,7 +1500,7 @@ int ReadCommandLineParms(int argc, const char *argv[], INPUT_PARMS *ip,
if ( !ip->path[i] || !ip->path[i][0] )
{
len = strlen( p ) + strlen(szNameSuffix) + strlen( ext[i] );
if ( sz = (char*) inchi_malloc( (len+1)*sizeof(sz[0]) ) )
if ( (sz = (char*) inchi_malloc( (len+1)*sizeof(sz[0]) )) )
{
strcpy( sz, p );
strcat( sz, szNameSuffix );
Expand Down
11 changes: 5 additions & 6 deletions src/formats/chemdrawcdx.cpp
View file
Expand Up @@ -299,7 +299,7 @@ bool ChemDrawBinaryXFormat::TopLevelParse

else if(ok && tag==kCDXObj_Graphic)
{
while(tag = cdxr.ReadNext())
while( (tag = cdxr.ReadNext()) )
{
stringstream& ss = cdxr.data();
if(tag == kCDXProp_Arrow_Type)
Expand All @@ -323,7 +323,7 @@ bool ChemDrawBinaryXFormat::DoReaction(CDXReader& cdxr, OBReaction* pReact)
{
CDXTag tag;
CDXObjectID id;
while(tag = cdxr.ReadNext())
while( (tag = cdxr.ReadNext()) )
{
if(tag == kCDXProp_ReactionStep_Reactants)
{
Expand Down Expand Up @@ -457,7 +457,7 @@ bool ChemDrawBinaryXFormat::DoFragmentImpl(CDXReader& cdxr, OBMol* pmol,
string aliastext;

//Read all node properties
while(tag = cdxr.ReadNext())
while( (tag = cdxr.ReadNext()) )
{
switch(tag)
{
Expand Down Expand Up @@ -550,7 +550,7 @@ bool ChemDrawBinaryXFormat::DoFragmentImpl(CDXReader& cdxr, OBMol* pmol,
int order=1, bgnIdx, endIdx ;
UINT16 stereo=0;

while(tag = cdxr.ReadNext())
while( (tag = cdxr.ReadNext()) )
{
switch(tag)
{
Expand Down Expand Up @@ -613,7 +613,7 @@ string ChemDrawBinaryXFormat::DoText(CDXReader& cdxr)
{
CDXTag tag;
string text;
while(tag=cdxr.ReadNext())
while( (tag=cdxr.ReadNext()) )
{
stringstream& ss = cdxr.data();
switch(tag)
Expand Down Expand Up @@ -833,4 +833,3 @@ string CDXReader::TagName(map<CDXTag, string>& enummap, CDXTag tag)
}

} //namespace

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