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diff --git a/output.dat b/AAoutput.dat
similarity index 100%
rename from output.dat
rename to AAoutput.dat
diff --git a/CommonRoutines.H b/CommonRoutines.H
index c56b53b..6b12f5d 100644
--- a/CommonRoutines.H
+++ b/CommonRoutines.H
@@ -53,9 +53,9 @@ bool getDoubleFromString(double &retVal, string s,
bool getDouble(double &retVal, double defaultValue);
-bool getInt(int &retVal, int defaultValue);
+bool getInt(long int &retVal, int defaultValue);
-bool getIntFromString(int &retVal, string s, int lowBounds, int hiBounds);
+bool getIntFromString(long int &retVal, string s, int lowBounds, long int hiBounds);
int getIntInput(string prompt, int defaultVal, int lowBounds, int hiBounds);
@@ -78,7 +78,7 @@ bool fileExists(string fn);
void getValidDoubleTokens (double &retVal, ifstream &ifs, double low,
double hi, string validLabel, int errorCode);
-void getValidIntTokens (int &retVal, ifstream &ifs, int low,
+void getValidIntTokens (long int &retVal, ifstream &ifs, int low,
int hi, string validLabel, int errorCode);
void getValidCharTokens (string &retVal, ifstream &ifs,
@@ -103,5 +103,3 @@ int findAAindex(char ch);
//===========================================================================
//======================= END OF CommonRoutines.H ========================
//===========================================================================
-
-
diff --git a/CommonRoutines.cpp b/CommonRoutines.cpp
index 306280f..410172e 100644
--- a/CommonRoutines.cpp
+++ b/CommonRoutines.cpp
@@ -35,9 +35,11 @@
#include <iostream>
#include <fstream>
#include <vector>
+#include <cstring>
#include "CommonRoutines.H"
using namespace std;
+const long int HI_BOUND = 1000000000000000001;
//---------------------------------------------------------------------------
bool isNum(char ch) {
@@ -85,7 +87,7 @@ bool getDoubleFromString(double &retVal, string s,
lhTok = strtok((char *)s.c_str(), ".");
rhTok = strtok(NULL, "\n");
- int lhs, rhs;
+ long int lhs, rhs;
if(rhTok == NULL) {
if(getIntFromString(lhs, lhTok, -1, 101)) {
retVal = (double) lhs;
@@ -96,8 +98,10 @@ bool getDoubleFromString(double &retVal, string s,
}
}
+ // cout << "rhTok: " << rhTok << endl;
+ // cout << "getIntFromString: " << getIntFromString(rhs, rhTok, -1, HI_BOUND) << endl;
if(getIntFromString(lhs, lhTok, -1, 101) &&
- getIntFromString(rhs, rhTok, -1, 10001)) {
+ getIntFromString(rhs, rhTok, -1, HI_BOUND)) {
// rhs should be divided accordingly
int divisor = 1;
@@ -118,7 +122,7 @@ bool getDoubleFromString(double &retVal, string s,
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
-bool getIntFromString(int &retVal, string s, int lowBounds, int hiBounds) {
+bool getIntFromString(long int &retVal, string s, int lowBounds, long int hiBounds) {
//**********************************************************************
// PRE : defaultValue has been set
@@ -139,10 +143,16 @@ bool getIntFromString(int &retVal, string s, int lowBounds, int hiBounds) {
if(!isNum(currCh))
return(false);
else {
- int currMult = (int)pow(10,len-i-1);
- retVal += currMult * ((int)currCh - 48);
+ long int currMult = (long int)pow(10,len-i-1);
+ retVal += currMult * ((long int)currCh - 48);
}
}
+
+ // Debugging purpose
+ // cout << "retVal: " << retVal << endl;
+ // cout << "lowBounds: " << lowBounds << endl;
+ // cout << "hiBounds: " << hiBounds << endl;
+ // cout << "(retVal > lowBounds) && (retVal < hiBounds): " << ((retVal > lowBounds) && (retVal < hiBounds)) << endl;
if((retVal > lowBounds) && (retVal < hiBounds))
return(true);
else
@@ -196,7 +206,7 @@ bool getDouble(double &retVal, double defaultValue) {
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
-bool getInt(int &retVal, int defaultValue) {
+bool getInt(long int &retVal, int defaultValue) {
//**********************************************************************
// PRE : defaultValue has been set
@@ -377,7 +387,7 @@ void getValidDoubleTokens (double &retVal, ifstream &ifs, double low,
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
-void getValidIntTokens (int &retVal, ifstream &ifs, int low,
+void getValidIntTokens (long int &retVal, ifstream &ifs, int low,
int hi, string validLabel, int errorCode) {
//**********************************************************************
@@ -449,7 +459,7 @@ int getIntInput(string prompt, int defaultVal, int lowBounds, int hiBounds) {
//**********************************************************************
bool finished = false;
- int retVal;
+ long int retVal;
while(!finished) {
cout << prompt;
@@ -688,5 +698,3 @@ int findAAindex(char ch) {
//===========================================================================
//===================== END OF CommonRoutines.cpp ==========================
//===========================================================================
-
-
diff --git a/Makefile b/Makefile
index c49a584..cf08cc7 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
COMPILER = g++
-CCFLAGS = -g
+CCFLAGS = -g -fpermissive
rMotifGen: RandomMotifs.cpp SequenceClass.o CommonRoutines.o SubstitutionMatrices.o PSSM.o
${COMPILER} ${CCFLAGS} -o rMotifGen RandomMotifs.cpp SequenceClass.o CommonRoutines.o SubstitutionMatrices.o PSSM.o
diff --git a/PSSM.cpp b/PSSM.cpp
index 7ec0e8e..f29f966 100644
--- a/PSSM.cpp
+++ b/PSSM.cpp
@@ -112,6 +112,7 @@ void PSSM::checkForValidPSSM() {
else {
if(!checkColOrientation()) {
if(!checkRowOrientation()) {
+ cerr << "Invalid orientation" << endl;
errorVal = 29; // INCORRECTLY FORMATTED PSSM FILE
return;
}
@@ -205,6 +206,7 @@ bool PSSM::checkColOrientation() {
double tmpD;
ss >> tmpS;
if(!getDoubleFromString(tmpD, tmpS, 0.0, 10000.0)) {
+ cerr << "Invalid string reading in col orientation" << endl;
errorVal = 29;
return(false);
}
@@ -286,6 +288,7 @@ bool PSSM::checkRowOrientation() {
// MAKE SURE EACH COLUMN IS A POSITIVE DOUBLE VALUE
if(!getDoubleFromString(tmpD, tmpS, 0.0, 10000.0)) {
+ cerr << "Invalid string reading in row orientation" << endl;
errorVal = 29;
return(false);
}
diff --git a/README b/README
index 18502c2..ba0164f 100644
--- a/README
+++ b/README
@@ -107,6 +107,7 @@ RUNNING rMotifGen
motif<X>Type= // Where X=1..numMotifs -- the value can
// be 'U' for user defined, 'R' for random
// or 'P' for PSSM
+ motif<X>PSSMFILE= // PSSM filename if motif<X>Type=P
motif<X>Seq= // Only Valid if Type = 'U' -- consensus motif
motif<X>PctSeqsContain= // Percentage of sequences that contain this
// motif
diff --git a/RandomMotifs.cpp b/RandomMotifs.cpp
index 9d66902..5e59a90 100644
--- a/RandomMotifs.cpp
+++ b/RandomMotifs.cpp
@@ -505,7 +505,7 @@ void getRandomMotifInfo(ifstream &infile, char *&motif_createTypeArr,
string motifLabel = setMotifLabel(i);
string currLabel = motifLabel + "Len";
- int tmpint;
+ long int tmpint;
if(infile.eof()) { exit(26); }
getValidIntTokens(tmpint, infile, 0, 101, currLabel, 18);
motif_lenArr[i] = tmpint;
@@ -580,7 +580,7 @@ void getPAMValue(PAM **&motif_PAMArr, ifstream &infile,
//**********************************************************************
string currLabel = motifLabel + "PAM";
- int pamVal;
+ long int pamVal;
if(infile.eof()) { exit(26); }
getValidIntTokens(pamVal, infile, -1, 501, currLabel, 17);
motif_PAMArr[i] = new PAM(pamVal);
@@ -601,9 +601,9 @@ void fileMode(string FN, char seqType){
double *ResiduePcts;
char *ResidueLabels;
- int seqLen;
- int numMotifs;
- int numSeqs;
+ long int seqLen;
+ long int numMotifs;
+ long int numSeqs;
bool finished;
char *motif_createTypeArr;
bool *motif_isPalindromicArr;
@@ -675,7 +675,7 @@ void fileMode(string FN, char seqType){
}
motif_PSSMArr[i] = currPSSM;
currLabel = motifLabel + "PctSeqsContain";
- int tmpint;
+ long int tmpint;
if(infile.eof()) { exit(26); }
getValidIntTokens(tmpint, infile, -1, 101, currLabel, 16);
motif_pctSeqConsArr[i] = tmpint;
@@ -872,7 +872,3 @@ int main(int argc, char *argv[]) {
//============================================================================
//--------------------------- END OF RandomMotifs.cpp ------------------------
//============================================================================
-
-
-
-
diff --git a/SequenceClass.cpp b/SequenceClass.cpp
index 45c121f..92035c1 100644
--- a/SequenceClass.cpp
+++ b/SequenceClass.cpp
@@ -144,7 +144,7 @@ string SequenceClass::randomPSSMSeq(PSSM *P) {
}
}
if(!nextFound) {
- s+= P->residueArr[P->totRows - 1];
+ s+= P->residueArr[P->totCols - 1];
}
}
return(s);
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