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ghulsghuls
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Fix whitespaces issues in the code.
 - Replace 4 spaces with 1 TAB, so code does align properly. - Remove trailing spaces and TABs. - Replace lines which consist of only whitespaces with an empty line.
1 parent b70d16e commit 516e5ec

22 files changed

+349
-349
lines changed

‎formatMotifs.pl‎

Lines changed: 72 additions & 72 deletions
Large diffs are not rendered by default.

‎src/Alignment.cpp‎

Lines changed: 61 additions & 61 deletions
Large diffs are not rendered by default.

‎src/Alignment.h‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,7 @@ struct AlignMatCell{
5555

5656
//Alignment record
5757
class AlignRec{
58-
private:
58+
private:
5959
int alignL;
6060
int numAligned;
6161
public:
@@ -94,7 +94,7 @@ class AlignRec{
9494

9595
//Alignment record
9696
class MultiAlignRec{
97-
private:
97+
private:
9898
int alignL;
9999
int numAligned;
100100
public:
@@ -122,8 +122,8 @@ class MultiAlignRec{
122122
};
123123

124124
//Alignment method
125-
class Alignment
126-
{
125+
class Alignment
126+
{
127127
protected:
128128
double gapOpen;
129129
double gapExtend;
@@ -164,9 +164,9 @@ class Alignment
164164
//Trim edges of a motif
165165
Motif* TrimEdges(Motif* in, int &start_offset, int &stop_offset, int minLen=IC_win_len, bool allowExclusive=false);
166166

167-
//Destructor
167+
//Destructor
168168
virtual ~Alignment(){for(int i=0; i<2; i++){delete alignSection[i];delete alignSectionTmp[i];} delete alignSection;delete alignSectionTmp;};
169-
169+
170170
};
171171

172172

‎src/ColumnComp.cpp‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ double PearsonCorrelation::Compare(Motif* M_A, int colA, Motif* M_B, int colB)
4646
double sum_diff1_sq=0, sum_diff2_sq=0;
4747
double score=0;
4848
double mean1=0, mean2=0;
49-
49+
5050
//Calc means
5151
for(i=0; i<B; i++) {
5252
mean1+=M_A->f[colA][i];
@@ -66,7 +66,7 @@ double PearsonCorrelation::Compare(Motif* M_A, int colA, Motif* M_B, int colB)
6666
diff2 = M_B->f[colB][i]-mean2;
6767

6868
num += diff1*diff2;
69-
69+
7070
sum_diff1_sq += (diff1*diff1);
7171
sum_diff2_sq += (diff2*diff2);
7272
}
@@ -89,7 +89,7 @@ double ALLR::Compare(Motif* M_A, int colA, Motif* M_B, int colB)
8989
LLR1 += (M_B->n[colB][i] * M_A->pwm[colA][i]);
9090
LLR2 += (M_A->n[colA][i] * M_B->pwm[colB][i]);
9191
}
92-
92+
9393
if(denom==0)
9494
return(min);
9595
else{
@@ -107,7 +107,7 @@ double ALLR_LL::Compare(Motif* M_A, int colA, Motif* M_B, int colB)
107107
LLR1 += (M_B->n[colB][i] * M_A->pwm[colA][i]);
108108
LLR2 += (M_A->n[colA][i] * M_B->pwm[colB][i]);
109109
}
110-
110+
111111
if(denom==0)
112112
return(min);
113113
else{
@@ -138,7 +138,7 @@ double ChiSq::Compare(Motif* M_A, int colA, Motif* M_B, int colB)
138138
CS2+=((M_B->n[colB][i]+1-exp2)*(M_B->n[colB][i]+1-exp2))/exp2;
139139
}
140140
x = (CS1+CS2);
141-
141+
142142
return(1-gsl_cdf_chisq_P(x, 3));
143143
}
144144

@@ -159,7 +159,7 @@ double KullbackLieber::Compare(Motif* M_A, int colA, Motif* M_B, int colB)
159159
{
160160
int i;
161161
double KL1=0, KL2=0;
162-
162+
163163
for(i=0; i<B; i++){
164164
if(M_A->f[colA][i]==0 || M_B->f[colB][i]==0){}
165165
else{

‎src/ColumnComp.h‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
#include "Motif.h"
3737

3838
class ColumnComp{
39-
protected:
39+
protected:
4040
double max;
4141
double min;
4242
double expected;
@@ -48,7 +48,7 @@ class ColumnComp{
4848
//Accessors
4949
double GetMax(){return max;}
5050
double GetMin(){return min;}
51-
51+
5252
//Actual comparison method
5353
virtual double Compare(Motif* M_A, int colA, Motif* M_B, int colB)=0;
5454

@@ -73,7 +73,7 @@ class ALLR : public ColumnComp
7373
public:
7474
//Constructor
7575
ALLR():ColumnComp(){max=2; min=-15; expected=0; /*max, min & expected unknown*/};
76-
76+
7777
//ALLR compare
7878
double Compare(Motif* M_A, int colA, Motif* M_B, int colB);
7979
};
@@ -84,18 +84,18 @@ class ALLR_LL : public ColumnComp
8484
public:
8585
//Constructor
8686
ALLR_LL():ColumnComp(){max=2; min=-2; expected=0; /*max, min & expected unknown*/};
87-
87+
8888
//ALLR compare
8989
double Compare(Motif* M_A, int colA, Motif* M_B, int colB);
9090
};
9191

92-
//Pearson's Chi-squared
92+
//Pearson's Chi-squared
9393
class ChiSq : public ColumnComp
9494
{
9595
public:
9696
//Constructor
9797
ChiSq():ColumnComp(){max=1; min=0; expected=0; /*max, min & expected unknown*/};
98-
98+
9999
//ALLR compare
100100
double Compare(Motif* M_A, int colA, Motif* M_B, int colB);
101101
};
@@ -107,7 +107,7 @@ class SumSqDiff : public ColumnComp
107107
public:
108108
//Constructor
109109
SumSqDiff():ColumnComp(){max=2; min=0; expected=0; /*max, min & expected unknown*/};
110-
110+
111111
//ALLR compare
112112
double Compare(Motif* M_A, int colA, Motif* M_B, int colB);
113113
};
@@ -118,7 +118,7 @@ class KullbackLieber : public ColumnComp
118118
public:
119119
//Constructor
120120
KullbackLieber():ColumnComp(){max=12; min=0; expected=0; /*max, min & expected unknown*/};
121-
121+
122122
//ALLR compare
123123
double Compare(Motif* M_A, int colA, Motif* M_B, int colB);
124124
};

‎src/Motif.cpp‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -80,7 +80,7 @@ void Motif::Reset()
8080
for(i=0; i<len; i++)
8181
for(j=0; j<B; j++)
8282
pwm[i][j]=0;
83-
83+
8484
for(i=0; i<len; i++)
8585
gaps[i]=0;
8686
members=1;
@@ -96,7 +96,7 @@ void Motif::RevCompMotif(Motif* out)
9696
out->members = members;
9797
for(int i=0; i<len; i++)
9898
{
99-
out->f[(len-i)-1][0] = f[i][3]; out->n[(len-i)-1][0] = n[i][3]; out->pwm[(len-i)-1][0] = pwm[i][3];
99+
out->f[(len-i)-1][0] = f[i][3]; out->n[(len-i)-1][0] = n[i][3]; out->pwm[(len-i)-1][0] = pwm[i][3];
100100
out->f[(len-i)-1][3] = f[i][0]; out->n[(len-i)-1][3] = n[i][0]; out->pwm[(len-i)-1][3] = pwm[i][0];
101101
out->f[(len-i)-1][1] = f[i][2]; out->n[(len-i)-1][1] = n[i][2]; out->pwm[(len-i)-1][1] = pwm[i][2];
102102
out->f[(len-i)-1][2] = f[i][1]; out->n[(len-i)-1][2] = n[i][1]; out->pwm[(len-i)-1][2] = pwm[i][1];
@@ -113,10 +113,10 @@ void Motif::RevCompColumn(int i)
113113
{
114114
double tmp_f, tmp_n, tmp_pwm;
115115
tmp_f=f[i][0]; tmp_n=n[i][0]; tmp_pwm=pwm[i][0];
116-
f[i][0] = f[i][3]; n[i][0] = n[i][3]; pwm[i][0] = pwm[i][3];
116+
f[i][0] = f[i][3]; n[i][0] = n[i][3]; pwm[i][0] = pwm[i][3];
117117
f[i][3]=tmp_f; n[i][3]=tmp_n; pwm[i][3]=tmp_pwm;
118118
tmp_f=f[i][1]; tmp_n=n[i][1]; tmp_pwm=pwm[i][1];
119-
f[i][1] = f[i][2]; n[i][1] = n[i][2]; pwm[i][1] = pwm[i][2];
119+
f[i][1] = f[i][2]; n[i][1] = n[i][2]; pwm[i][1] = pwm[i][2];
120120
f[i][2]=tmp_f; n[i][2]=tmp_n; pwm[i][2]=tmp_pwm;
121121
}
122122
//Clone a motif
@@ -153,7 +153,7 @@ char Motif::ColConsensus(int i)
153153
two_base_l[4]='K'; two_base_l[5]='M';
154154
three_base_l[0]='V'; three_base_l[1]='H';
155155
three_base_l[2]='D'; three_base_l[3]='B';
156-
156+
157157
two_base_c[0]=f[i][1]+f[i][3]; two_base_c[1]=f[i][0]+f[i][2];
158158
two_base_c[2]=f[i][0]+f[i][3]; two_base_c[3]=f[i][1]+f[i][2];
159159
two_base_c[4]=f[i][2]+f[i][3]; two_base_c[5]=f[i][0]+f[i][1];
@@ -166,7 +166,7 @@ char Motif::ColConsensus(int i)
166166
for(j=0; j<4; j++)
167167
sum+=f[i][j];
168168

169-
169+
170170
if(f[i][0]/sum>=CONS1) {curr='A';}
171171
else if(f[i][1]/sum>=CONS1) {curr='C';}
172172
else if(f[i][2]/sum>=CONS1) {curr='G';}
@@ -223,7 +223,7 @@ void Motif::PrintMotif(FILE* out, bool famNames)
223223
printf("%c\n", ColConsensus(i));
224224
}
225225
printf("XX\n");
226-
}else{
226+
}else{
227227
if(famNames)
228228
fprintf(out, "DE\t%s_%s\n", famName, name);
229229
else

‎src/Motif.h‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -66,10 +66,10 @@ class Motif {
6666

6767
//Copy a motif
6868
void CopyMotif(Motif* out);
69-
69+
7070
//Consensus letter for a column (taken from f)
7171
char ColConsensus(int i);
72-
72+
7373
//Find the information content of a column in f
7474
double Info(int i);
7575

@@ -78,7 +78,7 @@ class Motif {
7878

7979
//Print the motif's consensus
8080
void PrintMotifConsensus();
81-
81+
8282
//log base 2
8383
double log_2(double x){ return(log(x) / LOG_2);}
8484

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