void print_table(str s, const Dtable& T, bool latex, Slist labels) {
int SIZE = 7;
int MAXSIZE = 10;
int MAXLINE = 50;
int STANDARDSIZE = 1;
bool square(true);
int l = T.size();
if (MAXLINE<l) printf("Cautious, table is of size %d, only %d will be displayed \n",l,MAXLINE);
int cc = T[0].size();
for (int i=0; i<l; i++) if (T[i].size()!=cc) square = false;
int max = max_row(T);
List maxRow = initList(max);
if (square) {
Table sizestr = initTable(l,max);
for (int i=0; i<l; i++) {
for (int j=0; j<max; j++) {
int sz = f(T[i][j]).size()+1;
sizestr[i][j] = sz<MAXSIZE ? sz : MAXSIZE;
}
}
maxRow = max_on_row(sizestr);
}
else maxRow = initList(max,STANDARDSIZE);
str et = latex ? " &" : "|";
str slash = latex ? " \\\\ \n" : "\n";
str rrr(T[0].size(),'r');
printf("%s", s.c_str());
printf("\n");
bool labelsB = isnull(labels);
str space(6,' ');
printf("%s", space.c_str());
//rnc 10/25/15
printf("Obs. made ");
for (int j=0; j<6;j++){
//for (int j=0; j<max; j++) {
str s = (j==max-1) ? slash : et;
printf("%s%s",format(maxRow[j],f(j)).c_str(),s.c_str());
}
printf("initial& fibers&obs'rvd&percent& wght'd\\\\ \n");
for (int i=0; i<l && i<MAXLINE; i++) {
str pre = labelsB ? f(i) : format(11,labels[i]);
printf("%3s %s",pre.c_str(),et.c_str());
int c = T[i].size();
if (c==0) printf("\n");
for (int j=0; j<c; j++) {
str s = (j==c-1) ? slash : et;
str num = T[i][j]==-1 ? "" : f(T[i][j]).c_str();
printf("%s%s",format(maxRow[j],num).c_str(),s.c_str());
}
}
printf("\n");
}
void print_mult_Dtable_latex(str s, str ss, Dtable T, double multX) {
printf("# %s \n Output data in %s \n\n",s.c_str(),ss.c_str());
FILE* pFile;
pFile = fopen(ss.c_str(),"w");
if (!pFile) {
printf("File opening failed \n"); fl();
myexit(1);
}
fprintf(pFile,"x ");
for (int i=0; i<T.size(); i++) fprintf(pFile,"%d ",i);
fprintf(pFile,"\n");
int maxrow = max_row(T);
for (int j=0; j<maxrow; j++) {
fprintf(pFile,"%f ",j*multX);
for (int i=0; i<T.size(); i++) {
if (j<T[i].size()) fprintf(pFile,"%f ",T[i][j]);
else fprintf(pFile,"0 ");
}
fprintf(pFile,"\n");
}
fclose(pFile);
}
void make_square(Table& T) {
int max = max_row(T);
for (int i=0; i<T.size(); i++) {
if (T[i].size()<max) T[i].resize(max);
}
}
/** Run alignment algorithm.
\param first_last Last aligned position in first sequence (output)
\param second_last Last aligned position in second sequence (output)
*/
void align(int& first_last, int& second_last) const {
adjust_matrix_size();
limit_range();
make_frame();
ASSERT_TRUE(!local() || max_errors() == -1);
int& r_row = first_last;
int& r_col = second_last;
r_row = r_col = -1;
for (int row = 0; row <= max_row(); row++) {
int start_col = min_col(row);
int stop_col = max_col(row);
int min_score_col = start_col;
for (int col = start_col; col <= stop_col; col++) {
ASSERT_TRUE(col >= 0 && col < side());
ASSERT_TRUE(in(row, col));
int match = at(row - 1, col - 1) +
substitution(row, col);
int gap1 = at(row, col - 1) + gap_penalty();
int gap2 = at(row - 1, col) + gap_penalty();
int score = std::min(match, std::min(gap1, gap2));
if (local()) {
score = std::min(score, 0);
}
at(row, col) = score;
if (score < at(row, min_score_col)) {
min_score_col = col;
}
track(row, col) = (score == match) ? MATCH :
(score == gap1) ? COL_INC :
ROW_INC;
}
if (max_errors() != -1 &&
at(row, min_score_col) > max_errors()) {
break;
}
r_row = row;
r_col = min_score_col;
}
if (max_errors() == -1) {
// col -> max_col in this row
ASSERT_TRUE(in(max_row(), max_col(max_row())));
ASSERT_EQ(r_row, max_row());
r_col = max_col(max_row());
// if stopped earlier because of gap range
int last_row = contents().first_size() - 1;
int last_col = contents().second_size() - 1;
if (r_row == last_row) {
while (r_col < last_col) {
r_col += 1;
track(r_row, r_col) = COL_INC;
}
} else if (r_col == last_col) {
while (r_row < last_row) {
r_row += 1;
track(r_row, r_col) = ROW_INC;
}
} else {
throw Exception("row and column are not last");
}
}
}
