--- /dev/null
+/**
+ * Author: Mark Larkin
+ *
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
+ *
+ * @author Mark Larkin, Conway Institute, UCD. mark.larkin@ucd.ie
+ *
+ * Changes:
+ *
+ * 2007-12-03, Andreas Wilm (UCD): replaced gets with fgets, and
+ * got rid of some compiler warning
+ *
+ */
+#ifdef HAVE_CONFIG_H
+ #include "config.h"
+#endif
+#include <iostream>
+#include <algorithm>
+#include "Utility.h"
+#include "general/userparams.h"
+
+namespace clustalw
+{
+
+/** constructor
+ */
+Utility::Utility()
+{
+ quiet=false;
+}
+
+
+/**
+ * Removes trailing blanks from a string
+ */
+void Utility::rTrim(string *str)
+{
+ string::reverse_iterator rit = str->rbegin();
+
+ while(rit != str->rend() && isspace(*rit))
+ {
+ str->erase((++rit).base());
+ }
+}
+
+/**
+ * Removes trailing blanks from a string
+ * @param str String to remove trailing blanks from.
+ * @return Pointer to the processed string
+ */
+char * Utility::rTrim(char *str)
+{
+ register int p;
+
+ p = strlen(str) - 1;
+
+ while (isspace(str[p]))
+ {
+ p--;
+ }
+
+ str[p + 1] = EOS;
+
+ return str;
+}
+
+/**
+ * Replace blanks in a string with underscores. Also replaces , ; : ( or ) with _.
+ * @param str String to process.
+ * @return Pointer to the processed string
+ */
+char * Utility::blankToUnderscore(char *str)
+{
+ int i, p;
+
+ p = strlen(str) - 1;
+
+ for (i = 0; i <= p; i++)
+ if ((str[i] == ' ') || (str[i] == ';') || (str[i] == ',') || (str[i] ==
+ '(') || (str[i] == ')') || (str[i] == ':'))
+ {
+ str[i] = '_';
+ }
+
+ return str;
+}
+
+/**
+ * Replace blanks in a string with underscores. Also replaces , ; : ( or ) with _.
+ * @param str String to process.
+ * @return Pointer to the processed string
+ */
+string Utility::blankToUnderscore(string str)
+{
+ int i, p;
+
+ p = str.size() - 1;
+
+ for (i = 0; i <= p; i++)
+ if ((str[i] == ' ') || (str[i] == ';') || (str[i] == ',') || (str[i] ==
+ '(') || (str[i] == ')') || (str[i] == ':'))
+ {
+ str[i] = '_';
+ }
+
+ return str;
+}
+
+/**
+ *
+ * @param instr
+ * @return
+ */
+char Utility::getChoice(string instr)
+{
+ cout << instr << ": ";
+ cout.flush();
+ char choice;
+ cin.get(choice);
+ // We only want one character, so we ignore the rest.
+ if(choice != '\n')
+ {
+ cin.ignore(150, '\n');
+ }
+ cin.clear();
+ if(isalpha(choice) || isNumeric(choice))
+ {
+ return choice;
+ }
+ else if(choice == '\n')
+ {
+ return '\n';
+ }
+ else
+ {
+ return ' ';
+ }
+}
+
+bool Utility::isNumeric(char ch)
+{
+ if(ch >= '0' && ch <= '9')
+ {
+ return true;
+ }
+ return false;
+}
+
+
+/**
+ *
+ * @param instr
+ * @param outstr
+ */
+void Utility::getStr(string instr, string& outstr)
+{
+ cout << instr << ": ";
+ cout.flush();
+ string temp;
+ getline(cin, temp, '\n');
+ outstr = temp;
+ cin.clear();
+}
+
+/**
+ *
+ * @param instr
+ * @param minx
+ * @param maxx
+ * @param def
+ * @return
+ */
+double Utility::getReal(const char *instr, double minx, double maxx, double def)
+{
+ int status;
+ float ret;
+ char line[MAXLINE];
+
+ while (true)
+ {
+ fprintf(stdout, "%s (%.1f-%.1f) [%.1f]: ", instr, minx, maxx, def);
+ //gets(line);
+ fgets(line, MAXLINE, stdin);
+ status = sscanf(line, "%f", &ret);
+ if (status == EOF)
+ {
+ return def;
+ }
+ if (ret > maxx)
+ {
+ fprintf(stderr, "ERROR: Max. value=%.1f\n\n", maxx);
+ continue;
+ }
+ if (ret < minx)
+ {
+ fprintf(stderr, "ERROR: Min. value=%.1f\n\n", minx);
+ continue;
+ }
+ break;
+ }
+ return (double)ret;
+}
+
+/**
+ *
+ * @param instr
+ * @param minx
+ * @param maxx
+ * @param def
+ * @return
+ */
+int Utility::getInt(const char *instr, int minx, int maxx, int def)
+{
+ int ret, status;
+ char line[MAXLINE];
+
+ while (true)
+ {
+ fprintf(stdout, "%s (%d..%d) [%d]: ", instr, minx, maxx, def);
+ //gets(line);
+ fgets(line, MAXLINE, stdin);
+ status = sscanf(line, "%d", &ret);
+ if (status == EOF)
+ {
+ return def;
+ }
+ if (ret > maxx)
+ {
+ fprintf(stderr, "ERROR: Max. value=%d\n\n", maxx);
+ continue;
+ }
+ if (ret < minx)
+ {
+ fprintf(stderr, "ERROR: Min. value=%d\n\n", minx);
+ continue;
+ }
+ break;
+ }
+ return ret;
+}
+
+/**
+ *
+ * @param line
+ * @param code
+ * @return
+ */
+bool Utility::lineType(char *line, const char *code)
+{
+ // AW: introduced sanity check
+ int n;
+ if (strlen(line)<strlen(code))
+ n=strlen(line);
+ else
+ n=strlen(code);
+
+ return (strncmp(line, code, strlen(code)) == 0);
+}
+
+/**
+ *
+ * @param line
+ * @return
+ */
+bool Utility::blankLine(char *line)
+{
+ int i;
+
+ for (i = 0; line[i] != '\n' && line[i] != EOS; i++)
+ {
+ if (isdigit(line[i]) || isspace(line[i]) || (line[i] == '*') ||
+ (line[i] == ':') || (line[i] == '.'))
+ ;
+ else
+ {
+ return false;
+ }
+ }
+ return true;
+}
+
+/**
+ *
+ * @param str
+ * @param path
+ */
+void Utility::getPath(string str, string *path)
+{
+ int i;
+ string _temp;
+ _temp = str;
+
+ for (i = _temp.length() - 1; i > - 1; --i)
+ {
+ if (str[i] == DIRDELIM)
+ {
+ i = - 1;
+ break;
+ }
+ if (str[i] == '.')
+ {
+ break;
+ }
+ }
+
+ if (i < 0)
+ {
+ _temp += ".";
+ }
+ else
+ {
+ _temp = _temp.substr(0, i + 1);
+ }
+ *path = _temp;
+}
+
+/**
+ *
+ * @param title
+ * @param prompt
+ * @return
+ *
+ *
+ */
+char Utility::promptForYesNo(char *title, const char *prompt)
+{
+ cout << "\n" << title << "\n";
+ string promptMessage = string(prompt) + "(y/n) ? [y]";
+
+ string answer;
+ getStr(promptMessage, answer);
+
+ if(!answer.empty())
+ {
+ if ((answer[0] != 'n') && (answer[0] != 'N'))
+ {
+ return ('y');
+ }
+ }
+ return ('n');
+}
+
+/**
+ *
+ * @param title
+ * @param prompt
+ * @return
+ *
+ */
+char Utility::promptForYesNo(const char *title, const char *prompt)
+{
+ cout << "\n" << title << "\n";
+ string promptMessage = string(prompt) + "(y/n) ? [y]";
+
+ string answer;
+ getStr(promptMessage, answer);
+
+ if(!answer.empty())
+ {
+ if ((answer[0] != 'n') && (answer[0] != 'N'))
+ {
+ return ('y');
+ }
+ }
+ return ('n');
+}
+
+/**
+ *
+ * @param msg
+ */
+void Utility::error( char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap, msg);
+ fprintf(stderr, "\n\nERROR: ");
+ vfprintf(stderr, msg, ap);
+ fprintf(stderr, "\n\n");
+ va_end(ap);
+}
+
+/**
+ *
+ * @param msg
+ */
+void Utility::warning( char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap, msg);
+ fprintf(stderr, "\n\nWARNING: ");
+ vfprintf(stderr, msg, ap);
+ fprintf(stderr, "\n\n");
+ va_end(ap);
+}
+
+/**
+ *
+ * @param msg
+ */
+void Utility::error( const char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap, msg);
+ fprintf(stderr, "\n\nERROR: ");
+ vfprintf(stderr, msg, ap);
+ fprintf(stderr, "\n\n");
+ va_end(ap);
+}
+
+/**
+ *
+ * @param msg
+ */
+void Utility::warning( const char *msg,...)
+{
+ va_list ap;
+
+ va_start(ap, msg);
+ fprintf(stderr, "\n\nWARNING: ");
+ vfprintf(stderr, msg, ap);
+ fprintf(stderr, "\n\n");
+ va_end(ap);
+}
+
+/**
+ *
+ * @param msg
+ */
+void Utility::info( char *msg,...)
+{
+ va_list ap;
+ va_start(ap, msg);
+
+ if(! quiet)
+ {
+ fprintf(stdout, "\n");
+ vfprintf(stdout, msg, ap);
+ va_end(ap);
+ }
+}
+
+/**
+ *
+ * @param msg
+ */
+void Utility::info(const char *msg,...)
+{
+ va_list ap;
+ if(! quiet)
+ {
+ va_start(ap, msg);
+ fprintf(stdout, "\n");
+ vfprintf(stdout, msg, ap);
+ va_end(ap);
+ }
+}
+
+
+
+/**
+ *
+ */
+void Utility::myname( char *myname)
+{
+ strcpy(myname, "clustalw\0");
+}
+
+
+
+/**
+ * Change:
+ * Mark 25-1-2007. I made this change to get around the problem of having to keep track
+ * of output indexes in the alignment stage. This function returns the next unique id.
+ */
+unsigned long Utility::getUniqueSequenceIdentifier()
+{
+ static unsigned long nextSequenceIdentifier = MinIdentifier;
+ return nextSequenceIdentifier++;
+}
+
+void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj)
+{
+ // Dont do anything. This is here to allow the function to be added to QTUtility.
+ // Polymorphism wont work with different functions in the classes.
+}
+
+
+double Utility::average(std::vector<double>& v)
+{
+ double tmp = 0.0;
+ std::vector<double>::iterator i;
+
+ if (v.size() == 0)
+ return 0.0;
+
+ for (i=v.begin(); i != v.end(); i++)
+ tmp += *i;
+ return (tmp / v.size());
+}
+
+double Utility::stdDev(std::vector<double>& v)
+{
+ std::vector<double>::iterator i;
+ double tmp = 0.0;
+ double avg = average(v);
+
+ if (v.size() == 0)
+ return 0.0;
+
+ for(i=v.begin(); i != v.end(); ++i)
+ tmp += (*i - avg) * (*i - avg);
+ return sqrt(tmp / v.size());
+}
+
+double Utility::median(std::vector<double> v)
+{
+ // From Moo & Koenig, "Accelerated C++:
+ typedef vector<double>::size_type vec_sz;
+ vec_sz size = v.size();
+
+ if (v.size() == 0)
+ return 0.0;
+
+ std::sort(v.begin(), v.end());
+ vec_sz mid = size/2;
+ return size % 2 == 0 ? (v[mid] + v[mid-1]) / 2 : v[mid];
+}
+
+}
+
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