diff trimal_repo/source/utils.h @ 0:b15a3147e604 draft

"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

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+++ b/trimal_repo/source/utils.h	Fri Mar 25 17:10:43 2022 +0000
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+/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+   ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+
+    trimAl v1.4: a tool for automated alignment trimming in large-scale
+                 phylogenetics analyses.
+
+    readAl v1.4: a tool for automated alignment conversion among different
+                 formats.
+
+    2009-2015 Capella-Gutierrez S. and Gabaldon, T.
+              [scapella, tgabaldon]@crg.es
+
+    This file is part of trimAl/readAl.
+
+    trimAl/readAl are free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, the last available version.
+
+    trimAl/readAl are distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.
+
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
+***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
+
+#ifndef UTILS_H
+#define UTILS_H
+
+#include <string.h>
+#include <stdlib.h>
+
+#include <fstream>
+#include <iostream>
+
+/** \brief Utils class.
+ *
+ * This class implements util methods.
+ */
+
+using namespace std;
+
+class utils {
+
+ public:
+  /** \brief Vector initialization.
+   * \param vector The vector that will be initializated.
+   * \param tam The size of the vector.
+   * \param valor The initialization value of all positions of the vector.
+   *
+   * This method is used to initializate all positions of a vector with a given value.
+   */
+  static void initlVect(int *vector, int tam, int valor);
+  static void initlVect(float *vector, int tam, float valor);
+
+  /** \brief Integer vector copying.
+   * \param vect1 Vector that we want to copy.
+   * \param vect2 Destination vector of the copy.
+   * \param tam Vectors size.
+   *
+   * This method copies integer vector 1 to integer vector 2.
+   */
+  static void copyVect(int *vect1, int *vect2, int tam);
+
+  /** \brief Float vector copying.
+   * \param vect1 Vector that we want to copy.
+   * \param vect2 Destination vector of the copy.
+   * \param tam Vectors size.
+   *
+   * This method copies float vector 1 to float vector 2.
+   */
+  static void copyVect(float *vect1, float *vect2, int tam);
+
+  /** \brief Round double to inferior integer method.
+   * \param number The number that will be rounded.
+   * \return the rounded number.
+   *
+   * This method rounds a double number to the inferior integer.
+   */
+  static int roundToInf(double number);
+
+  /** \brief Round double to integer method.
+   * \param number The number that will be rounded.
+   * \return the rounded number.
+   *
+   * This method rounds a double number to a integer.
+   */
+  static int roundInt(double number);
+
+  /** \brief Round double to greater integer method.
+   * \param number The number that will be rounded.
+   * \return the rounded number.
+   *
+   * This method rounds a double number to the greater integer.
+   */
+  static int roundToSup(double number);
+
+  /** \brief Maximum of two numbers method.
+   * \param x The first number.
+   * \param y The second number.
+   * \return The maximum between the two given numbers.
+   *
+   * This method returns the maximum between the two numbers given as parameters.
+   */
+  static int max(int x, int y);
+
+  static float max(float x, float y);
+
+  static double max(double x, double y);
+
+  static int min(int x, int y);
+
+  static float min(float x, float y);
+
+  static double min(double x, double y);
+
+  // static bool getArg(int argc, char *argv[], int *var, char *argument, char *abrevArg);
+  /** \brief String-is-number checking.
+   * \param num The string we want to check.
+   * \return \b true if the string is a number, \b false if not.
+   *
+   * This method checks if the given string is a float number.
+   */
+  static bool isNumber(char *num);
+
+  /** \brief String comparing method.
+   * \param a The first string that will be compared.
+   * \param b The second string that will be compared.
+   * \return \b true if the two strings are the same, \b false if not.
+   *
+   * This method compares the two strings given, and returns \b true if the two strings are equal.
+   */
+  static bool compare(char *a, char *b);
+
+  /** \brief Removing spaces method.
+   * \param in The string that we want to clean.
+   * \param out The destination of the clean string.
+   *
+   * This method removes spaces in the input string and put the result in the output string.
+   */
+  static void removeSpaces(char *in, char *out);
+
+  /** \brief Quicksort sorting method.
+   * \a param list The vector that we want to sort.
+   * \a param ini The first element of the vector.
+   * \a param fin The last element of the vector.
+   *
+   * This method sorts the vector using the quicksort method.
+   */
+  static void quicksort(float *list, int ini, int fin);
+
+  /** \brief Swapping elements method
+   * \param a One element to swap.
+   * \param b Other element to swap.
+   *
+   * This method swaps the values in a and b.
+   */
+  static void swap(float *a, float *b);
+
+  /** \brief Quicksort sorting method.
+   * \a param list The vector that we want to sort.
+   * \a param ini The first element of the vector.
+   * \a param fin The last element of the vector.
+   *
+   * This method sorts the vector using the quicksort method.
+   */
+  static void quicksort(int *list, int ini, int fin);
+
+  /** \brief Swapping elements method
+   * \param a One element to swap.
+   * \param b Other element to swap.
+   *
+   * This method swaps the values in a and b.
+   */
+  static void swap(int *a, int *b);
+
+  static bool checkFile(ifstream &file);
+
+  static char* readLine(ifstream &file);
+
+  static char* trimLine(string nline);
+
+  static char* readLineMEGA(ifstream &file);
+
+  static string getReverse(string toReverse);
+
+  static string removeCharacter(char c, string line);
+
+  static int checkTypeAlignment(int, int, string *);
+
+  static int* readNumbers(string);
+
+  static int* readNumbers_StartEnd(string);
+
+  static void quicksort(int **, int, int);
+
+  static void swap(int **, int **);
+
+  static char determineColor(char res, string column);
+
+  static bool lookForPattern(string, string, float);
+
+};
+#endif