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annotate clustalomega/clustal-omega-0.2.0/src/hhalign/list.h @ 0:ff1768533a07

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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author clustalomega
date Tue, 07 Jun 2011 17:04:25 -0400
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1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
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2
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3 /*********************************************************************
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4 * Clustal Omega - Multiple sequence alignment
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5 *
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6 * Copyright (C) 2010 University College Dublin
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7 *
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8 * Clustal-Omega is free software; you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation; either version 2 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * This file is part of Clustal-Omega.
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14 *
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15 ********************************************************************/
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16
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17 /*
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18 * RCS $Id: list.h 143 2010-10-14 13:11:14Z andreas $
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19 */
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20
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21 // list.h
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22
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23
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24 //////////////////////////////////////////////////////////////////////////////
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25 // Double-linked list implementation with head and tail dummy elements
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26 // We set head->prev=head and tail->next=tail.
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27 // This makes sure that repeated current=current->next; ends up in tail
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28 // and repeated current=current->prev; ends up in head.
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29 // head and tail optionally contain a NULL element of Typ defined by method Null(Typ)
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30 //////////////////////////////////////////////////////////////////////////////
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31
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32 template<class Typ>
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33 class List
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34 {
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35 protected:
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36 template<class Typ1>
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37 class ListEl //elements of List; essentially a data structure
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38 {
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39 public:
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40 Typ1 data; //Typ is type of data to be stored in list
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41 ListEl* prev; //points to previous list element
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42 ListEl* next; //points to next list element
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43 ListEl() : prev(0), next(0) {}
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44 ListEl(Typ1 d) : data(d), prev(0), next(0) {}
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45 ListEl(ListEl* p, ListEl* n) : prev(p), next(n) {}
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46 ListEl(Typ1 d, ListEl* p, ListEl* n) : data(d), prev(p), next(n) {}
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47 };
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48
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49 ListEl<Typ>* head; //points to dummy element at beginning of list
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50 ListEl<Typ>* tail; //points to dummy element at end of list
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51 ListEl<Typ>* current; //current element position within list
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52 int size; //Number of elements in list
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53
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54 // Use QUICKSORT to sort list in asscending order between two list elements
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55 void SortList(ListEl<Typ>*, ListEl<Typ>*, int);
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56 // Use QUICKSORT to sort list of pointers by comparing elements they point to
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57 void SortPointerList(ListEl<Typ>*, ListEl<Typ>*);
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58
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59 // Swap two list elements by making a flat copy (don't need two copies of data)
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60 // Warning: Gets slow if Typ is composite type with many variables (>=5)
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61 void SwapContent(ListEl<Typ>* e1, ListEl<Typ>* e2)
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62 { Typ d; if (e1!=e2) {d=e1->data; e1->data=e2->data; e2->data=d;} }
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63
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64 public:
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65 //////////////////////////////////////////////////////////////////////////////
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66 // General methods
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67 List();
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68 List(Typ d);
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69 ~List();
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70 List<Typ>& operator=(List<Typ>&);
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71
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72 // Set Null element that will be returned when trying to read from an empty list
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73 void Null(Typ null) {head->data = tail->data = null;}
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74
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75
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76 //////////////////////////////////////////////////////////////////////////////
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77 // Methods that act at the end of the list
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78
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79 // Insert Element after LAST element of list (and return address of data element)
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80 Typ* Push(Typ);
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81
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82 // Remove and return LAST element of list. Returns head->data if list empty
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83 Typ Pop();
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84
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85 // return LAST element of list. Returns null element in head->data if list empty
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86 Typ ReadLast() {return tail->prev->data;}
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87
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88
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89 //////////////////////////////////////////////////////////////////////////////
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90 // Methods that act at the beginning of the list
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91
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92 // Insert element as FIRST element of list (and return address of data element)
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93 Typ* Enqueue(Typ);
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94
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95 // Remove and return element at BEGINNING of list. Returns head->data if list empty
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96 Typ Dequeue();
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97
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98 // return FIRST element of list. Returns null element in head->data if list empty
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99 Typ ReadFirst() {if (size) return head->next->data; else return head->data;}
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100
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101
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102 //////////////////////////////////////////////////////////////////////////////
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103 // Methods that work with 'current' position in the list
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104
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105 // Advances current position by 1 and reads next element; returns head->data if at end of list.
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106 Typ ReadNext();
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107
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108 // Reads current element again
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109 Typ ReadCurrent();
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110
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111 // Moves current position back by 1 and reads previous element; returns head->data if at beginning of list.
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112 Typ ReadPrevious();
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113
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114 // Advances current position by 1 and reads address of next element; returns NULL if at end of list.
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115 Typ* ReadNextAddress();
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116
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117 // Reads address of current element again, returns NULL if at end of list
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118 Typ* ReadCurrentAddress();
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119
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120 // Sets current position to k and reads k'th element (first=1). Returns head->data if current points to no data element
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121 Typ Read(int);
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122
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123 // Inserts element AFTER CURRENT element; current element will be set to inserted element
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124 void Insert(Typ);
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125
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126 // Removes and returns element at CURRENT position. New position is one BEFORE current position.
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127 // Returns head->data if current points to no data element. After Reset() delete first element (not 0'th)
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128 Typ Delete();
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129
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130 // Overwrites data at current position with new data
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131 void Overwrite(Typ d) {current->data=d;}
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132
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133 // Reset current position to 0 (one BEFORE the first)
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134 int Reset() {current = head; return size;}
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135
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136 // Reset current position to End (one AFTER the last)
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137 int SetToEnd() {current = tail; return size;}
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138
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139
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140 //////////////////////////////////////////////////////////////////////////////
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141 // Methods that return information about the list
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142
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143 // Return number of list elements (size>=0)
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144 int Size() {return size;}
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145
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146 // return true if end of list, i.e. ReadNext would give tail->data (i.e. current position >= Size)
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147 char End() {return (current==tail || current==tail->prev);}
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148 char End(void* curr) {return ( curr == tail || curr == tail->prev);}
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149
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150 // return true if start of list, i.e. ReadPrevious would give head->data (i.e. current position <=1)
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151 char Start() {return (current==head || current==head->next);}
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152
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153 // Get current position within list (0 <= pos <= Size+1)
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154 int GetPos();
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155
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156 //print out list (elements assumed int)
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157 void PrintList();
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158
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159 // Get largest data element (Null element for empty list)
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160 Typ Largest();
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161
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162 // Get smallest data element (Null element for empty list)
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163 Typ Smallest();
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164
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165 //////////////////////////////////////////////////////////////////////////////
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166 // Methods that manipulate the list as a whole
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167
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168 // Reverse list
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169 void Reverse();
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170
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171 // Copies list into list object
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172 void Copy(List<Typ>* list);
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173
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174 // Appends a copy of list to class object
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175 void AppendCopy(List<Typ>* list);
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176
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177 // Appends list to class object list
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178 void Append(List<Typ>* list);
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179
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180 // Use QUICKSORT to sort list in ascending order. Use only for UNSORTED lists, otherwise time O(N^2) instead of O(N*log(N))
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181 /* void SortList() {if (size>1) SortList(head->next, tail->prev);} */
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182 void SortList() {if (size>1) SortList(head->next, tail->prev, size);}
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183 void QuickSort() {if (size>1) SortList(head->next, tail->prev, size);}
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184
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185 // Use QUICKSORT to sort list of pointers in ascending order. Use only for UNSORTED lists, otherwwise time O(N^2)!
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186 void SortPointerList() {if (size>1) SortPointerList(head->next, tail->prev);}
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187 void QuickSortPointer() {if (size>1) SortPointerList(head->next, tail->prev);}
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188
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189 // Use INSERTSORT to sort list in asscending order. Use only for PRESORTED lists, otherwise time O(N^2)!
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190 void ResortList();
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191 };
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192
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193