1 | // NodeUtils.java |
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2 | // |
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3 | // (c) 1999-2001 PAL Development Core Team |
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4 | // |
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5 | // This package may be distributed under the |
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6 | // terms of the Lesser GNU General Public License (LGPL) |
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7 | |
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8 | |
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9 | package de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree; |
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10 | |
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11 | import java.io.*; |
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12 | |
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13 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.io.FormattedOutput; |
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14 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.BranchLimits; |
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15 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; |
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16 | |
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17 | |
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18 | /** |
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19 | * Helper routines for dealing with nodes. |
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20 | * |
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21 | * @version $Id: NodeUtils.java,v 1.19 2002/01/08 02:09:53 alexi Exp $ |
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22 | * |
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23 | * @author Alexei Drummond |
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24 | * @author Korbinian Strimmer |
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25 | */ |
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26 | public class NodeUtils { |
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27 | |
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28 | /** |
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29 | * Converts lengths to heights, *without* assuming contemporaneous |
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30 | * tips. |
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31 | */ |
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32 | public static void lengths2Heights(Node root) { |
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33 | |
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34 | lengths2Heights(root, getGreatestDistance(root)); |
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35 | } |
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36 | |
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37 | /** |
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38 | * Converts lengths to heights, but maintains tip heights. |
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39 | */ |
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40 | public static void lengths2HeightsKeepTips(Node node, boolean useMax) { |
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41 | |
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42 | if (!node.isLeaf()) { |
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43 | for (int i = 0; i < node.getChildCount(); i++) { |
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44 | lengths2HeightsKeepTips(node.getChild(i), useMax); |
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45 | } |
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46 | |
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47 | double totalHL = 0.0; |
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48 | double maxHL = 0.0; |
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49 | double hl = 0.0; |
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50 | double maxH = 0.0; |
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51 | double h = 0.0; |
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52 | for (int i = 0; i < node.getChildCount(); i++) { |
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53 | h = node.getChild(i).getNodeHeight(); |
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54 | hl = node.getChild(i).getBranchLength() + h; |
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55 | if (hl > maxHL) maxHL = hl; |
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56 | if (h > maxH) maxH = h; |
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57 | totalHL += hl; |
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58 | } |
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59 | if (useMax) { |
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60 | hl = maxHL; // set parent height to maximum parent height implied by children |
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61 | } else { |
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62 | hl = totalHL / node.getChildCount(); // get mean parent height |
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63 | if (hl < maxH) hl = maxHL; // if mean parent height is not greater than all children height, fall back on max parent height. |
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64 | } |
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65 | node.setNodeHeight(hl); // set new parent height |
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66 | |
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67 | // change lengths in children to reflect changes. |
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68 | for (int i = 0; i < node.getChildCount(); i++) { |
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69 | h = node.getChild(i).getNodeHeight(); |
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70 | node.getChild(i).setBranchLength(hl - h); |
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71 | } |
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72 | } |
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73 | } |
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74 | |
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75 | |
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76 | /** |
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77 | * sets this nodes height value to newHeight and all children's |
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78 | * height values based on length of branches. |
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79 | */ |
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80 | private static void lengths2Heights(Node node, double newHeight) { |
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81 | |
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82 | if (!node.isRoot()) { |
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83 | newHeight -= node.getBranchLength(); |
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84 | node.setNodeHeight(newHeight); |
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85 | } else { |
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86 | node.setNodeHeight(newHeight); |
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87 | } |
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88 | |
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89 | for (int i = 0; i < node.getChildCount(); i++) { |
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90 | lengths2Heights(node.getChild(i), newHeight); |
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91 | } |
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92 | } |
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93 | |
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94 | /** |
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95 | * Exchange field info between two nodes. Specifically |
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96 | * identifiers, branch lengths, node heights and branch length |
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97 | * SEs. |
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98 | */ |
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99 | public static void exchangeInfo(Node node1, Node node2) { |
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100 | |
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101 | Identifier swaps; |
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102 | double swapd; |
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103 | |
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104 | swaps = node1.getIdentifier(); |
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105 | node1.setIdentifier(node2.getIdentifier()); |
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106 | node2.setIdentifier(swaps); |
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107 | |
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108 | swapd = node1.getBranchLength(); |
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109 | node1.setBranchLength(node2.getBranchLength()); |
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110 | node2.setBranchLength(swapd); |
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111 | |
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112 | swapd = node1.getNodeHeight(); |
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113 | node1.setNodeHeight(node2.getNodeHeight()); |
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114 | node2.setNodeHeight(swapd); |
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115 | |
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116 | swapd = node1.getBranchLengthSE(); |
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117 | node1.setBranchLengthSE(node2.getBranchLengthSE()); |
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118 | node2.setBranchLengthSE(swapd); |
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119 | } |
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120 | |
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121 | /** |
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122 | * determines branch lengths of this and all descendent nodes |
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123 | * from heights |
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124 | */ |
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125 | public static void heights2Lengths(Node node) { |
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126 | heights2Lengths(node, true); //respect minimum |
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127 | } |
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128 | |
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129 | /** |
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130 | * determines branch lengths of this and all descendent nodes |
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131 | * from heights |
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132 | */ |
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133 | public static void heights2Lengths(Node node, boolean respectMinimum) { |
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134 | |
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135 | for (int i = 0; i < node.getChildCount(); i++) { |
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136 | heights2Lengths(node.getChild(i)); |
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137 | } |
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138 | |
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139 | if (node.isRoot()) { |
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140 | node.setBranchLength(0.0); |
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141 | } |
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142 | else { |
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143 | node.setBranchLength(node.getParent().getNodeHeight() - node.getNodeHeight()); |
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144 | if (respectMinimum && (node.getBranchLength() < BranchLimits.MINARC)) |
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145 | { |
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146 | node.setBranchLength(BranchLimits.MINARC); |
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147 | } |
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148 | } |
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149 | } |
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150 | |
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151 | /** |
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152 | * determines branch lengths of this node and its immediate descendent nodes |
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153 | * from heights. |
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154 | */ |
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155 | public static void localHeights2Lengths(Node node, boolean respectMinimum) { |
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156 | |
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157 | for (int i = 0; i < node.getChildCount(); i++) { |
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158 | Node child = node.getChild(i); |
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159 | |
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160 | child.setBranchLength(node.getNodeHeight() - child.getNodeHeight()); |
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161 | } |
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162 | |
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163 | if (node.isRoot()) { |
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164 | node.setBranchLength(0.0); |
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165 | } |
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166 | else { |
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167 | node.setBranchLength(node.getParent().getNodeHeight() - node.getNodeHeight()); |
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168 | if (respectMinimum && (node.getBranchLength() < BranchLimits.MINARC)) |
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169 | { |
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170 | node.setBranchLength(BranchLimits.MINARC); |
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171 | } |
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172 | } |
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173 | } |
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174 | |
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175 | |
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176 | /** |
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177 | * Get the distance to furthest leaf from this nodes parent. |
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178 | */ |
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179 | private static double getGreatestDistance(Node node) { |
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180 | |
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181 | double distance = 0.0; |
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182 | if (!node.isLeaf()) { |
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183 | if (!node.isRoot()) { |
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184 | distance = node.getBranchLength(); |
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185 | } |
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186 | double max = getGreatestDistance(node.getChild(0)); |
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187 | double posmax = 0.0; |
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188 | for (int i = 1; i < node.getChildCount(); i++) { |
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189 | posmax = getGreatestDistance(node.getChild(i)); |
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190 | if (posmax > max) max = posmax; |
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191 | } |
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192 | distance += max; |
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193 | |
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194 | return distance; |
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195 | } else { |
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196 | return node.getBranchLength(); |
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197 | } |
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198 | } |
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199 | |
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200 | /** |
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201 | * Finds the largest child (in terms of node height). |
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202 | */ |
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203 | public static double findLargestChild(Node node) { |
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204 | // find child with largest height |
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205 | double max = node.getChild(0).getNodeHeight(); |
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206 | for (int j = 1; j < node.getChildCount(); j++) |
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207 | { |
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208 | if (node.getChild(j).getNodeHeight() > max) |
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209 | { |
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210 | max = node.getChild(j).getNodeHeight(); |
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211 | } |
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212 | } |
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213 | return max; |
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214 | } |
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215 | |
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216 | /** |
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217 | * remove child |
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218 | * |
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219 | * @param node child node to be removed |
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220 | */ |
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221 | public static void removeChild(Node parent, Node child) |
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222 | { |
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223 | int rm = -1; |
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224 | for (int i = 0; i < parent.getChildCount(); i++) |
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225 | { |
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226 | if (child == parent.getChild(i)) |
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227 | { |
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228 | rm = i; |
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229 | break; |
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230 | } |
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231 | } |
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232 | |
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233 | parent.removeChild(rm); |
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234 | } |
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235 | |
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236 | /** |
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237 | * remove internal branch (collapse node with its parent) |
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238 | * |
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239 | * @param node node associated with internal branch |
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240 | */ |
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241 | public static void removeBranch(Node node) |
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242 | { |
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243 | if (node.isRoot() || node.isLeaf()) |
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244 | { |
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245 | throw new IllegalArgumentException("INTERNAL NODE REQUIRED (NOT ROOT)"); |
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246 | } |
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247 | |
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248 | Node parent = node.getParent(); |
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249 | |
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250 | // add childs of node to parent |
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251 | // (node still contains the link to childs |
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252 | // to allow later restoration) |
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253 | int numChilds = node.getChildCount(); |
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254 | for (int i = 0; i < numChilds; i++) |
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255 | { |
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256 | parent.addChild(node.getChild(i)); |
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257 | } |
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258 | |
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259 | // remove node from parent |
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260 | // (link to parent is restored and the |
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261 | // position is stored) |
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262 | int rm = -1; |
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263 | for (int i = 0; i < parent.getChildCount(); i++) |
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264 | { |
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265 | if (node == parent.getChild(i)) |
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266 | { |
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267 | rm = i; |
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268 | break; |
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269 | } |
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270 | } |
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271 | parent.removeChild(rm); |
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272 | node.setParent(parent); |
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273 | node.setNumber(rm); |
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274 | } |
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275 | |
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276 | /** |
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277 | * restore internal branch |
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278 | * |
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279 | * @param node node associated with internal branch |
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280 | */ |
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281 | public static void restoreBranch(Node node) |
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282 | { |
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283 | if (node.isRoot() || node.isLeaf()) |
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284 | { |
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285 | throw new IllegalArgumentException("INTERNAL NODE REQUIRED (NOT ROOT)"); |
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286 | } |
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287 | |
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288 | Node parent = node.getParent(); |
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289 | |
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290 | // remove childs of node from parent and make node their parent |
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291 | int numChilds = node.getChildCount(); |
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292 | for (int i = 0; i < numChilds; i++) |
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293 | { |
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294 | Node c = node.getChild(i); |
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295 | removeChild(parent, c); |
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296 | c.setParent(node); |
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297 | } |
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298 | |
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299 | // insert node into parent |
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300 | parent.insertChild(node, node.getNumber()); |
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301 | } |
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302 | |
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303 | |
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304 | |
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305 | /** |
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306 | * join two childs, introducing a new node/branch in the tree |
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307 | * that replaces the first child |
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308 | * |
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309 | * @param n1 number of first child |
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310 | * @param n2 number of second child |
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311 | */ |
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312 | public static void joinChilds(Node node, int n1, int n2) { |
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313 | |
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314 | if (n1 == n2) { |
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315 | throw new IllegalArgumentException("CHILDREN MUST BE DIFFERENT"); |
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316 | } |
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317 | |
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318 | int c1, c2; |
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319 | if (n2 < n1) |
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320 | { |
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321 | c1 = n2; |
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322 | c2 = n1; |
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323 | } |
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324 | else |
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325 | { |
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326 | c1 = n1; |
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327 | c2 = n2; |
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328 | } |
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329 | |
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330 | Node newNode = NodeFactory.createNode(); |
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331 | |
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332 | Node child1 = node.getChild(c1); |
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333 | Node child2 = node.getChild(c2); |
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334 | |
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335 | node.setChild(c1, newNode); |
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336 | newNode.setParent(node); |
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337 | node.removeChild(c2); // now parent of child2 = null |
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338 | |
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339 | newNode.addChild(child1); |
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340 | newNode.addChild(child2); |
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341 | } |
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342 | |
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343 | /** |
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344 | * determine preorder successor of this node |
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345 | * |
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346 | * @return next node |
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347 | */ |
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348 | public static Node preorderSuccessor(Node node) { |
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349 | |
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350 | Node next = null; |
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351 | |
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352 | if (node.isLeaf()) { |
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353 | Node cn = node, ln = null; // Current and last node |
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354 | |
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355 | // Go up |
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356 | do |
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357 | { |
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358 | if (cn.isRoot()) |
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359 | { |
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360 | next = cn; |
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361 | break; |
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362 | } |
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363 | ln = cn; |
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364 | cn = cn.getParent(); |
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365 | } |
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366 | while (cn.getChild(cn.getChildCount()-1) == ln); |
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367 | |
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368 | // Determine next node |
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369 | if (next == null) |
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370 | { |
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371 | // Go down one node |
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372 | for (int i = 0; i < cn.getChildCount()-1; i++) |
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373 | { |
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374 | if (cn.getChild(i) == ln) |
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375 | { |
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376 | next = cn.getChild(i+1); |
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377 | break; |
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378 | } |
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379 | } |
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380 | } |
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381 | } |
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382 | else |
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383 | { |
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384 | next = node.getChild(0); |
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385 | } |
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386 | |
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387 | return next; |
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388 | } |
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389 | |
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390 | /** |
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391 | * determine postorder successor of a node |
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392 | * |
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393 | * @return next node |
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394 | */ |
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395 | public static Node postorderSuccessor(Node node) { |
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396 | |
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397 | Node cn = null; |
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398 | Node parent = node.getParent(); |
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399 | |
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400 | if (node.isRoot()) |
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401 | { |
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402 | cn = node; |
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403 | } |
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404 | else |
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405 | { |
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406 | |
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407 | // Go up one node |
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408 | if (parent.getChild(parent.getChildCount()-1) == node) { |
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409 | return parent; |
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410 | } |
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411 | // Go down one node |
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412 | for (int i = 0; i < parent.getChildCount()-1; i++) |
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413 | { |
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414 | if (parent.getChild(i) == node) |
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415 | { |
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416 | cn = parent.getChild(i+1); |
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417 | break; |
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418 | } |
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419 | } |
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420 | } |
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421 | |
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422 | // Go down until leaf |
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423 | while (cn.getChildCount() > 0) |
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424 | { |
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425 | |
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426 | cn = cn.getChild(0); |
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427 | } |
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428 | |
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429 | return cn; |
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430 | } |
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431 | |
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432 | /** |
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433 | * prints node in New Hamshire format. |
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434 | */ |
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435 | static void printNH(PrintWriter out, Node node, |
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436 | boolean printLengths, boolean printInternalLabels) { |
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437 | |
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438 | printNH(out, node, printLengths, printInternalLabels, 0, true); |
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439 | } |
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440 | |
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441 | |
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442 | static int printNH(PrintWriter out, Node node, |
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443 | boolean printLengths, boolean printInternalLabels, int column, boolean breakLines) { |
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444 | |
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445 | if (breakLines) column = breakLine(out, column); |
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446 | |
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447 | if (!node.isLeaf()) |
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448 | { |
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449 | out.print("("); |
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450 | column++; |
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451 | |
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452 | for (int i = 0; i < node.getChildCount(); i++) |
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453 | { |
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454 | if (i != 0) |
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455 | { |
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456 | out.print(","); |
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457 | column++; |
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458 | } |
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459 | |
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460 | column = printNH(out, node.getChild(i), printLengths, printInternalLabels, column, breakLines); |
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461 | } |
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462 | |
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463 | out.print(")"); |
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464 | column++; |
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465 | } |
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466 | |
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467 | if (!node.isRoot()) |
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468 | { |
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469 | if (node.isLeaf() || printInternalLabels) |
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470 | { |
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471 | if (breakLines) column = breakLine(out, column); |
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472 | |
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473 | String id = node.getIdentifier().toString(); |
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474 | out.print(id); |
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475 | column += id.length(); |
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476 | } |
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477 | |
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478 | if (printLengths) |
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479 | { |
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480 | out.print(":"); |
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481 | column++; |
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482 | |
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483 | if (breakLines) column = breakLine(out, column); |
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484 | |
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485 | column += FormattedOutput.getInstance().displayDecimal(out, node.getBranchLength(), 7); |
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486 | } |
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487 | } |
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488 | |
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489 | return column; |
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490 | } |
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491 | |
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492 | private static int breakLine(PrintWriter out, int column) |
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493 | { |
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494 | if (column > 70) |
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495 | { |
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496 | out.println(); |
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497 | column = 0; |
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498 | } |
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499 | |
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500 | return column; |
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501 | } |
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502 | /** |
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503 | * Returns the first nodes in this tree that has the |
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504 | * required identifiers. |
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505 | * @return null if none of the identifiers names match nodes in tree, else return array which may have |
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506 | * null "blanks" for corresponding identifiers that do not match any node in the tree |
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507 | */ |
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508 | public static final Node[] findByIdentifier(Node node, String[] identifierNames) { |
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509 | Node[] nodes = new Node[identifierNames.length]; |
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510 | boolean foundSomething = false; |
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511 | for(int i = 0 ; i < nodes.length ; i++) { |
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512 | nodes[i] = findByIdentifier(node,identifierNames[i]); |
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513 | foundSomething = foundSomething||(nodes[i]!=null); |
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514 | } |
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515 | if(!foundSomething) { |
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516 | return null; |
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517 | } |
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518 | return nodes; |
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519 | } |
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520 | /** |
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521 | * Returns the first nodes in this tree that has the |
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522 | * required identifiers. |
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523 | */ |
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524 | public static final Node[] findByIdentifier(Node node, Identifier[] identifiers) { |
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525 | Node[] nodes = new Node[identifiers.length]; |
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526 | for(int i = 0 ; i < nodes.length ; i++) { |
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527 | nodes[i] = findByIdentifier(node,identifiers[i]); |
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528 | } |
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529 | return nodes; |
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530 | } |
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531 | /** |
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532 | * Returns the first node in this tree that has the |
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533 | * required identifier. |
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534 | */ |
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535 | public static final Node findByIdentifier(Node node, Identifier identifier) { |
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536 | return findByIdentifier(node,identifier.getName()); |
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537 | } |
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538 | /** |
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539 | * Returns the first node in this tree that has the |
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540 | * required identifier. |
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541 | */ |
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542 | public static final Node findByIdentifier(Node node, String identifierName) { |
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543 | |
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544 | |
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545 | if (node.getIdentifier().getName().equals(identifierName)) { |
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546 | return node; |
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547 | } else { |
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548 | Node pos = null; |
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549 | for (int i = 0; i < node.getChildCount(); i++) { |
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550 | pos = findByIdentifier(node.getChild(i), identifierName); |
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551 | if (pos != null) return pos; |
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552 | } |
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553 | |
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554 | return pos; |
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555 | } |
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556 | } |
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557 | |
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558 | /** |
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559 | * Root tree at this node. |
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560 | */ |
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561 | public static Node root(Node node) { |
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562 | |
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563 | if (!node.isRoot()) { |
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564 | |
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565 | Node myParent = node.getParent(); |
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566 | removeChild(myParent, node); |
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567 | |
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568 | root(myParent); |
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569 | |
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570 | while (myParent.getChildCount() == 1) { |
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571 | myParent = myParent.getChild(0); |
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572 | } |
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573 | |
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574 | node.addChild(myParent); |
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575 | lengths2Heights(node); |
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576 | } |
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577 | return node; |
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578 | } |
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579 | |
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580 | /** |
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581 | * Root the tree above the node with this identifier. |
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582 | */ |
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583 | public static Node rootAbove(Identifier id, Node root) { |
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584 | return rootAbove(findByIdentifier(root, id)); |
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585 | } |
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586 | |
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587 | /** |
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588 | * Root tree above this node; |
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589 | */ |
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590 | public static Node rootAbove(Node node) { |
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591 | |
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592 | if (!node.isRoot()) { |
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593 | |
---|
594 | Node root = NodeFactory.createNode(); |
---|
595 | |
---|
596 | Node myParent = node.getParent(); |
---|
597 | removeChild(myParent, node); |
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598 | |
---|
599 | root(myParent); |
---|
600 | |
---|
601 | while (myParent.getChildCount() == 1) { |
---|
602 | myParent = myParent.getChild(0); |
---|
603 | } |
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604 | |
---|
605 | root.addChild(myParent); |
---|
606 | root.addChild(node); |
---|
607 | |
---|
608 | lengths2Heights(root); |
---|
609 | |
---|
610 | return root; |
---|
611 | |
---|
612 | } else return node; |
---|
613 | } |
---|
614 | |
---|
615 | /** |
---|
616 | * determine distance to root |
---|
617 | * |
---|
618 | * @return distance to root |
---|
619 | */ |
---|
620 | public static double getDistanceToRoot(Node node) |
---|
621 | { |
---|
622 | if (node.isRoot()) |
---|
623 | { |
---|
624 | return 0.0; |
---|
625 | } |
---|
626 | else |
---|
627 | { |
---|
628 | return node.getBranchLength() + getDistanceToRoot(node.getParent()); |
---|
629 | } |
---|
630 | } |
---|
631 | |
---|
632 | /** |
---|
633 | * Return the number of terminal leaves below this node or 1 if this is |
---|
634 | * a terminal leaf. |
---|
635 | */ |
---|
636 | public static int getLeafCount(Node node) { |
---|
637 | |
---|
638 | int count = 0; |
---|
639 | if (!node.isLeaf()) { |
---|
640 | for (int i = 0; i < node.getChildCount(); i++) { |
---|
641 | count += getLeafCount(node.getChild(i)); |
---|
642 | } |
---|
643 | } else { |
---|
644 | count = 1; |
---|
645 | } |
---|
646 | return count; |
---|
647 | } |
---|
648 | /** |
---|
649 | * For two nodes in the tree true if the first node is the ancestor of the second |
---|
650 | * |
---|
651 | * @param possibleAncestor the node that may be the ancestor of the other node |
---|
652 | * @param node the node that may have the other node as it's ancestor |
---|
653 | */ |
---|
654 | public static boolean isAncestor(Node possibleAncestor, Node node) { |
---|
655 | if(node==possibleAncestor) { |
---|
656 | return true; |
---|
657 | } |
---|
658 | while(!node.isRoot()){ |
---|
659 | node = node.getParent(); |
---|
660 | if(node==possibleAncestor) { |
---|
661 | return true; |
---|
662 | } |
---|
663 | } |
---|
664 | return false; |
---|
665 | } |
---|
666 | |
---|
667 | /** |
---|
668 | * For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor) |
---|
669 | * |
---|
670 | * @param nodes the nodes to check, is okay if array elements are null! |
---|
671 | * @returns null if a at least one node is disjoint from the others nodes disjoint |
---|
672 | */ |
---|
673 | public static Node getFirstCommonAncestor(Node[] nodes) { |
---|
674 | Node currentCA = nodes[0]; |
---|
675 | for(int i = 1; i < nodes.length ;i++) { |
---|
676 | if(currentCA!=null&&nodes[i]!=null) { |
---|
677 | currentCA = getFirstCommonAncestor(currentCA,nodes[i]); |
---|
678 | if(currentCA==null) { |
---|
679 | return null; |
---|
680 | } |
---|
681 | } |
---|
682 | } |
---|
683 | return currentCA; |
---|
684 | } |
---|
685 | /** |
---|
686 | * For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor) |
---|
687 | * |
---|
688 | * @param nodeOne |
---|
689 | * @param nodeTwo |
---|
690 | * @returns null if two nodes disjoint (from different trees). May also return either nodeOne or nodeTwo if one node is an ancestor of the other |
---|
691 | */ |
---|
692 | public static Node getFirstCommonAncestor(Node nodeOne, Node nodeTwo) { |
---|
693 | if(isAncestor(nodeTwo, nodeOne)) { |
---|
694 | return nodeTwo; |
---|
695 | } |
---|
696 | if(isAncestor(nodeOne, nodeTwo)) { |
---|
697 | return nodeOne; |
---|
698 | } |
---|
699 | while(!nodeTwo.isRoot()) { |
---|
700 | nodeTwo = nodeTwo.getParent(); |
---|
701 | if(isAncestor(nodeTwo, nodeOne)) { |
---|
702 | return nodeTwo; |
---|
703 | } |
---|
704 | } |
---|
705 | return null; |
---|
706 | } |
---|
707 | |
---|
708 | /** returns number of branches centered around an internal node in an unrooted tree */ |
---|
709 | public static final int getUnrootedBranchCount(Node center) { |
---|
710 | if (center.isRoot()) { |
---|
711 | return center.getChildCount(); |
---|
712 | } |
---|
713 | else { |
---|
714 | return center.getChildCount()+1; |
---|
715 | } |
---|
716 | } |
---|
717 | |
---|
718 | /** Attempts to remove the root of a tree by making it polyficating (as opposed to bificating). |
---|
719 | */ |
---|
720 | public static final Node getUnrooted(Node root) { |
---|
721 | if(!root.isRoot()) { |
---|
722 | return root; //Already unrooted |
---|
723 | } |
---|
724 | Node left = root.getChild(0); |
---|
725 | Node right = root.getChild(1); |
---|
726 | /*if(left.getChildCount()==1) { |
---|
727 | if(l |
---|
728 | } */ |
---|
729 | if(left.getChildCount()>1) { |
---|
730 | return root(left); |
---|
731 | } |
---|
732 | if(right.getChildCount()>1) { |
---|
733 | return root(right); |
---|
734 | } |
---|
735 | return root; //Can't do much |
---|
736 | } |
---|
737 | } |
---|