4 package uk.ac.vamsas.objects.utils.trees;
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6 import uk.ac.vamsas.client.Vobject;
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7 import uk.ac.vamsas.client.VorbaId;
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9 public class SequenceNode extends BinaryNode {
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10 /** DOCUMENT ME!! */
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13 /** DOCUMENT ME!! */
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14 public boolean dummy = false;
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16 private boolean placeholder = false;
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19 * Creates a new SequenceNode object.
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21 public SequenceNode() {
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26 * Creates a new SequenceNode object.
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37 public SequenceNode(Vobject val, SequenceNode parent, float dist, String name) {
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38 super(val, parent, name);
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43 * Creates a new SequenceNode object.
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58 public SequenceNode(Vobject val, SequenceNode parent, String name,
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59 float dist, int bootstrap, boolean dummy) {
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60 super(val, parent, name);
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62 this.bootstrap = bootstrap;
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68 * true if node is created for the representation of polytomous
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71 public boolean isDummy() {
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76 * @param placeholder is true if the sequence referred to in the element node
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77 * is not actually present in the associated alignment
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79 public boolean isPlaceholder() {
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89 * @return DOCUMENT ME!
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91 public boolean setDummy(boolean newstate) {
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92 boolean oldstate = dummy;
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101 * @param Placeholder
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104 public void setPlaceholder(boolean Placeholder) {
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105 this.placeholder = Placeholder;
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109 * ascends the tree but doesn't stop until a non-dummy node is discovered.
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110 * This will probably break if the tree is a mixture of BinaryNodes and
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113 public SequenceNode AscendTree() {
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114 SequenceNode c = this;
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117 c = (SequenceNode) c.parent();
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118 } while ((c != null) && c.dummy);
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