jalviewX
File SequenceNode.java
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40% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| SequenceNode | 31 | 24 | 16 | 22 |
Contributing tests
This file is covered by 10 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.datamodel; | |
| 22 | ||
| 23 | import java.awt.Color; | |
| 24 | ||
| 25 | /** | |
| 26 | * DOCUMENT ME! | |
| 27 | * | |
| 28 | * @author $author$ | |
| 29 | * @version $Revision$ | |
| 30 | */ | |
| 31 | public class SequenceNode extends BinaryNode | |
| 32 | { | |
| 33 | /** DOCUMENT ME!! */ | |
| 34 | public double dist; | |
| 35 | ||
| 36 | /** DOCUMENT ME!! */ | |
| 37 | public int count; | |
| 38 | ||
| 39 | /** DOCUMENT ME!! */ | |
| 40 | public double height; | |
| 41 | ||
| 42 | /** DOCUMENT ME!! */ | |
| 43 | public float ycount; | |
| 44 | ||
| 45 | /** DOCUMENT ME!! */ | |
| 46 | public Color color = Color.black; | |
| 47 | ||
| 48 | /** DOCUMENT ME!! */ | |
| 49 | public boolean dummy = false; | |
| 50 | ||
| 51 | private boolean placeholder = false; | |
| 52 | ||
| 53 | /** | |
| 54 | * Creates a new SequenceNode object. | |
| 55 | */ | |
| 56 | 18 |  public SequenceNode() |
| 57 | { | |
| 58 | 18 | super(); |
| 59 | } | |
| 60 | ||
| 61 | /** | |
| 62 | * Creates a new SequenceNode object. | |
| 63 | * | |
| 64 | * @param val | |
| 65 | * DOCUMENT ME! | |
| 66 | * @param parent | |
| 67 | * DOCUMENT ME! | |
| 68 | * @param dist | |
| 69 | * DOCUMENT ME! | |
| 70 | * @param name | |
| 71 | * DOCUMENT ME! | |
| 72 | */ | |
| 73 | 0 | public SequenceNode(Object val, SequenceNode parent, float dist, |
| 74 | String name) | |
| 75 | { | |
| 76 | 0 | super(val, parent, name); |
| 77 | 0 | this.dist = dist; |
| 78 | } | |
| 79 | ||
| 80 | /** | |
| 81 | * Creates a new SequenceNode object. | |
| 82 | * | |
| 83 | * @param val | |
| 84 | * DOCUMENT ME! | |
| 85 | * @param parent | |
| 86 | * DOCUMENT ME! | |
| 87 | * @param name | |
| 88 | * DOCUMENT ME! | |
| 89 | * @param dist | |
| 90 | * DOCUMENT ME! | |
| 91 | * @param bootstrap | |
| 92 | * DOCUMENT ME! | |
| 93 | * @param dummy | |
| 94 | * DOCUMENT ME! | |
| 95 | */ | |
| 96 | 298 | public SequenceNode(Object val, SequenceNode parent, String name, |
| 97 | float dist, int bootstrap, boolean dummy) | |
| 98 | { | |
| 99 | 298 | super(val, parent, name); |
| 100 | 298 | this.dist = dist; |
| 101 | 298 | this.bootstrap = bootstrap; |
| 102 | 298 | this.dummy = dummy; |
| 103 | } | |
| 104 | ||
| 105 | /** | |
| 106 | * @param dummy | |
| 107 | * true if node is created for the representation of polytomous trees | |
| 108 | */ | |
| 109 | 34 | public boolean isDummy() |
| 110 | { | |
| 111 | 34 | return dummy; |
| 112 | } | |
| 113 | ||
| 114 | /* | |
| 115 | * @param placeholder is true if the sequence refered to in the element node | |
| 116 | * is not actually present in the associated alignment | |
| 117 | */ | |
| 118 | 370 | public boolean isPlaceholder() |
| 119 | { | |
| 120 | 370 | return placeholder; |
| 121 | } | |
| 122 | ||
| 123 | /** | |
| 124 | * DOCUMENT ME! | |
| 125 | * | |
| 126 | * @param newstate | |
| 127 | * DOCUMENT ME! | |
| 128 | * | |
| 129 | * @return DOCUMENT ME! | |
| 130 | */ | |
| 131 | 0 | public boolean setDummy(boolean newstate) |
| 132 | { | |
| 133 | 0 | boolean oldstate = dummy; |
| 134 | 0 | dummy = newstate; |
| 135 | ||
| 136 | 0 | return oldstate; |
| 137 | } | |
| 138 | ||
| 139 | /** | |
| 140 | * DOCUMENT ME! | |
| 141 | * | |
| 142 | * @param Placeholder | |
| 143 | * DOCUMENT ME! | |
| 144 | */ | |
| 145 | 38 | public void setPlaceholder(boolean Placeholder) |
| 146 | { | |
| 147 | 38 | this.placeholder = Placeholder; |
| 148 | } | |
| 149 | ||
| 150 | /** | |
| 151 | * ascends the tree but doesn't stop until a non-dummy node is discovered. | |
| 152 | * This will probably break if the tree is a mixture of BinaryNodes and | |
| 153 | * SequenceNodes. | |
| 154 | */ | |
| 155 | 140 | public SequenceNode AscendTree() |
| 156 | { | |
| 157 | 140 | SequenceNode c = this; |
| 158 | ||
| 159 | 140 | do |
| 160 | { | |
| 161 | 140 | c = (SequenceNode) c.parent(); |
| 162 | 140 | } while ((c != null) && c.dummy); |
| 163 | ||
| 164 | 140 | return c; |
| 165 | } | |
| 166 | ||
| 167 | /** | |
| 168 | * test if this node has a name that might be a label rather than a bootstrap | |
| 169 | * value | |
| 170 | * | |
| 171 | * @return true if node has a non-numeric label | |
| 172 | */ | |
| 173 | 0 | public boolean isSequenceLabel() |
| 174 | { | |
| 175 | 0 | if (name != null && name.length() > 0) |
| 176 | { | |
| 177 | 0 | for (int c = 0, s = name.length(); c < s; c++) |
| 178 | { | |
| 179 | 0 | char q = name.charAt(c); |
| 180 | 0 | if ('0' <= q && q <= '9') |
| 181 | { | |
| 182 | 0 | continue; |
| 183 | } | |
| 184 | 0 | return true; |
| 185 | } | |
| 186 | } | |
| 187 | 0 | return false; |
| 188 | } | |
| 189 | } |