Coverage Report
File SequenceNode.java
Coverage histogram
52% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| SequenceNode | 29 | 13 | 12 |
Contributing tests
This file is covered by 11 tests.
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Source view
| 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 | /** | |
| 24 | * DOCUMENT ME! | |
| 25 | * | |
| 26 | * @author $author$ | |
| 27 | * @version $Revision$ | |
| 28 | */ | |
| 29 | public class SequenceNode extends BinaryNode<SequenceI> | |
| 30 | { | |
| 31 | private boolean placeholder = false; | |
| 32 | ||
| 33 | /** | |
| 34 | * Creates a new SequenceNode object. | |
| 35 | */ | |
| 36 | 20 |  public SequenceNode() |
| 37 | { | |
| 38 | 20 | super(); |
| 39 | } | |
| 40 | ||
| 41 | 396 | public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent, |
| 42 | String name, double dist, int bootstrap, boolean dummy) | |
| 43 | { | |
| 44 | 396 | super(val, parent, name, dist, bootstrap, dummy); |
| 45 | } | |
| 46 | ||
| 47 | 0 | public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent, |
| 48 | String name, double dist, int bootstrap) | |
| 49 | { | |
| 50 | 0 | super(element, parent, name, dist, bootstrap); |
| 51 | } | |
| 52 | ||
| 53 | 0 | public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent, |
| 54 | String name, double dist) | |
| 55 | { | |
| 56 | 0 | super(element, parent, name, dist); |
| 57 | } | |
| 58 | ||
| 59 | /* | |
| 60 | * @param placeholder is true if the sequence refered to in the element node | |
| 61 | * is not actually present in the associated alignment | |
| 62 | */ | |
| 63 | 185 | public boolean isPlaceholder() |
| 64 | { | |
| 65 | 185 | return placeholder; |
| 66 | } | |
| 67 | ||
| 68 | /** | |
| 69 | * DOCUMENT ME! | |
| 70 | * | |
| 71 | * @param Placeholder | |
| 72 | * DOCUMENT ME! | |
| 73 | */ | |
| 74 | 38 | public void setPlaceholder(boolean Placeholder) |
| 75 | { | |
| 76 | 38 | this.placeholder = Placeholder; |
| 77 | } | |
| 78 | ||
| 79 | /** | |
| 80 | * test if this node has a name that might be a label rather than a bootstrap | |
| 81 | * value | |
| 82 | * | |
| 83 | * @return true if node has a non-numeric label | |
| 84 | */ | |
| 85 | 0 | public boolean isSequenceLabel() |
| 86 | { | |
| 87 | 0 | if (name != null && name.length() > 0) |
| 88 | { | |
| 89 | 0 | for (int c = 0, s = name.length(); c < s; c++) |
| 90 | { | |
| 91 | 0 | char q = name.charAt(c); |
| 92 | 0 | if ('0' <= q && q <= '9') |
| 93 | { | |
| 94 | 0 | continue; |
| 95 | } | |
| 96 | 0 | return true; |
| 97 | } | |
| 98 | } | |
| 99 | 0 | return false; |
| 100 | } | |
| 101 | } |