jalviewX
File Atom.java
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12% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Atom | 27 | 28 | 8 | 4 |
Contributing tests
This file is covered by 29 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 mc_view; | |
| 22 | ||
| 23 | import jalview.schemes.ResidueProperties; | |
| 24 | ||
| 25 | import java.awt.Color; | |
| 26 | ||
| 27 | public class Atom | |
| 28 | { | |
| 29 | public float x; | |
| 30 | ||
| 31 | public float y; | |
| 32 | ||
| 33 | public float z; | |
| 34 | ||
| 35 | public int number; | |
| 36 | ||
| 37 | public String name; | |
| 38 | ||
| 39 | public String resName; | |
| 40 | ||
| 41 | public int resNumber; | |
| 42 | ||
| 43 | public char insCode = ' '; | |
| 44 | ||
| 45 | public String resNumIns = null; | |
| 46 | ||
| 47 | public int type; | |
| 48 | ||
| 49 | Color color = Color.lightGray; | |
| 50 | ||
| 51 | public String chain; | |
| 52 | ||
| 53 | /** | |
| 54 | * this is a temporary value - designed to store the position in sequence that | |
| 55 | * this atom corresponds to after aligning the chain to a SequenceI object. Do | |
| 56 | * not rely on its value being correct when visualizing sequence colourings on | |
| 57 | * the structure - use the StructureSelectionManager's mapping instead. | |
| 58 | */ | |
| 59 | public int alignmentMapping = -1; | |
| 60 | ||
| 61 | public int atomIndex; | |
| 62 | ||
| 63 | public float occupancy = 0; | |
| 64 | ||
| 65 | public float tfactor = 0; | |
| 66 | ||
| 67 | // need these if we ever want to export Atom data | |
| 68 | // public boolean tfacset=true,occset=true; | |
| 69 | public boolean isSelected = false; | |
| 70 | ||
| 71 | 3254 |  public Atom(String str) |
| 72 | { | |
| 73 | 3254 | atomIndex = Integer.parseInt(str.substring(6, 11).trim()); |
| 74 | ||
| 75 | 3253 | name = str.substring(12, 15).trim(); |
| 76 | ||
| 77 | 3253 | resName = str.substring(17, 20); |
| 78 | // JAL-1828 treat MSE Selenomethionine as MET (etc) | |
| 79 | 3253 | resName = ResidueProperties.getCanonicalAminoAcid(resName); |
| 80 | ||
| 81 | 3253 | chain = str.substring(21, 22); |
| 82 | ||
| 83 | 3253 | resNumber = Integer.parseInt(str.substring(22, 26).trim()); |
| 84 | 3253 | resNumIns = str.substring(22, 27).trim(); |
| 85 | 3253 | insCode = str.substring(26, 27).charAt(0); |
| 86 | 3253 | this.x = (new Float(str.substring(30, 38).trim()).floatValue()); |
| 87 | 3253 | this.y = (new Float(str.substring(38, 46).trim()).floatValue()); |
| 88 | 3253 | this.z = (new Float(str.substring(47, 55).trim()).floatValue()); |
| 89 | // optional entries - see JAL-730 | |
| 90 | 3253 | String tm = str.substring(54, 60).trim(); |
| 91 | 3253 | if (tm.length() > 0) |
| 92 | { | |
| 93 | 3252 | occupancy = (new Float(tm)).floatValue(); |
| 94 | } | |
| 95 | else | |
| 96 | { | |
| 97 | 1 | occupancy = 1f; // default occupancy |
| 98 | // see note above: occset=false; | |
| 99 | } | |
| 100 | 3253 | tm = str.substring(60, 66).trim(); |
| 101 | 3253 | if (tm.length() > 0) |
| 102 | { | |
| 103 | 3252 | tfactor = (new Float(tm).floatValue()); |
| 104 | } | |
| 105 | else | |
| 106 | { | |
| 107 | 1 | tfactor = 1f; |
| 108 | // see note above: tfacset=false; | |
| 109 | } | |
| 110 | } | |
| 111 | ||
| 112 | 4948363 | @Override |
| 113 | public boolean equals(Object that) | |
| 114 | { | |
| 115 | 4948363 | if (this == that || that == null) |
| 116 | { | |
| 117 | 0 | return true; |
| 118 | } | |
| 119 | 4948363 | if (that instanceof Atom) |
| 120 | { | |
| 121 | 4948363 | Atom other = (Atom) that; |
| 122 | 4948363 | return other.resName.equals(this.resName) |
| 123 | && other.resNumber == this.resNumber | |
| 124 | && other.resNumIns.equals(this.resNumIns) | |
| 125 | && other.chain.equals(this.chain); | |
| 126 | } | |
| 127 | 0 | return false; |
| 128 | } | |
| 129 | ||
| 130 | 19160 | public Atom(float x, float y, float z) |
| 131 | { | |
| 132 | 19160 | this.x = x; |
| 133 | 19160 | this.y = y; |
| 134 | 19160 | this.z = z; |
| 135 | } | |
| 136 | } |