jalviewX
File StructureViewerModel.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| StructureViewerModel | 32 | 29 | 21 | 10 | ||
| StructureViewerModel.StructureData | 57 | 9 | 7 | 6 |
Contributing tests
This file is covered by 6 tests.
.
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 | import java.io.File; | |
| 24 | import java.util.ArrayList; | |
| 25 | import java.util.HashMap; | |
| 26 | import java.util.List; | |
| 27 | import java.util.Map; | |
| 28 | ||
| 29 | /** | |
| 30 | * A data bean to hold stored data about a structure viewer. | |
| 31 | */ | |
| 32 | public class StructureViewerModel | |
| 33 | { | |
| 34 | private int x; | |
| 35 | ||
| 36 | private int y; | |
| 37 | ||
| 38 | private int width; | |
| 39 | ||
| 40 | private int height; | |
| 41 | ||
| 42 | private boolean alignWithPanel; | |
| 43 | ||
| 44 | private boolean colourWithAlignPanel; | |
| 45 | ||
| 46 | private boolean colourByViewer; | |
| 47 | ||
| 48 | private String stateData = ""; | |
| 49 | ||
| 50 | private String viewId; | |
| 51 | ||
| 52 | // CHIMERA or JMOL (for projects from Jalview 2.9 on) | |
| 53 | private String type; | |
| 54 | ||
| 55 | private Map<File, StructureData> fileData = new HashMap<File, StructureData>(); | |
| 56 | ||
| 57 | public class StructureData | |
| 58 | { | |
| 59 | private String filePath; | |
| 60 | ||
| 61 | private String pdbId; | |
| 62 | ||
| 63 | private List<SequenceI> seqList; | |
| 64 | ||
| 65 | // TODO and possibly a list of chains? | |
| 66 | ||
| 67 | /** | |
| 68 | * Constructor given structure file path and id. | |
| 69 | * | |
| 70 | * @param pdbFile | |
| 71 | * @param id | |
| 72 | */ | |
| 73 | 60 |  public StructureData(String pdbFile, String id) |
| 74 | { | |
| 75 | 60 | this.filePath = pdbFile; |
| 76 | 60 | this.pdbId = id; |
| 77 | 60 | this.seqList = new ArrayList<SequenceI>(); |
| 78 | } | |
| 79 | ||
| 80 | 68 | public String getFilePath() |
| 81 | { | |
| 82 | 68 | return filePath; |
| 83 | } | |
| 84 | ||
| 85 | 0 | protected void setFilePath(String filePath) |
| 86 | { | |
| 87 | 0 | this.filePath = filePath; |
| 88 | } | |
| 89 | ||
| 90 | 8 | public String getPdbId() |
| 91 | { | |
| 92 | 8 | return pdbId; |
| 93 | } | |
| 94 | ||
| 95 | 0 | protected void setPdbId(String pdbId) |
| 96 | { | |
| 97 | 0 | this.pdbId = pdbId; |
| 98 | } | |
| 99 | ||
| 100 | 300 | public List<SequenceI> getSeqList() |
| 101 | { | |
| 102 | 300 | return seqList; |
| 103 | } | |
| 104 | ||
| 105 | 0 | protected void setSeqList(List<SequenceI> seqList) |
| 106 | { | |
| 107 | 0 | this.seqList = seqList; |
| 108 | } | |
| 109 | } | |
| 110 | ||
| 111 | 60 | public StructureViewerModel(int x, int y, int width, int height, |
| 112 | boolean alignWithPanel, boolean colourWithAlignPanel, | |
| 113 | boolean colourByViewer, String viewId, String type) | |
| 114 | { | |
| 115 | 60 | this.x = x; |
| 116 | 60 | this.y = y; |
| 117 | 60 | this.width = width; |
| 118 | 60 | this.height = height; |
| 119 | 60 | this.alignWithPanel = alignWithPanel; |
| 120 | 60 | this.colourWithAlignPanel = colourWithAlignPanel; |
| 121 | 60 | this.colourByViewer = colourByViewer; |
| 122 | 60 | this.viewId = viewId; |
| 123 | 60 | this.type = type; |
| 124 | } | |
| 125 | ||
| 126 | 28 | public int getX() |
| 127 | { | |
| 128 | 28 | return x; |
| 129 | } | |
| 130 | ||
| 131 | 0 | protected void setX(int x) |
| 132 | { | |
| 133 | 0 | this.x = x; |
| 134 | } | |
| 135 | ||
| 136 | 28 | public int getY() |
| 137 | { | |
| 138 | 28 | return y; |
| 139 | } | |
| 140 | ||
| 141 | 0 | protected void setY(int y) |
| 142 | { | |
| 143 | 0 | this.y = y; |
| 144 | } | |
| 145 | ||
| 146 | 28 | public int getWidth() |
| 147 | { | |
| 148 | 28 | return width; |
| 149 | } | |
| 150 | ||
| 151 | 0 | protected void setWidth(int width) |
| 152 | { | |
| 153 | 0 | this.width = width; |
| 154 | } | |
| 155 | ||
| 156 | 28 | public int getHeight() |
| 157 | { | |
| 158 | 28 | return height; |
| 159 | } | |
| 160 | ||
| 161 | 0 | public void setHeight(int height) |
| 162 | { | |
| 163 | 0 | this.height = height; |
| 164 | } | |
| 165 | ||
| 166 | 180 | public boolean isAlignWithPanel() |
| 167 | { | |
| 168 | 180 | return alignWithPanel; |
| 169 | } | |
| 170 | ||
| 171 | 120 | public void setAlignWithPanel(boolean alignWithPanel) |
| 172 | { | |
| 173 | 120 | this.alignWithPanel = alignWithPanel; |
| 174 | } | |
| 175 | ||
| 176 | 180 | public boolean isColourWithAlignPanel() |
| 177 | { | |
| 178 | 180 | return colourWithAlignPanel; |
| 179 | } | |
| 180 | ||
| 181 | 120 | public void setColourWithAlignPanel(boolean colourWithAlignPanel) |
| 182 | { | |
| 183 | 120 | this.colourWithAlignPanel = colourWithAlignPanel; |
| 184 | } | |
| 185 | ||
| 186 | 180 | public boolean isColourByViewer() |
| 187 | { | |
| 188 | 180 | return colourByViewer; |
| 189 | } | |
| 190 | ||
| 191 | 120 | public void setColourByViewer(boolean colourByViewer) |
| 192 | { | |
| 193 | 120 | this.colourByViewer = colourByViewer; |
| 194 | } | |
| 195 | ||
| 196 | 128 | public String getStateData() |
| 197 | { | |
| 198 | 128 | return stateData; |
| 199 | } | |
| 200 | ||
| 201 | 50 | public void setStateData(String stateData) |
| 202 | { | |
| 203 | 50 | this.stateData = stateData; |
| 204 | } | |
| 205 | ||
| 206 | 240 | public Map<File, StructureData> getFileData() |
| 207 | { | |
| 208 | 240 | return fileData; |
| 209 | } | |
| 210 | ||
| 211 | 0 | protected void setFileData(Map<File, StructureData> fileData) |
| 212 | { | |
| 213 | 0 | this.fileData = fileData; |
| 214 | } | |
| 215 | ||
| 216 | 2 | public String getViewId() |
| 217 | { | |
| 218 | 2 | return this.viewId; |
| 219 | } | |
| 220 | ||
| 221 | 16 | public String getType() |
| 222 | { | |
| 223 | 16 | return this.type; |
| 224 | } | |
| 225 | } |