Class |
Line # |
Actions |
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---|---|---|---|---|---|
StructureViewerModel | 32 | 29 | 21 | ||
StructureViewerModel.StructureData | 57 | 9 | 7 |
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 | 40 | public StructureData(String pdbFile, String id) |
74 | { | |
75 | 40 | this.filePath = pdbFile; |
76 | 40 | this.pdbId = id; |
77 | 40 | this.seqList = new ArrayList<SequenceI>(); |
78 | } | |
79 | ||
80 | 47 | public String getFilePath() |
81 | { | |
82 | 47 | return filePath; |
83 | } | |
84 | ||
85 | 0 | protected void setFilePath(String filePath) |
86 | { | |
87 | 0 | this.filePath = filePath; |
88 | } | |
89 | ||
90 | 7 | public String getPdbId() |
91 | { | |
92 | 7 | return pdbId; |
93 | } | |
94 | ||
95 | 0 | protected void setPdbId(String pdbId) |
96 | { | |
97 | 0 | this.pdbId = pdbId; |
98 | } | |
99 | ||
100 | 200 | public List<SequenceI> getSeqList() |
101 | { | |
102 | 200 | return seqList; |
103 | } | |
104 | ||
105 | 0 | protected void setSeqList(List<SequenceI> seqList) |
106 | { | |
107 | 0 | this.seqList = seqList; |
108 | } | |
109 | } | |
110 | ||
111 | 40 | public StructureViewerModel(int x, int y, int width, int height, |
112 | boolean alignWithPanel, boolean colourWithAlignPanel, | |
113 | boolean colourByViewer, String viewId, String type) | |
114 | { | |
115 | 40 | this.x = x; |
116 | 40 | this.y = y; |
117 | 40 | this.width = width; |
118 | 40 | this.height = height; |
119 | 40 | this.alignWithPanel = alignWithPanel; |
120 | 40 | this.colourWithAlignPanel = colourWithAlignPanel; |
121 | 40 | this.colourByViewer = colourByViewer; |
122 | 40 | this.viewId = viewId; |
123 | 40 | this.type = type; |
124 | } | |
125 | ||
126 | 12 | public int getX() |
127 | { | |
128 | 12 | return x; |
129 | } | |
130 | ||
131 | 0 | protected void setX(int x) |
132 | { | |
133 | 0 | this.x = x; |
134 | } | |
135 | ||
136 | 12 | public int getY() |
137 | { | |
138 | 12 | return y; |
139 | } | |
140 | ||
141 | 0 | protected void setY(int y) |
142 | { | |
143 | 0 | this.y = y; |
144 | } | |
145 | ||
146 | 12 | public int getWidth() |
147 | { | |
148 | 12 | return width; |
149 | } | |
150 | ||
151 | 0 | protected void setWidth(int width) |
152 | { | |
153 | 0 | this.width = width; |
154 | } | |
155 | ||
156 | 12 | public int getHeight() |
157 | { | |
158 | 12 | return height; |
159 | } | |
160 | ||
161 | 0 | public void setHeight(int height) |
162 | { | |
163 | 0 | this.height = height; |
164 | } | |
165 | ||
166 | 120 | public boolean isAlignWithPanel() |
167 | { | |
168 | 120 | return alignWithPanel; |
169 | } | |
170 | ||
171 | 80 | public void setAlignWithPanel(boolean alignWithPanel) |
172 | { | |
173 | 80 | this.alignWithPanel = alignWithPanel; |
174 | } | |
175 | ||
176 | 120 | public boolean isColourWithAlignPanel() |
177 | { | |
178 | 120 | return colourWithAlignPanel; |
179 | } | |
180 | ||
181 | 80 | public void setColourWithAlignPanel(boolean colourWithAlignPanel) |
182 | { | |
183 | 80 | this.colourWithAlignPanel = colourWithAlignPanel; |
184 | } | |
185 | ||
186 | 120 | public boolean isColourByViewer() |
187 | { | |
188 | 120 | return colourByViewer; |
189 | } | |
190 | ||
191 | 80 | public void setColourByViewer(boolean colourByViewer) |
192 | { | |
193 | 80 | this.colourByViewer = colourByViewer; |
194 | } | |
195 | ||
196 | 87 | public String getStateData() |
197 | { | |
198 | 87 | return stateData; |
199 | } | |
200 | ||
201 | 30 | public void setStateData(String stateData) |
202 | { | |
203 | 30 | this.stateData = stateData; |
204 | } | |
205 | ||
206 | 167 | public Map<File, StructureData> getFileData() |
207 | { | |
208 | 167 | 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 | 7 | public String getType() |
222 | { | |
223 | 7 | return this.type; |
224 | } | |
225 | } |