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Coverage Report

  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.structure

File StructureCommandsBase.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
22% of files have more coverage

Code metrics

16
50
16
1
286
153
24
0.48
3.12
16
1.5

Classes

Class Line # Actions
StructureCommandsBase 38 50 24
0.7560975675.6%
 

Contributing tests

This file is covered by 60 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.structure;
22   
23    import java.awt.Color;
24    import java.util.ArrayList;
25    import java.util.List;
26    import java.util.Map;
27    import java.util.Map.Entry;
28   
29    import jalview.bin.Console;
30   
31    /**
32    * A base class holding methods useful to all classes that implement commands
33    * for structure viewers
34    *
35    * @author gmcarstairs
36    *
37    */
 
38    public abstract class StructureCommandsBase implements StructureCommandsI
39    {
40    public static final String NAMESPACE_PREFIX = "jv_";
41   
42    private static final String CMD_SEPARATOR = ";";
43   
44    /**
45    * Returns something that separates concatenated commands
46    *
47    * @return
48    */
 
49  4719 toggle protected String getCommandSeparator()
50    {
51  4720 return CMD_SEPARATOR;
52    }
53   
54    /**
55    * Returns the lowest model number used by the structure viewer
56    *
57    * @return
58    */
 
59  2 toggle @Override
60    public int getModelStartNo()
61    {
62  2 return 0;
63    }
64   
65    /**
66    * Helper method to add one contiguous range to the AtomSpec model for the
67    * given value (creating the model if necessary). As used by Jalview,
68    * {@code value} is
69    * <ul>
70    * <li>a colour, when building a 'colour structure by sequence' command</li>
71    * <li>a feature value, when building a 'set Chimera attributes from features'
72    * command</li>
73    * </ul>
74    *
75    * @param map
76    * @param value
77    * @param model
78    * @param startPos
79    * @param endPos
80    * @param chain
81    */
 
82  57 toggle public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
83    Object value, String model, int startPos, int endPos,
84    String chain)
85    {
86    /*
87    * Get/initialize map of data for the colour
88    */
89  57 AtomSpecModel atomSpec = map.get(value);
90  57 if (atomSpec == null)
91    {
92  21 atomSpec = new AtomSpecModel();
93  21 map.put(value, atomSpec);
94    }
95   
96  57 atomSpec.addRange(model, startPos, endPos, chain);
97    }
98   
99    /**
100    * Makes a structure viewer attribute name for a Jalview feature type by
101    * prefixing it with "jv_", and replacing any non-alphanumeric characters with
102    * an underscore
103    *
104    * @param featureType
105    * @return
106    */
 
107  21 toggle protected String makeAttributeName(String featureType)
108    {
109  21 StringBuilder sb = new StringBuilder();
110  21 if (featureType != null)
111    {
112  20 for (char c : featureType.toCharArray())
113    {
114  171 sb.append(Character.isLetterOrDigit(c) ? c : '_');
115    }
116    }
117  21 String attName = NAMESPACE_PREFIX + sb.toString();
118  21 return attName;
119    }
120   
121    /**
122    * Traverse the map of colours/models/chains/positions to construct a list of
123    * 'color' commands (one per distinct colour used). The format of each command
124    * is specific to the structure viewer.
125    * <p>
126    * The default implementation returns a single command containing one command
127    * per colour, concatenated.
128    *
129    * @param colourMap
130    * @return
131    */
 
132  502 toggle @Override
133    public List<StructureCommandI> colourBySequence(
134    Map<Object, AtomSpecModel> colourMap)
135    {
136  502 List<StructureCommandI> commands = new ArrayList<>();
137  502 StringBuilder sb = new StringBuilder(colourMap.size() * 20);
138  502 boolean first = true;
139  502 for (Object key : colourMap.keySet())
140    {
141  2582 Color colour = (Color) key;
142  2582 final AtomSpecModel colourData = colourMap.get(colour);
143  2582 StructureCommandI command = getColourCommand(colourData, colour);
144  2582 if (!first)
145    {
146  2132 sb.append(getCommandSeparator());
147    }
148  2582 first = false;
149  2582 sb.append(command.getCommand());
150    }
151   
152  502 commands.add(new StructureCommand(sb.toString()));
153  502 return commands;
154    }
155   
156    /**
157    * Returns a command to colour the atoms represented by {@code atomSpecModel}
158    * with the colour specified by {@code colourCode}.
159    *
160    * @param atomSpecModel
161    * @param colour
162    * @return
163    */
 
164  2585 toggle protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
165    Color colour)
166    {
167  2585 String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
168  2585 return colourResidues(atomSpec, colour);
169    }
170   
171    /**
172    * Returns a command to colour the atoms described (in viewer command syntax)
173    * by {@code atomSpec} with the colour specified by {@code colourCode}
174    *
175    * @param atomSpec
176    * @param colour
177    * @return
178    */
179    protected abstract StructureCommandI colourResidues(String atomSpec,
180    Color colour);
181   
 
182  0 toggle @Override
183    public List<StructureCommandI> colourByResidues(
184    Map<String, Color> colours)
185    {
186  0 List<StructureCommandI> commands = new ArrayList<>();
187  0 for (Entry<String, Color> entry : colours.entrySet())
188    {
189  0 commands.add(colourResidue(entry.getKey(), entry.getValue()));
190    }
191  0 return commands;
192    }
193   
 
194  0 toggle private StructureCommandI colourResidue(String resName, Color col)
195    {
196  0 String atomSpec = getResidueSpec(resName);
197  0 return colourResidues(atomSpec, col);
198    }
199   
200    /**
201    * Helper method to append one start-end range to an atomspec string
202    *
203    * @param sb
204    * @param start
205    * @param end
206    * @param chain
207    * @param firstPositionForModel
208    */
 
209  230 toggle protected void appendRange(StringBuilder sb, int start, int end,
210    String chain, boolean firstPositionForModel, boolean isChimeraX)
211    {
212  230 if (!firstPositionForModel)
213    {
214  59 sb.append(",");
215    }
216  230 if (end == start)
217    {
218  54 sb.append(start);
219    }
220    else
221    {
222  176 sb.append(start).append("-").append(end);
223    }
224   
225  230 if (!isChimeraX)
226    {
227  119 sb.append(".");
228  119 if (!" ".equals(chain))
229    {
230  117 sb.append(chain);
231    }
232    }
233    }
234   
235    /**
236    * Returns the atom specifier meaning all occurrences of the given residue
237    *
238    * @param residue
239    * @return
240    */
241    protected abstract String getResidueSpec(String residue);
242   
 
243  0 toggle @Override
244    public List<StructureCommandI> setAttributes(
245    Map<String, Map<Object, AtomSpecModel>> featureValues)
246    {
247    // default does nothing, override where this is implemented
248  0 return null;
249    }
250   
 
251  0 toggle @Override
252    public List<StructureCommandI> startNotifications(String uri)
253    {
254  0 return null;
255    }
256   
 
257  39 toggle @Override
258    public List<StructureCommandI> stopNotifications()
259    {
260  39 return null;
261    }
262   
 
263  0 toggle @Override
264    public StructureCommandI getSelectedResidues()
265    {
266  0 return null;
267    }
268   
 
269  0 toggle @Override
270    public StructureCommandI listResidueAttributes()
271    {
272  0 return null;
273    }
274   
 
275  0 toggle @Override
276    public StructureCommandI getResidueAttributes(String attName)
277    {
278  0 return null;
279    }
280   
 
281  0 toggle @Override
282    public StructureCommandI restoreSession(String filePath)
283    {
284  0 return loadFile(filePath);
285    }
286    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.