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Coverage Report

  1. Project Clover database Thu Dec 4 2025 16:11:35 GMT
  2. Package jalview.gui

File PaintRefresher.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
30% of files have more coverage

Code metrics

62
83
7
1
276
202
39
0.47
11.86
7
5.57

Classes

Class Line # Actions
PaintRefresher 40 83 39
0.618421161.8%
 

Contributing tests

This file is covered by 199 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.gui;
22   
23    import jalview.datamodel.AlignmentI;
24    import jalview.datamodel.SequenceI;
25   
26    import java.awt.Component;
27    import java.util.ArrayList;
28    import java.util.HashMap;
29    import java.util.Iterator;
30    import java.util.List;
31    import java.util.Map;
32   
33    /**
34    * Route datamodel/view update events for a sequence set to any display
35    * components involved TODO: JV3 refactor to abstract gui/view package
36    *
37    * @author $author$
38    * @version $Revision$
39    */
 
40    public class PaintRefresher
41    {
42    private static final int ALIGNMENT_CHANGED = 1 << 0;
43    private static final int VALIDATE_SEQUENCES = 1 << 1;
44   
45    static Map<String, List<Component>> components = new HashMap<>();
46   
47    /**
48    * Add the given component to those registered under the given sequence set
49    * id. Does nothing if already added.
50    *
51    * @param comp
52    * @param al
53    */
 
54  1689 toggle public static void Register(Component comp, String seqSetId)
55    {
56  1689 if (components.containsKey(seqSetId))
57    {
58  1254 List<Component> comps = components.get(seqSetId);
59  1254 if (!comps.contains(comp))
60    {
61  1102 comps.add(comp);
62    }
63    }
64    else
65    {
66  435 List<Component> vcoms = new ArrayList<>();
67  435 vcoms.add(comp);
68  435 components.put(seqSetId, vcoms);
69    }
70    }
71   
72    /**
73    * Remove this component from all registrations. Also removes a registered
74    * sequence set id if there are no remaining components registered against it.
75    *
76    * @param comp
77    */
 
78  1532 toggle public static void RemoveComponent(Component comp)
79    {
80  1532 if (components == null)
81    {
82  0 return;
83    }
84   
85  1532 Iterator<String> it = components.keySet().iterator();
86  41221 while (it.hasNext())
87    {
88  39689 List<Component> comps = components.get(it.next());
89  39689 comps.remove(comp);
90  39689 if (comps.isEmpty())
91    {
92  269 it.remove();
93    }
94    }
95    }
96   
 
97  199 toggle public static void Refresh(Component source, String id)
98    {
99  199 Refresh(source, id, false, false);
100    }
101   
 
102  264 toggle public static void Refresh(Component source, String id,
103    boolean alignmentChanged, boolean validateSequences)
104    {
105  264 List<Component> comps = components.get(id);
106   
107  264 int mode = (alignmentChanged ? ALIGNMENT_CHANGED : 0) | (validateSequences ? VALIDATE_SEQUENCES : 0);
108  264 if (comps == null)
109    {
110  0 return;
111    }
112  264 repaintComponents(source, mode, comps.toArray(new Component[comps.size()]));
113    }
114   
 
115  264 toggle public static void repaintComponents(Component source, int mode,
116    Component... comps)
117    {
118  1453 for (int i = 0; i < comps.length; i++)
119    {
120  1189 Component comp = comps[i];
121  1189 if (comp == null)
122    {
123  0 continue;
124    }
125  1189 if (comp instanceof AlignmentPanel)
126    {
127  364 if ((mode & VALIDATE_SEQUENCES) != 0 && source instanceof AlignmentPanel)
128    {
129  149 validateSequences(((AlignmentPanel) source).av.getAlignment(),
130    ((AlignmentPanel) comp).av.getAlignment());
131    }
132  364 if ((mode & ALIGNMENT_CHANGED) != 0)
133    {
134  149 ((AlignmentPanel) comp).alignmentChanged();
135    }
136    }
137  825 else if (comp instanceof IdCanvas)
138    {
139    // BH 2019.04.22 fixes JS problem of repaint() consolidation
140    // that occurs in JavaScript but not Java [JAL-3226]
141  407 ((IdCanvas) comp).setNoFastPaint();
142    }
143  418 else if (comp instanceof SeqCanvas)
144    {
145    // BH 2019.04.22 fixes JS problem of repaint() consolidation
146    // that occurs in JavaScript but not Java [JAL-3226]
147  407 ((SeqCanvas) comp).setNoFastPaint();
148    }
149  1189 comp.repaint();
150    }
151    }
152   
 
153  149 toggle static void validateSequences(AlignmentI source, AlignmentI comp)
154    {
155  149 SequenceI[] a1;
156  149 if (source.getHiddenSequences().getSize() > 0)
157    {
158  130 a1 = source.getHiddenSequences().getFullAlignment()
159    .getSequencesArray();
160    }
161    else
162    {
163  19 a1 = source.getSequencesArray();
164    }
165   
166  149 SequenceI[] a2;
167  149 if (comp.getHiddenSequences().getSize() > 0)
168    {
169  129 a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
170    }
171    else
172    {
173  20 a2 = comp.getSequencesArray();
174    }
175   
176  149 int i, iSize = a1.length, j, jSize = a2.length;
177   
178  149 if (iSize == jSize)
179    {
180  149 return;
181    }
182   
183  0 boolean exists = false;
184  0 for (i = 0; i < iSize; i++)
185    {
186  0 exists = false;
187   
188  0 for (j = 0; j < jSize; j++)
189    {
190  0 if (a2[j] == a1[i])
191    {
192  0 exists = true;
193  0 break;
194    }
195    }
196   
197  0 if (!exists)
198    {
199  0 if (i < comp.getHeight())
200    {
201    // TODO: the following does not trigger any recalculation of
202    // height/etc, or maintain the dataset
203  0 if (comp.getDataset() != source.getDataset())
204    {
205    // raise an implementation warning here - not sure if this situation
206    // will ever occur
207  0 jalview.bin.Console.errPrintln(
208    "IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
209    }
210  0 List<SequenceI> alsq = comp.getSequences();
211  0 synchronized (alsq)
212    {
213  0 alsq.add(i, a1[i]);
214    }
215    }
216    else
217    {
218  0 comp.addSequence(a1[i]);
219    }
220   
221  0 if (comp.getHiddenSequences().getSize() > 0)
222    {
223  0 a2 = comp.getHiddenSequences().getFullAlignment()
224    .getSequencesArray();
225    }
226    else
227    {
228  0 a2 = comp.getSequencesArray();
229    }
230   
231  0 jSize = a2.length;
232    }
233    }
234   
235  0 iSize = a1.length;
236  0 jSize = a2.length;
237   
238  0 for (j = 0; j < jSize; j++)
239    {
240  0 exists = false;
241  0 for (i = 0; i < iSize; i++)
242    {
243  0 if (a2[j] == a1[i])
244    {
245  0 exists = true;
246  0 break;
247    }
248    }
249   
250  0 if (!exists)
251    {
252  0 comp.deleteSequence(a2[j]);
253    }
254    }
255    }
256   
 
257  21 toggle static AlignmentPanel[] getAssociatedPanels(String id)
258    {
259  21 List<Component> comps = components.get(id);
260  21 if (comps == null)
261    {
262  1 return new AlignmentPanel[0];
263    }
264  20 List<AlignmentPanel> tmp = new ArrayList<>();
265  20 for (Component comp : comps)
266    {
267  145 if (comp instanceof AlignmentPanel)
268    {
269  42 tmp.add((AlignmentPanel) comp);
270    }
271    }
272  20 return tmp.toArray(new AlignmentPanel[tmp.size()]);
273    }
274   
275   
276    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.