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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:56:54 GMT
  2. Package jalview.gui

File PaintRefresher.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
36% of files have more coverage

Code metrics

56
80
6
1
265
193
35
0.44
13.33
6
5.83

Classes

Class Line # Actions
PaintRefresher 40 80 35
0.591549359.2%
 

Contributing tests

This file is covered by 190 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    static Map<String, List<Component>> components = new HashMap<>();
43   
44    /**
45    * Add the given component to those registered under the given sequence set
46    * id. Does nothing if already added.
47    *
48    * @param comp
49    * @param al
50    */
 
51  1551 toggle public static void Register(Component comp, String seqSetId)
52    {
53  1551 if (components.containsKey(seqSetId))
54    {
55  1151 List<Component> comps = components.get(seqSetId);
56  1151 if (!comps.contains(comp))
57    {
58  1019 comps.add(comp);
59    }
60    }
61    else
62    {
63  400 List<Component> vcoms = new ArrayList<>();
64  400 vcoms.add(comp);
65  400 components.put(seqSetId, vcoms);
66    }
67    }
68   
69    /**
70    * Remove this component from all registrations. Also removes a registered
71    * sequence set id if there are no remaining components registered against it.
72    *
73    * @param comp
74    */
 
75  1156 toggle public static void RemoveComponent(Component comp)
76    {
77  1156 if (components == null)
78    {
79  0 return;
80    }
81   
82  1156 Iterator<String> it = components.keySet().iterator();
83  57784 while (it.hasNext())
84    {
85  56628 List<Component> comps = components.get(it.next());
86  56628 comps.remove(comp);
87  56628 if (comps.isEmpty())
88    {
89  206 it.remove();
90    }
91    }
92    }
93   
 
94  109 toggle public static void Refresh(Component source, String id)
95    {
96  109 Refresh(source, id, false, false);
97    }
98   
 
99  173 toggle public static void Refresh(Component source, String id,
100    boolean alignmentChanged, boolean validateSequences)
101    {
102  173 List<Component> comps = components.get(id);
103   
104  173 if (comps == null)
105    {
106  0 return;
107    }
108   
109  173 for (Component comp : comps)
110    {
111  762 if (comp == source)
112    {
113  77 continue;
114    }
115  685 if (comp instanceof AlignmentPanel)
116    {
117  170 if (validateSequences && source instanceof AlignmentPanel)
118    {
119  71 validateSequences(((AlignmentPanel) source).av.getAlignment(),
120    ((AlignmentPanel) comp).av.getAlignment());
121    }
122  170 if (alignmentChanged)
123    {
124  71 ((AlignmentPanel) comp).alignmentChanged();
125    }
126    }
127  515 else if (comp instanceof IdCanvas)
128    {
129    // BH 2019.04.22 fixes JS problem of repaint() consolidation
130    // that occurs in JavaScript but not Java [JAL-3226]
131  250 ((IdCanvas) comp).fastPaint = false;
132    }
133  265 else if (comp instanceof SeqCanvas)
134    {
135    // BH 2019.04.22 fixes JS problem of repaint() consolidation
136    // that occurs in JavaScript but not Java [JAL-3226]
137  250 ((SeqCanvas) comp).fastPaint = false;
138    }
139  684 comp.repaint();
140    }
141    }
142   
 
143  71 toggle static void validateSequences(AlignmentI source, AlignmentI comp)
144    {
145  71 SequenceI[] a1;
146  71 if (source.getHiddenSequences().getSize() > 0)
147    {
148  71 a1 = source.getHiddenSequences().getFullAlignment()
149    .getSequencesArray();
150    }
151    else
152    {
153  0 a1 = source.getSequencesArray();
154    }
155   
156  71 SequenceI[] a2;
157  71 if (comp.getHiddenSequences().getSize() > 0)
158    {
159  70 a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
160    }
161    else
162    {
163  1 a2 = comp.getSequencesArray();
164    }
165   
166  71 int i, iSize = a1.length, j, jSize = a2.length;
167   
168  71 if (iSize == jSize)
169    {
170  71 return;
171    }
172   
173  0 boolean exists = false;
174  0 for (i = 0; i < iSize; i++)
175    {
176  0 exists = false;
177   
178  0 for (j = 0; j < jSize; j++)
179    {
180  0 if (a2[j] == a1[i])
181    {
182  0 exists = true;
183  0 break;
184    }
185    }
186   
187  0 if (!exists)
188    {
189  0 if (i < comp.getHeight())
190    {
191    // TODO: the following does not trigger any recalculation of
192    // height/etc, or maintain the dataset
193  0 if (comp.getDataset() != source.getDataset())
194    {
195    // raise an implementation warning here - not sure if this situation
196    // will ever occur
197  0 jalview.bin.Console.errPrintln(
198    "IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
199    }
200  0 List<SequenceI> alsq = comp.getSequences();
201  0 synchronized (alsq)
202    {
203  0 alsq.add(i, a1[i]);
204    }
205    }
206    else
207    {
208  0 comp.addSequence(a1[i]);
209    }
210   
211  0 if (comp.getHiddenSequences().getSize() > 0)
212    {
213  0 a2 = comp.getHiddenSequences().getFullAlignment()
214    .getSequencesArray();
215    }
216    else
217    {
218  0 a2 = comp.getSequencesArray();
219    }
220   
221  0 jSize = a2.length;
222    }
223    }
224   
225  0 iSize = a1.length;
226  0 jSize = a2.length;
227   
228  0 for (j = 0; j < jSize; j++)
229    {
230  0 exists = false;
231  0 for (i = 0; i < iSize; i++)
232    {
233  0 if (a2[j] == a1[i])
234    {
235  0 exists = true;
236  0 break;
237    }
238    }
239   
240  0 if (!exists)
241    {
242  0 comp.deleteSequence(a2[j]);
243    }
244    }
245    }
246   
 
247  1623 toggle static AlignmentPanel[] getAssociatedPanels(String id)
248    {
249  1623 List<Component> comps = components.get(id);
250  1623 if (comps == null)
251    {
252  1 return new AlignmentPanel[0];
253    }
254  1622 List<AlignmentPanel> tmp = new ArrayList<>();
255  1622 for (Component comp : comps)
256    {
257  7544 if (comp instanceof AlignmentPanel)
258    {
259  2135 tmp.add((AlignmentPanel) comp);
260    }
261    }
262  1622 return tmp.toArray(new AlignmentPanel[tmp.size()]);
263    }
264   
265    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 10:04:05 GMT using coverage data from Mon Nov 18 2024 10:03:47 GMT.
  • OpenClover is free and open-source software.