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Coverage Report

  1. Project Clover database Mon Nov 11 2024 20:42:03 GMT
  2. Package jalview.appletgui

File PaintRefresher.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

58
84
6
1
262
195
38
0.45
14
6
6.33

Classes

Class Line # Actions
PaintRefresher 39 84 38
0.00%
 

Contributing tests

No tests hitting this source file were found.

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.appletgui;
22   
23    import jalview.datamodel.AlignmentI;
24    import jalview.datamodel.SequenceI;
25   
26    import java.awt.Component;
27    import java.util.Hashtable;
28    import java.util.Iterator;
29    import java.util.List;
30    import java.util.Map;
31    import java.util.Vector;
32   
33    /**
34    * DOCUMENT ME!
35    *
36    * @author $author$
37    * @version $Revision$
38    */
 
39    public class PaintRefresher
40    {
41    static Map<String, Vector<Component>> components;
42   
43    /**
44    * DOCUMENT ME!
45    *
46    * @param comp
47    * DOCUMENT ME!
48    * @param al
49    * DOCUMENT ME!
50    */
 
51  0 toggle public static void Register(Component comp, String seqSetId)
52    {
53  0 if (components == null)
54    {
55  0 components = new Hashtable<>();
56    }
57   
58  0 if (components.containsKey(seqSetId))
59    {
60  0 Vector<Component> comps = components.get(seqSetId);
61  0 if (!comps.contains(comp))
62    {
63  0 comps.addElement(comp);
64    }
65    }
66    else
67    {
68  0 Vector<Component> vcoms = new Vector<>();
69  0 vcoms.addElement(comp);
70  0 components.put(seqSetId, vcoms);
71    }
72    }
73   
 
74  0 toggle public static void RemoveComponent(Component comp)
75    {
76  0 if (components == null)
77    {
78  0 return;
79    }
80   
81  0 Iterator<String> it = components.keySet().iterator();
82  0 while (it.hasNext())
83    {
84  0 Vector<Component> comps = components.get(it.next());
85  0 comps.removeElement(comp);
86  0 if (comps.isEmpty())
87    {
88  0 it.remove();
89    }
90    }
91    }
92   
 
93  0 toggle public static void Refresh(Component source, String id)
94    {
95  0 Refresh(source, id, false, false);
96    }
97   
 
98  0 toggle public static void Refresh(Component source, String id,
99    boolean alignmentChanged, boolean validateSequences)
100    {
101  0 if (components == null)
102    {
103  0 return;
104    }
105   
106  0 Component comp;
107  0 Vector<Component> comps = components.get(id);
108   
109  0 if (comps == null)
110    {
111  0 return;
112    }
113   
114  0 Iterator<Component> it = comps.iterator();
115  0 while (it.hasNext())
116    {
117  0 comp = it.next();
118   
119  0 if (comp == source)
120    {
121  0 continue;
122    }
123   
124  0 if (!comp.isValid())
125    {
126  0 it.remove();
127    }
128  0 else if (validateSequences && comp instanceof AlignmentPanel
129    && source instanceof AlignmentPanel)
130    {
131  0 validateSequences(((AlignmentPanel) source).av.getAlignment(),
132    ((AlignmentPanel) comp).av.getAlignment());
133    }
134   
135  0 if (comp instanceof AlignmentPanel && alignmentChanged)
136    {
137  0 ((AlignmentPanel) comp).alignmentChanged();
138    }
139   
140  0 comp.repaint();
141    }
142    }
143   
 
144  0 toggle static void validateSequences(AlignmentI source, AlignmentI comp)
145    {
146  0 SequenceI[] a1;
147  0 if (source.getHiddenSequences().getSize() > 0)
148    {
149  0 a1 = source.getHiddenSequences().getFullAlignment()
150    .getSequencesArray();
151    }
152    else
153    {
154  0 a1 = source.getSequencesArray();
155    }
156   
157  0 SequenceI[] a2;
158  0 if (comp.getHiddenSequences().getSize() > 0)
159    {
160  0 a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
161    }
162    else
163    {
164  0 a2 = comp.getSequencesArray();
165    }
166   
167  0 int i, iSize = a1.length, j, jSize = a2.length;
168   
169  0 if (iSize == jSize)
170    {
171  0 return;
172    }
173   
174  0 boolean exists = false;
175  0 for (i = 0; i < iSize; i++)
176    {
177  0 exists = false;
178   
179  0 for (j = 0; j < jSize; j++)
180    {
181  0 if (a2[j] == a1[i])
182    {
183  0 exists = true;
184  0 break;
185    }
186    }
187   
188  0 if (!exists)
189    {
190  0 if (i < comp.getHeight())
191    {
192    // TODO: the following does not trigger any recalculation of
193    // height/etc, or maintain the dataset
194  0 List<SequenceI> alsq = comp.getSequences();
195  0 synchronized (alsq)
196    {
197  0 alsq.add(i, a1[i]);
198    }
199    }
200    else
201    {
202  0 comp.addSequence(a1[i]);
203    }
204   
205  0 if (comp.getHiddenSequences().getSize() > 0)
206    {
207  0 a2 = comp.getHiddenSequences().getFullAlignment()
208    .getSequencesArray();
209    }
210    else
211    {
212  0 a2 = comp.getSequencesArray();
213    }
214   
215  0 jSize = a2.length;
216    }
217    }
218   
219  0 iSize = a1.length;
220  0 jSize = a2.length;
221   
222  0 for (j = 0; j < jSize; j++)
223    {
224  0 exists = false;
225  0 for (i = 0; i < iSize; i++)
226    {
227  0 if (a2[j] == a1[i])
228    {
229  0 exists = true;
230  0 break;
231    }
232    }
233   
234  0 if (!exists)
235    {
236  0 comp.deleteSequence(a2[j]);
237    }
238    }
239    }
240   
 
241  0 toggle public static AlignmentPanel[] getAssociatedPanels(String id)
242    {
243  0 Vector<Component> comps = components.get(id);
244  0 Vector<Component> tmp = new Vector<>();
245  0 int i, iSize = comps.size();
246  0 for (i = 0; i < iSize; i++)
247    {
248  0 if (comps.elementAt(i) instanceof AlignmentPanel)
249    {
250  0 tmp.addElement(comps.elementAt(i));
251    }
252    }
253  0 AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
254  0 for (int ix = 0; ix < result.length; ix++)
255    {
256  0 result[ix] = (AlignmentPanel) tmp.elementAt(ix);
257    }
258   
259  0 return result;
260    }
261   
262    }