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Coverage Report

  1. Project Clover database Mon Dec 1 2025 13:17:41 GMT
  2. Package jalview.workers

File ConsensusThread.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

24
64
13
1
265
162
33
0.52
4.92
13
2.54

Classes

Class Line # Actions
ConsensusThread 33 64 33
0.871287187.1%
 

Contributing tests

This file is covered by 203 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.workers;
22   
23    import jalview.analysis.AAFrequency;
24    import jalview.api.AlignViewportI;
25    import jalview.api.AlignmentViewPanel;
26    import jalview.datamodel.AlignmentAnnotation;
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.Annotation;
29    import jalview.datamodel.ProfilesI;
30    import jalview.datamodel.SequenceI;
31    import jalview.renderer.ResidueShaderI;
32   
 
33    public class ConsensusThread extends AlignCalcWorker
34    {
 
35  528 toggle public ConsensusThread(AlignViewportI alignViewport,
36    AlignmentViewPanel alignPanel)
37    {
38  528 super(alignViewport, alignPanel);
39    }
40   
 
41  1568 toggle @Override
42    public void run()
43    {
44  1568 if (calcMan.isPending(this))
45    {
46  28 return;
47    }
48  1540 calcMan.notifyStart(this);
49    // long started = System.currentTimeMillis();
50  1540 try
51    {
52  1540 AlignmentAnnotation consensus = getConsensusAnnotation();
53  1540 AlignmentAnnotation gap = getGapAnnotation();
54  1540 if ((consensus == null && gap == null) || calcMan.isPending(this))
55    {
56  114 calcMan.workerComplete(this);
57  114 return;
58    }
59  1427 while (!calcMan.notifyWorking(this))
60    {
61    // jalview.bin.Console.errPrintln("Thread
62    // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
63  1 try
64    {
65  1 if (ap != null)
66    {
67  1 ap.paintAlignment(false, false);
68    }
69  1 Thread.sleep(200);
70    } catch (Exception ex)
71    {
72  0 ex.printStackTrace();
73    }
74    }
75  1426 if (alignViewport.isClosed())
76    {
77  0 abortAndDestroy();
78  0 return;
79    }
80  1426 AlignmentI alignment = alignViewport.getAlignment();
81   
82  1426 int aWidth = -1;
83   
84  ? if (alignment == null || (aWidth = alignment.getWidth()) < 0)
85    {
86  0 calcMan.workerComplete(this);
87  0 return;
88    }
89   
90  1426 eraseConsensus(aWidth);
91  1426 computeConsensus(alignment);
92  1426 updateResultAnnotation(true);
93   
94  1423 if (ap != null)
95    {
96  1423 ap.paintAlignment(true, true);
97    }
98    } catch (OutOfMemoryError error)
99    {
100  0 calcMan.disableWorker(this);
101  0 ap.raiseOOMWarning("calculating consensus", error);
102    } finally
103    {
104    /*
105    * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
106    * - alignment was edited at same time as calculation was running
107    */
108  1540 calcMan.workerComplete(this);
109    }
110    }
111   
112    /**
113    * Clear out any existing consensus annotations
114    *
115    * @param aWidth
116    * the width (number of columns) of the annotated alignment
117    */
 
118  1426 toggle protected void eraseConsensus(int aWidth)
119    {
120  1426 AlignmentAnnotation consensus = getConsensusAnnotation();
121  1426 if (consensus != null)
122    {
123  1426 consensus.annotations = new Annotation[aWidth];
124    }
125  1426 AlignmentAnnotation gap = getGapAnnotation();
126  1426 if (gap != null)
127    {
128  1415 gap.annotations = new Annotation[aWidth];
129    }
130    }
131   
132    /**
133    * @param alignment
134    */
 
135  1421 toggle protected void computeConsensus(AlignmentI alignment)
136    {
137   
138  1421 SequenceI[] aseqs = getSequences();
139  1421 int width = alignment.getWidth();
140  1421 ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
141    true);
142   
143  1421 alignViewport.setSequenceConsensusHash(hconsensus);
144  1421 setColourSchemeConsensus(hconsensus);
145    }
146   
147    /**
148    * @return
149    */
 
150  4284 toggle protected SequenceI[] getSequences()
151    {
152  4284 return alignViewport.getAlignment().getSequencesArray();
153    }
154   
155    /**
156    * @param hconsensus
157    */
 
158  1421 toggle protected void setColourSchemeConsensus(ProfilesI hconsensus)
159    {
160  1421 ResidueShaderI cs = alignViewport.getResidueShading();
161  1421 if (cs != null)
162    {
163  1418 cs.setConsensus(hconsensus);
164    }
165    }
166   
167    /**
168    * Get the Consensus annotation for the alignment
169    *
170    * @return
171    */
 
172  4396 toggle protected AlignmentAnnotation getConsensusAnnotation()
173    {
174  4396 return alignViewport.getAlignmentConsensusAnnotation();
175    }
176   
177    /**
178    * Get the Gap annotation for the alignment
179    *
180    * @return
181    */
 
182  4400 toggle protected AlignmentAnnotation getGapAnnotation()
183    {
184  4400 return alignViewport.getAlignmentGapAnnotation();
185    }
186   
187    /**
188    * update the consensus annotation from the sequence profile data using
189    * current visualization settings.
190    */
 
191  19 toggle @Override
192    public void updateAnnotation()
193    {
194  19 updateResultAnnotation(false);
195    }
196   
 
197  1440 toggle public void updateResultAnnotation(boolean immediate)
198    {
199  1440 AlignmentAnnotation consensus = getConsensusAnnotation();
200  1440 ProfilesI hconsensus = (ProfilesI) getViewportConsensus();
201  1440 if (immediate || !calcMan.isWorking(this) && consensus != null
202    && hconsensus != null)
203    {
204  1437 deriveConsensus(consensus, hconsensus);
205  1434 AlignmentAnnotation gap = getGapAnnotation();
206  1434 if (gap != null)
207    {
208  1421 deriveGap(gap, hconsensus);
209    }
210    }
211    }
212   
213    /**
214    * Convert the computed consensus data into the desired annotation for
215    * display.
216    *
217    * @param consensusAnnotation
218    * the annotation to be populated
219    * @param hconsensus
220    * the computed consensus data
221    */
 
222  1437 toggle protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
223    ProfilesI hconsensus)
224    {
225   
226  1437 long nseq = getSequences().length;
227  1434 consensusAnnotation.setNoOfSequencesIncluded(nseq);
228  1434 AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
229    hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
230    alignViewport.isIgnoreGapsConsensus(),
231    alignViewport.isShowSequenceLogo(), nseq);
232    // TODO: JAL-4425 - from JAL-4392 - uncommenting this line will mean consensus annotation is hidden if only one sequence is shown.
233    // consensusAnnotation.hasData=hconsensus.getCount()>1;
234   
235    }
236   
237    /**
238    * Convert the computed consensus data into a gap annotation row for display.
239    *
240    * @param gapAnnotation
241    * the annotation to be populated
242    * @param hconsensus
243    * the computed consensus data
244    */
 
245  1421 toggle protected void deriveGap(AlignmentAnnotation gapAnnotation,
246    ProfilesI hconsensus)
247    {
248  1421 long nseq = getSequences().length;
249  1421 gapAnnotation.setNoOfSequencesIncluded(nseq);
250  1421 AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
251    hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
252    nseq);
253    }
254   
255    /**
256    * Get the consensus data stored on the viewport.
257    *
258    * @return
259    */
 
260  1440 toggle protected Object getViewportConsensus()
261    {
262    // TODO convert ComplementConsensusThread to use Profile
263  1440 return alignViewport.getSequenceConsensusHash();
264    }
265    }
  • Report generated by OpenClover v 4.4.1 on Mon Dec 1 2025 13:27:33 GMT using coverage data from Mon Dec 1 2025 13:27:18 GMT.
  • OpenClover is free and open-source software.