Clover icon

Coverage Report

  1. Project Clover database Fri Nov 15 2024 13:56:46 GMT
  2. Package jalview.workers

File ConsensusThread.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

24
62
13
1
263
160
33
0.53
4.77
13
2.54

Classes

Class Line # Actions
ConsensusThread 33 62 33
0.787878878.8%
 

Contributing tests

This file is covered by 186 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  463 toggle public ConsensusThread(AlignViewportI alignViewport,
36    AlignmentViewPanel alignPanel)
37    {
38  463 super(alignViewport, alignPanel);
39    }
40   
 
41  1039 toggle @Override
42    public void run()
43    {
44  1039 if (calcMan.isPending(this))
45    {
46  0 return;
47    }
48  1039 calcMan.notifyStart(this);
49    // long started = System.currentTimeMillis();
50  1039 try
51    {
52  1039 AlignmentAnnotation consensus = getConsensusAnnotation();
53  1039 AlignmentAnnotation gap = getGapAnnotation();
54  1039 if ((consensus == null && gap == null) || calcMan.isPending(this))
55    {
56  64 calcMan.workerComplete(this);
57  64 return;
58    }
59  975 while (!calcMan.notifyWorking(this))
60    {
61    // jalview.bin.Console.errPrintln("Thread
62    // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
63  0 try
64    {
65  0 if (ap != null)
66    {
67  0 ap.paintAlignment(false, false);
68    }
69  0 Thread.sleep(200);
70    } catch (Exception ex)
71    {
72  0 ex.printStackTrace();
73    }
74    }
75  975 if (alignViewport.isClosed())
76    {
77  0 abortAndDestroy();
78  0 return;
79    }
80  975 AlignmentI alignment = alignViewport.getAlignment();
81   
82  975 int aWidth = -1;
83   
84  ? if (alignment == null || (aWidth = alignment.getWidth()) < 0)
85    {
86  0 calcMan.workerComplete(this);
87  0 return;
88    }
89   
90  975 eraseConsensus(aWidth);
91  975 computeConsensus(alignment);
92  975 updateResultAnnotation(true);
93   
94  972 if (ap != null)
95    {
96  972 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  1039 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  975 toggle protected void eraseConsensus(int aWidth)
119    {
120  975 AlignmentAnnotation consensus = getConsensusAnnotation();
121  975 if (consensus != null)
122    {
123  975 consensus.annotations = new Annotation[aWidth];
124    }
125  975 AlignmentAnnotation gap = getGapAnnotation();
126  975 if (gap != null)
127    {
128  968 gap.annotations = new Annotation[aWidth];
129    }
130    }
131   
132    /**
133    * @param alignment
134    */
 
135  971 toggle protected void computeConsensus(AlignmentI alignment)
136    {
137   
138  971 SequenceI[] aseqs = getSequences();
139  971 int width = alignment.getWidth();
140  971 ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
141    true);
142   
143  971 alignViewport.setSequenceConsensusHash(hconsensus);
144  971 setColourSchemeConsensus(hconsensus);
145    }
146   
147    /**
148    * @return
149    */
 
150  2936 toggle protected SequenceI[] getSequences()
151    {
152  2936 return alignViewport.getAlignment().getSequencesArray();
153    }
154   
155    /**
156    * @param hconsensus
157    */
 
158  971 toggle protected void setColourSchemeConsensus(ProfilesI hconsensus)
159    {
160  971 ResidueShaderI cs = alignViewport.getResidueShading();
161  971 if (cs != null)
162    {
163  969 cs.setConsensus(hconsensus);
164    }
165    }
166   
167    /**
168    * Get the Consensus annotation for the alignment
169    *
170    * @return
171    */
 
172  2994 toggle protected AlignmentAnnotation getConsensusAnnotation()
173    {
174  2994 return alignViewport.getAlignmentConsensusAnnotation();
175    }
176   
177    /**
178    * Get the Gap annotation for the alignment
179    *
180    * @return
181    */
 
182  2997 toggle protected AlignmentAnnotation getGapAnnotation()
183    {
184  2997 return alignViewport.getAlignmentGapAnnotation();
185    }
186   
187    /**
188    * update the consensus annotation from the sequence profile data using
189    * current visualization settings.
190    */
 
191  17 toggle @Override
192    public void updateAnnotation()
193    {
194  17 updateResultAnnotation(false);
195    }
196   
 
197  988 toggle public void updateResultAnnotation(boolean immediate)
198    {
199  988 AlignmentAnnotation consensus = getConsensusAnnotation();
200  988 ProfilesI hconsensus = (ProfilesI) getViewportConsensus();
201  988 if (immediate || !calcMan.isWorking(this) && consensus != null
202    && hconsensus != null)
203    {
204  985 deriveConsensus(consensus, hconsensus);
205  983 AlignmentAnnotation gap = getGapAnnotation();
206  983 if (gap != null)
207    {
208  976 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  985 toggle protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
223    ProfilesI hconsensus)
224    {
225   
226  985 long nseq = getSequences().length;
227  983 AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
228    hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
229    alignViewport.isIgnoreGapsConsensus(),
230    alignViewport.isShowSequenceLogo(), nseq);
231    // TODO: JAL-4425 - from JAL-4392 - uncommenting this line will mean consensus annotation is hidden if only one sequence is shown.
232    // consensusAnnotation.hasData=hconsensus.getCount()>1;
233   
234    }
235   
236    /**
237    * Convert the computed consensus data into a gap annotation row for display.
238    *
239    * @param gapAnnotation
240    * the annotation to be populated
241    * @param hconsensus
242    * the computed consensus data
243    */
 
244  976 toggle protected void deriveGap(AlignmentAnnotation gapAnnotation,
245    ProfilesI hconsensus)
246    {
247  976 long nseq = getSequences().length;
248  976 AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
249    hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
250    nseq);
251    }
252   
253    /**
254    * Get the consensus data stored on the viewport.
255    *
256    * @return
257    */
 
258  988 toggle protected Object getViewportConsensus()
259    {
260    // TODO convert ComplementConsensusThread to use Profile
261  988 return alignViewport.getSequenceConsensusHash();
262    }
263    }
  • Report generated by OpenClover v 4.4.1 on Fri Nov 15 2024 14:04:22 GMT using coverage data from Fri Nov 15 2024 14:04:05 GMT.
  • OpenClover is free and open-source software.