1 package jalview.workers;
3 import java.util.Hashtable;
5 import jalview.analysis.StructureFrequency;
6 import jalview.analysis.StructureFrequency;
7 import jalview.api.AlignCalcWorkerI;
8 import jalview.api.AlignViewportI;
9 import jalview.api.AlignmentViewPanel;
10 import jalview.datamodel.AlignmentAnnotation;
11 import jalview.datamodel.AlignmentI;
12 import jalview.datamodel.Annotation;
14 public class StrucConsensusThread extends AlignCalcWorker implements
17 public StrucConsensusThread(AlignViewportI alignViewport,
18 AlignmentViewPanel alignPanel)
20 super(alignViewport, alignPanel);
23 AlignmentAnnotation strucConsensus;
25 Hashtable[] hStrucConsensus;
32 if (calcMan.isPending(this))
36 calcMan.notifyStart(this);
37 while (!calcMan.notifyWorking(this))
43 // ap.paintAlignment(false);
47 } catch (Exception ex)
52 if (alignViewport.isClosed())
56 AlignmentI alignment = alignViewport.getAlignment();
60 if (alignment == null || (aWidth = alignment.getWidth()) < 0)
62 calcMan.workerComplete(this);
65 strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
66 hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
67 strucConsensus.annotations = null;
68 strucConsensus.annotations = new Annotation[aWidth];
70 hStrucConsensus = new Hashtable[aWidth];
72 AlignmentAnnotation[] aa = alignViewport.getAlignment()
73 .getAlignmentAnnotation();
74 AlignmentAnnotation rnaStruc = null;
75 // select rna struct to use for calculation
76 for (int i = 0; i < aa.length; i++)
78 if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
84 // check to see if its valid
86 if (rnaStruc == null || !rnaStruc.isValidStruc())
88 calcMan.workerComplete(this);
93 jalview.analysis.StructureFrequency.calculate(
94 alignment.getSequencesArray(), 0, alignment.getWidth(),
95 hStrucConsensus, true, rnaStruc);
96 } catch (ArrayIndexOutOfBoundsException x)
98 calcMan.workerComplete(this);
101 alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
102 // TODO AlignmentAnnotation rnaStruc!!!
103 updateResultAnnotation(true);
104 if (alignViewport.getGlobalColourScheme() != null)
106 alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
109 } catch (OutOfMemoryError error)
111 calcMan.workerCannotRun(this);
114 // hconsensus = null;
115 ap.raiseOOMWarning("calculating RNA structure consensus", error);
118 calcMan.workerComplete(this);
121 ap.paintAlignment(true);
128 * update the consensus annotation from the sequence profile data using
129 * current visualization settings.
132 public void updateAnnotation()
134 updateResultAnnotation(false);
137 public void updateResultAnnotation(boolean immediate)
139 if (immediate || !calcMan.isWorking(this) && strucConsensus != null
140 && hStrucConsensus != null)
142 StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
143 0, hStrucConsensus.length,
144 alignViewport.getIgnoreGapsConsensus(),
145 alignViewport.isShowSequenceLogo());