1 package jalview.workers;
3 import java.util.Hashtable;
5 import jalview.analysis.AAFrequency;
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 AlignCalcWorkerI
16 public StrucConsensusThread(AlignViewportI alignViewport,
17 AlignmentViewPanel alignPanel)
19 super(alignViewport, alignPanel);
25 calcMan.notifyStart(this);
26 while (!calcMan.notifyWorking(this))
32 ap.paintAlignment(false);
36 } catch (Exception ex)
41 if (alignViewport.isClosed())
45 AlignmentI alignment = alignViewport.getAlignment();
49 if (alignment == null || (aWidth = alignment.getWidth()) < 0)
51 calcMan.workerComplete(this);
54 AlignmentAnnotation strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
55 Hashtable[] hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
56 strucConsensus.annotations = null;
57 strucConsensus.annotations = new Annotation[aWidth];
59 hStrucConsensus = new Hashtable[aWidth];
61 AlignmentAnnotation[] aa = alignViewport.getAlignment()
62 .getAlignmentAnnotation();
63 AlignmentAnnotation rnaStruc = null;
64 // select rna struct to use for calculation
65 for (int i = 0; i < aa.length; i++)
67 if (aa[i].getRNAStruc() != null)
73 // check to see if its valid
75 if (rnaStruc==null || !rnaStruc.isValidStruc())
77 calcMan.workerComplete(this);
81 jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
82 alignment.getWidth(), hStrucConsensus, true, rnaStruc);
83 alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
84 // TODO AlignmentAnnotation rnaStruc!!!
85 updateResultAnnotation(true);
86 if (alignViewport.getGlobalColourScheme()!= null)
88 alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
91 } catch (OutOfMemoryError error)
93 calcMan.workerCannotRun(this);
97 ap.raiseOOMWarning("calculating RNA structure consensus", error);
100 calcMan.workerComplete(this);
103 ap.paintAlignment(true);
108 * update the consensus annotation from the sequence profile data using
109 * current visualization settings.
111 public void updateAnnotation()
113 updateResultAnnotation(false);
116 public void updateResultAnnotation(boolean immediate)
118 AlignmentAnnotation strucConsensus = alignViewport
119 .getAlignmentStrucConsensusAnnotation();
120 Hashtable[] hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
121 if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
123 StructureFrequency.completeConsensus(strucConsensus,
124 hStrucConsensus, 0, hStrucConsensus.length,
125 alignViewport.getIgnoreGapsConsensus(),
126 alignViewport.isShowSequenceLogo());