site/j2s/jalview/workers/ComplementConsensusThread.js

   1 Clazz.declarePackage ("jalview.workers");\r
   2 Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () {\r
   3 c$ = Clazz.decorateAsClass (function () {\r
   4 this.mappings = null;\r
   5 Clazz.instantialize (this, arguments);\r
   6 }, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread);\r
   7 Clazz.overrideMethod (c$, "getNewWorker", \r
   8 function () {\r
   9 return  new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap);\r
  10 });\r
  11 Clazz.overrideMethod (c$, "getConsensusAnnotation", \r
  12 function () {\r
  13 return this.alignViewport.getComplementConsensusAnnotation ();\r
  14 });\r
  15 Clazz.overrideMethod (c$, "getViewportConsensus", \r
  16 function () {\r
  17 return this.alignViewport.getComplementConsensusHash ();\r
  18 });\r
  19 Clazz.defineMethod (c$, "initializeCalc", \r
  20 function () {\r
  21 this.mappings = this.alignment.getCodonFrames ();\r
  22 return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", []));\r
  23 });\r
  24 Clazz.overrideMethod (c$, "computeConsensus", \r
  25 function () {\r
  26 for (var i = 0; i < 3; i++) {\r
  27 try {\r
  28 jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast);\r
  29 break;\r
  30 } catch (e) {\r
  31 if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) {\r
  32 } else {\r
  33 throw e;\r
  34 }\r
  35 }\r
  36 }\r
  37 });\r
  38 Clazz.overrideMethod (c$, "finalizeCalc", \r
  39 function () {\r
  40 this.alignViewport.setComplementConsensusHash (this.hconsensus);\r
  41 });\r
  42 Clazz.overrideMethod (c$, "deriveConsensus", \r
  43 function (consensusAnnotation, consensusData) {\r
  44 jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length);\r
  45 }, "jalview.datamodel.AlignmentAnnotation,~A");\r
  46 });\r