site/j2s/jalview/workers/StrucConsensusThread.js

   1 Clazz.declarePackage ("jalview.workers");\r
   2 Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency"], function () {\r
   3 c$ = Clazz.decorateAsClass (function () {\r
   4 this.rnaStruc = null;\r
   5 this.strucConsensus = null;\r
   6 this.hStrucConsensus = null;\r
   7 this.nseq = -1;\r
   8 this.aa = null;\r
   9 this.arr = null;\r
  10 Clazz.instantialize (this, arguments);\r
  11 }, jalview.workers, "StrucConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);\r
  12 Clazz.overrideMethod (c$, "getNewWorker", \r
  13 function () {\r
  14 return  new jalview.workers.StrucConsensusThread (this.alignViewport, this.ap);\r
  15 });\r
  16 Clazz.overrideMethod (c$, "run1", \r
  17 function (state) {\r
  18 if (this.alignViewport.isClosed ()) {\r
  19 this.abortAndDestroy ();\r
  20 return;\r
  21 }while (!Thread.interrupted ()) {\r
  22 try {\r
  23 switch (state) {\r
  24 case 0:\r
  25 if (this.calcMan.isPending (this)) return;\r
  26 this.calcMan.notifyStart (this);\r
  27 state = 3;\r
  28 break;\r
  29 case 3:\r
  30 while (!this.calcMan.notifyWorking (this)) {\r
  31 if (this.ap != null) {\r
  32 this.ap.paintAlignment (false);\r
  33 }try {\r
  34 if (this.sleepAndReturn (200, state)) return;\r
  35 } catch (e) {\r
  36 if (Clazz.exceptionOf (e, InterruptedException)) {\r
  37 state = 2;\r
  38 break;\r
  39 } else {\r
  40 throw e;\r
  41 }\r
  42 }\r
  43 }\r
  44 if (this.alignViewport.isClosed ()) {\r
  45 this.abortAndDestroy ();\r
  46 state = 2;\r
  47 break;\r
  48 }this.alignment = this.alignViewport.getAlignment ();\r
  49 this.aWidth = -1;\r
  50 if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) {\r
  51 state = 2;\r
  52 }this.strucConsensus = this.alignViewport.getAlignmentStrucConsensusAnnotation ();\r
  53 this.hStrucConsensus = this.alignViewport.getRnaStructureConsensusHash ();\r
  54 this.strucConsensus.annotations = null;\r
  55 this.strucConsensus.annotations =  new Array (this.aWidth);\r
  56 this.hStrucConsensus =  new Array (this.aWidth);\r
  57 this.aa = this.alignViewport.getAlignment ().getAlignmentAnnotation ();\r
  58 for (var i = 0; i < this.aa.length; i++) {\r
  59 if (this.aa[i].getRNAStruc () != null && this.aa[i].isValidStruc ()) {\r
  60 this.rnaStruc = this.aa[i];\r
  61 break;\r
  62 }}\r
  63 if (this.rnaStruc == null || !this.rnaStruc.isValidStruc ()) {\r
  64 this.calcMan.workerComplete (this);\r
  65 return;\r
  66 }this.arr = this.alignment.getSequencesArray ();\r
  67 this.nseq = this.arr.length;\r
  68 state = 4;\r
  69 break;\r
  70 case 4:\r
  71 this.iFirst = this.iLast;\r
  72 this.iLast = Math.min (this.iLast + this.nPer, this.aWidth);\r
  73 if (this.iLast == this.iFirst) {\r
  74 state = 2;\r
  75 } else {\r
  76 jalview.analysis.StructureFrequency.calculate (this.arr, 0, this.alignment.getWidth (), this.hStrucConsensus, true, this.rnaStruc);\r
  77 if (this.sleepAndReturn (0, state)) return;\r
  78 }break;\r
  79 case 2:\r
  80 this.alignViewport.setRnaStructureConsensusHash (this.hStrucConsensus);\r
  81 this.updateResultAnnotation (true);\r
  82 if (this.alignViewport.getGlobalColourScheme () != null) {\r
  83 this.alignViewport.getGlobalColourScheme ().setConsensus (this.hStrucConsensus);\r
  84 }this.notifyDone ();\r
  85 return;\r
  86 }\r
  87 } catch (e$$) {\r
  88 if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {\r
  89 var error = e$$;\r
  90 {\r
  91 this.calcMan.workerCannotRun (this);\r
  92 this.ap.raiseOOMWarning ("calculating RNA structure consensus", error);\r
  93 }\r
  94 } else {\r
  95 var e = e$$;\r
  96 {\r
  97 System.out.println ("Error in ConsensusThread: " + e);\r
  98 e.printStackTrace ();\r
  99 this.calcMan.workerComplete (this);\r
 100 }\r
 101 }\r
 102 }\r
 103 }\r
 104 }, "~N");\r
 105 Clazz.overrideMethod (c$, "updateAnnotation", \r
 106 function () {\r
 107 this.updateResultAnnotation (false);\r
 108 });\r
 109 Clazz.defineMethod (c$, "updateResultAnnotation", \r
 110 function (immediate) {\r
 111 if (immediate || !this.calcMan.isWorking (this) && this.strucConsensus != null && this.hStrucConsensus != null) {\r
 112 jalview.analysis.StructureFrequency.completeConsensus (this.strucConsensus, this.hStrucConsensus, 0, this.hStrucConsensus.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), this.nseq);\r
 113 }}, "~B");\r
 114 });\r