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  1. Jalview
  2. JAL-4443

Add support for PaSiMap analysis in JalviewJS

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.4.0
    • Fix Version/s: 2.12.0
    • Component/s: jalview-j2s
    • Labels:

      Description

      PaSiMap relies on some java ops not yet supported in java2script:
      e.g. in jalview.analysis.ccAnalysis:

      double newH = Arrays.stream(MiscMath.elementwiseMultiply(hValues, eigenMatrix.getRow(hIndex))).sum() / Arrays.stream(MiscMath.elementwiseMultiply(hValues, hValues)).sum();
      hValues[hIndex] = newH;

      this involves spliterators - which result in:
      ERROR: Error computing cc_analysis: TypeError: this.$finals$.accumulator.accept$O$D is not a function
      at Object.eval [as accept$D] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/ReduceOps.js:616:27)
      at Object.eval (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/Spliterators.js:592:8)
      at Object.eval [as forEachRemaining$java_util_function_Consumer] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/Spliterator.js:162:6)
      at clazz.eval [as copyInto$java_util_stream_Sink$java_util_Spliterator] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/AbstractPipeline.js:205:13)
      at clazz.eval [as wrapAndCopyInto$java_util_stream_Sink$java_util_Spliterator] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/AbstractPipeline.js:197:6)
      at Object.eval [as evaluateSequential$java_util_stream_PipelineHelper$java_util_Spliterator] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/ReduceOps.js:673:15)
      at clazz.eval [as evaluate$java_util_stream_TerminalOp] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/AbstractPipeline.js:50:195)
      at clazz.eval [as collect$java_util_function_Supplier$java_util_function_ObjDoubleConsumer$java_util_function_BiConsumer] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/DoublePipeline.js:565:13)
      at clazz.eval [as sum$] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/java/util/stream/DoublePipeline.js:381:20)
      at Object.eval [as run$] (https://www.jalview.org/jalview-js/test-release/swingjs/j2s/jalview/analysis/ccAnalysis.js:111:106)

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            Assignee:
            Unassigned Unassigned
            Reporter:
            jprocter James Procter
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              Created:
              Updated: