Examples of org.bmdrc.nmr.Nmr2dCHUnit

org.bmdrc.nmr.Nmr2dCHUnit
@author SungBo Hwang, CSB


    private void __setStartPeak(Nmr2dCHUnitList theMedianPeakInMergeHMQCAndHMBC) {
        Nmr2dCHUnitList theStartPeakSetInHMQC = new Nmr2dCHUnitList();


        for (Object thePeak : this.getHMQCPeakList()) {
            Nmr2dCHUnit theClosestPeak = this.__getClosestPeak(theMedianPeakInMergeHMQCAndHMBC, (Nmr2dCHUnit) thePeak);


            this.__setStartPeakListInHMBC().addPeak(theClosestPeak);
            this.__setStartPeakListInHMQC().addPeak((Nmr2dCHUnit) thePeak);
        }
    }

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        return thePeakData;
    }


    private Nmr2dCHUnit __getPeakDataInSparkFormat(String theFileString) {
        String[] theSplitedString = theFileString.split(this.SPACE_STRING);
        Nmr2dCHUnit thePeak = new Nmr2dCHUnit();


        thePeak.setCarbonShift(Double.parseDouble(theSplitedString[this.CARBON_CHEMICAL_SHIFT_2D_INDEX_IN_SPARKY]));
        thePeak.setHydrogenShift(Double.parseDouble(theSplitedString[this.HYDROGEN_CHEMICAL_SHIFT_2D_INDEX_IN_SPARKY]));
        thePeak.setIntensity(Double.parseDouble(theSplitedString[this.INTENSITY_2D_INDEX_IN_SPARKY]));


        return thePeak;
    }

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        return thePeak;
    }


    private Nmr2dCHUnit __readACDLabFileFormat(String theFileString) throws NumberFormatException {
        String[] theSplitedString = theFileString.split(this.TAB_STRING);
        Nmr2dCHUnit thePeak = new Nmr2dCHUnit();


        if (!theFileString.isEmpty() && theSplitedString.length >= 8) {
            thePeak.setCarbonShift(Double.parseDouble(theSplitedString[this.CARBON_CHEMICAL_SHIFT_2D_INDEX_IN_ACD]));
            thePeak.setHydrogenShift(Double.parseDouble(theSplitedString[this.HYDROGEN_CHEMICAL_SHIFT_2D_INDEX_IN_ACD]));
            thePeak.setIntensity(Double.parseDouble(theSplitedString[this.INTENSITY_2D_INDEX_IN_ACD]));
        }


        return thePeak;
    }

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        return theMedianPeakData;
    }


    private Nmr2dCHUnitList __getClusterPeakList(Nmr1dUnit the1HPeak, Nmr1dUnit the13CPeak, Nmr2dCHUnitList theCopiedPeakData) {
        Nmr2dCHUnit theClassStandardPeak = this.__getClassStandardPeak(the1HPeak, the13CPeak);
        Nmr2dCHUnit theStartPeak = this.__getClosestPeak(theCopiedPeakData, theClassStandardPeak);
        Nmr2dCHUnitList thePeakList = new Nmr2dCHUnitList();


        if (this.__containRange(theStartPeak, theClassStandardPeak) && this.__containHydrogenRange(theStartPeak, (Nmr1dUnit) the1HPeak)) {
            int theIndexOfStartPeak = this.__getIndexOfSamePeakIn2D(theCopiedPeakData, theStartPeak);

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            }
        }
    }


    private Nmr2dCHUnit __getClassStandardPeak(Nmr1dUnit the1HPeak, Nmr1dUnit the13CPeak) {
        Nmr2dCHUnit theClassStandardPeak = new Nmr2dCHUnit();


        theClassStandardPeak.setCarbonShift(the13CPeak.getChemicalShift());
        theClassStandardPeak.setHydrogenShift(the1HPeak.getChemicalShift());


        return theClassStandardPeak;
    }

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        return false;
    }


    private Nmr2dCHUnit __getClosestPeak(Nmr2dCHUnitList thePeakData, Nmr2dCHUnit theCheckPeak) {
        Nmr2dCHUnit theClosestPeak = new Nmr2dCHUnit();
        double theMinimumDistance = Math.sqrt(2.0);


        for (Object thePeak : thePeakData) {
            if (!this.__isSamePeak((Nmr2dCHUnit) thePeak, theCheckPeak)) {
                double theDistance = this.__calculateDistance((Nmr2dCHUnit) thePeak, theCheckPeak);

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        return true;
    }


    private Nmr2dCHUnit __getMedianPosition(Nmr2dCHUnitList thePeakList) {
        Nmr2dCHUnit theMedianPosition = new Nmr2dCHUnit();
        double theSumOfCarbonShift = 0;
        double theSumOfHydrogenShift = 0;


        for (int i = 0; i < thePeakList.size(); i++) {
            theSumOfCarbonShift += thePeakList.get(i).getCarbonShift();
            theSumOfHydrogenShift += thePeakList.get(i).getHydrogenShift();
        }


        theMedianPosition.setCarbonShift(theSumOfCarbonShift / thePeakList.size());
        theMedianPosition.setHydrogenShift(theSumOfHydrogenShift / thePeakList.size());


        return theMedianPosition;
    }

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    private Nmr2dCHUnitList __generateCriterionPeakList() {
        Nmr2dCHUnitList theCriterionPeakList = new Nmr2dCHUnitList();


        for (int qi = 0, qEnd = this.getHMQC().getMedianPeak().size(); qi < qEnd; qi++) {
            Nmr2dCHUnit theClosestPeak = this.__getClosestPeak(this.getMergedHmbcAndHmqc(), this.getHMQC().getMedianPeak().get(qi));


            theCriterionPeakList.addPeak(theClosestPeak);
        }


        return theCriterionPeakList;

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        return theCriterionPeakList;
    }


    private Nmr2dCHUnit __getClosestPeak(Nmr2dCHUnitList thePeakList, Nmr2dCHUnit theCheckPeak) {
        Nmr2dCHUnit theClosestPeak = new Nmr2dCHUnit();
        double theMinimumDistance = MAXIMUM_DISTANCE_IN_NMR_2D;


        for (Nmr2dCHUnit thePeak : thePeakList.getPeakList()) {
            if (!__isSamePeak(thePeak, theCheckPeak)) {
                double theDistance = Math.sqrt(Math.pow(thePeak.getCarbonShift() / this.MAXIMUM_CARBON_NMR_CHEMICAL_SHIFT - theCheckPeak.getCarbonShift() / this.MAXIMUM_CARBON_NMR_CHEMICAL_SHIFT, 2.0)

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                continue;
            }


            String[] theSplitedString = theLines.get(i).split(" ");
            List<Double> thePeakDataArray = new java.util.ArrayList<Double>();
            Nmr2dCHUnit thePeak = new Nmr2dCHUnit();


            for (int j = 0; j < theSplitedString.length; j++) {
                if (!theSplitedString[j].isEmpty() && !theSplitedString[j].contains("?-?")) {
                    thePeakDataArray.add(Double.parseDouble(theSplitedString[j].toString()));
                }
            }


            thePeak.setCarbonShift(thePeakDataArray.get(this.SPARKY_CARBON_SHIFT_INDEX));
            thePeak.setHydrogenShift(thePeakDataArray.get(this.SPARKY_HYDROGEN_SHIFT_INDEX));
            thePeak.setIntensity(thePeakDataArray.get(this.SPARKY_INTENSITY_INDEX));


            this.setPeak().addPeak(thePeak);
        }
    }

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Related Classes of org.bmdrc.nmr.Nmr2dCHUnit

modify_file.HydrogenQueryGeneratorInNmr2d

org.bmdrc.nmr.abstracts.AbstractNmr2d

org.bmdrc.nmr.tool.CarbonQueryGenerator

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