Examples of org.bmdrc.nmr.Nmr2dCHUnitList

org.bmdrc.nmr.Nmr2dCHUnitList
@author labwindows

        this.set13CNMRFilePath(new String());
        this.setHMQCFilePath(new String());
        this.setHMBCFilePath(new String());
        this.set1HPeakList(new Nmr1dUnitList());
        this.set13CPeakList(new Nmr1dUnitList());
        this.setHMQCPeakList(new Nmr2dCHUnitList());
        this.__setStartPeakListInHMBC(new Nmr2dCHUnitList());
        this.__setStartPeakListInHMQC(new Nmr2dCHUnitList());
    }

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            Integer theTotalNumberOfHydrogen, Integer theTypeOfInputFileFormat) throws FileNotFoundException, IOException {
        this.set1HPeakList(this.__read1DNMRACDLabFileFormat(this.get1HNMRFilePath(), theTotalNumberOfHydrogen));
        this.set13CPeakList(this.__read1DNMRACDLabFileFormat(this.get13CNMRFilePath(), theTotalNumberOfCarbon));
        this.setHMQCPeakList(this.__convertMedianPeakInHMQC(theTypeOfInputFileFormat));


        Nmr2dCHUnitList theMedianPeakInMergeHMQCAndHMBC = this.__convertMedianPeakInMergeHMBCAndHMQC(theTotalNumberOfCarbon, theTotalNumberOfHydrogen, theTypeOfInputFileFormat);
        List<Nmr2dCHUnitList> theSortedByCarbonPeak = this.__sortedByShift(theMedianPeakInMergeHMQCAndHMBC, this.get13CPeakList(), Nmr2dCHUnit.CARBON_SHIFT_INDEX);
        List<Nmr2dCHUnitList> theSortedByHydrogenPeak = this.__sortedByShift(theMedianPeakInMergeHMQCAndHMBC, this.get1HPeakList(), Nmr2dCHUnit.HYDROGEN_SHIFT_INDEX);


        this.__setStartPeak(theMedianPeakInMergeHMQCAndHMBC);
        this.__printInitializeCondition(theSortedByCarbonPeak, theSortedByHydrogenPeak);

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        this.setFrame().setLogTextArea().append(Integer.toString(theSortedByHydrogenPeak.size()));
        this.setFrame().setLogTextArea().append(this.END_LINE);
    }


    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);

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    }


    private Nmr2dCHUnitList __readNMRDataFile(String thePeakDataFilePath, Integer theTypeOfInputFileFormat) throws FileNotFoundException, IOException {
        List<String> theFileInformationList = this.__readLines(thePeakDataFilePath);
        String theResultFileInformation = new String();
        Nmr2dCHUnitList thePeakData = new Nmr2dCHUnitList();
        int theLine = 2;


        theFileInformationList.remove(this.FIRST_INDEX);
        theFileInformationList.remove(this.FIRST_INDEX);


        for (String theFileString : theFileInformationList) {
            if (!theFileString.isEmpty()) {
                if (theTypeOfInputFileFormat == this.SPARKY_FILE_FORMAT) {
                    thePeakData.addPeak(this.__getPeakDataInSparkFormat(theFileString));
                } else if (theTypeOfInputFileFormat == this.ACD_FILE_FORMAT) {
                    try {
                        thePeakData.addPeak(this.__readACDLabFileFormat(theFileString));
                    } catch (NumberFormatException e) {
                        this.setFrame().setLogTextArea().append(thePeakDataFilePath + " " + theLine++ + "th Line is Error!!\n");
                    }
                }
            }

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        return theFileStringList;
    }


    private Nmr2dCHUnitList __convertMedianPeakInMergeHMBCAndHMQC(Integer theNumberOfCarbon, Integer theNumberOfHydrogen, Integer theTypeOfInputFileFormat) {
        Nmr2dCHUnitList theHMQCPeakData = new Nmr2dCHUnitList();
        Nmr2dCHUnitList theHMBCPeakData = new Nmr2dCHUnitList();
        Nmr1dUnitList the1HPeakData = this.__read1DNMRACDLabFileFormat(this.get1HNMRFilePath(), theNumberOfHydrogen);;
        Nmr1dUnitList the13CPeakData = this.__read1DNMRACDLabFileFormat(this.get13CNMRFilePath(), theNumberOfCarbon);
        Nmr2dCHUnitList theMedianPeakInHMBC = new Nmr2dCHUnitList();
        Nmr2dCHUnitList theMedianPeakInHMQC = new Nmr2dCHUnitList();


        List<Nmr1dUnitList> theSortedByCarbonPeak = new ArrayList<>();
        List<Nmr1dUnitList> theSortedByHydrogenPeak = new ArrayList<>();
        try {
            theHMQCPeakData = this.__readNMRDataFile(this.getHMQCFilePath(), theTypeOfInputFileFormat);

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    private Double __getTolerenceOfCarbonInHMBC() {
        return (double) 1000 / this.getNmrResolution();
    }


    private Nmr2dCHUnitList convertMedianPeak(Nmr2dCHUnitList the2dPeakList, Nmr1dUnitList the1HNmrPeakList, Nmr1dUnitList the13CNmrPeakList) {
        Nmr2dCHUnitList theMedianPeakData = new Nmr2dCHUnitList();
        Nmr2dCHUnitList theCopiedPeakData = new Nmr2dCHUnitList(the2dPeakList);
        List<Nmr2dCHUnitList> theMedianPeakSet = new ArrayList<>();


        //실질적으로 Median Peak를 뽑아냄
        for (Object the1HPeak : the1HNmrPeakList) {
            for (Object the13CPeak : the13CNmrPeakList) {
                Nmr2dCHUnitList theClusterPeakList = this.__getClusterPeakList((Nmr1dUnit) the1HPeak, (Nmr1dUnit) the13CPeak, theCopiedPeakData);


                if (!theClusterPeakList.isEmpty()) {
                    theMedianPeakData.addPeak(this.__getMedianPosition(theClusterPeakList));
                }
            }
        }

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    }


    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);


            theCopiedPeakData.remove(theIndexOfStartPeak);
            thePeakList.addPeak(theStartPeak);


            this.__getClusterPeakList(theCopiedPeakData, thePeakList);
        }


        return thePeakList;

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    private List<Nmr2dCHUnitList> __initializeSortedGroup(Nmr1dUnitList theStandard1DPeakList) {
        List<Nmr2dCHUnitList> theSortedByShift = new ArrayList<>();


        for (int pi = 0, pEnd = theStandard1DPeakList.size(); pi < pEnd; pi++) {
            theSortedByShift.add(new Nmr2dCHUnitList());
        }


        return theSortedByShift;
    }

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        return theIndexOfTypeOfPeak;
    }


    private Nmr2dCHUnitList __convertMedianPeakInHMQC(Integer theTypeOfInputFileFormat) throws FileNotFoundException, IOException {
        Nmr2dCHUnitList thePeakList = this.__readNMRDataFile(this.getHMQCFilePath(), theTypeOfInputFileFormat);
        Nmr2dCHUnitList theMedianPeakData = new Nmr2dCHUnitList();
        Nmr2dCHUnitList thePeakData = new Nmr2dCHUnitList(thePeakList);
        List<Nmr2dCHUnitList> theSortedByCarbonPeak = this.__sortedByShift(thePeakData, this.get13CPeakList(), Nmr2dCHUnit.CARBON_SHIFT_INDEX);


        for (int i = 0; i < theSortedByCarbonPeak.size(); i++) {
            theMedianPeakData.addPeak(this.__getMedianPosition(theSortedByCarbonPeak.get(i)));
        }

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        this.setMergedHmbcAndHmqc().addPeakList(this.getHMBC().getMedianPeak());
        this.setMergedHmbcAndHmqc().addPeakList(this.getHMQC().getMedianPeak());
    }


    public void generateCarbonQuery() {
        Nmr2dCHUnitList theCriterionPeakList = new Nmr2dCHUnitList();
        List<Integer> theNumberOfBoundHydrogenList = new ArrayList<>();


        this.__generateGroupByCarbonShift();
        this.__generateGroupByHydrogenShift();

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Related Classes of org.bmdrc.nmr.Nmr2dCHUnitList

modify_file.HydrogenQueryGeneratorInNmr2d

org.bmdrc.nmr.abstracts.AbstractNmr2d

org.bmdrc.nmr.tool.CarbonQueryGenerator

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