Package org.bmdrc.nmr

Examples of org.bmdrc.nmr.Nmr2dCHUnitList

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    }

    private void __initializeGroupByCarbonShift(int theSizeOfArray) {
        for (int pi = 0; pi < theSizeOfArray; pi++) {
            this.setGroupByCarbonShift().add(new Nmr2dCHUnitList());
        }
    }
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        this.__removeEmptyGroupInHydrogenShift();
    }

    private void __initializeGroupByHydrogenShift(int theSizeOfArray) {
        for (int pi = 0; pi < theSizeOfArray; pi++) {
            this.setGroupByHydrogenShift().add(new Nmr2dCHUnitList());
        }
    }
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        return itsMedianPeak;
    }
   
    public void fromSpark(String theSparkFile) {
        List<String> theLines = this.__readLines(theSparkFile);
        this.setPeak(new Nmr2dCHUnitList());

        this.__removeIndexLine(theLines);
        this.__addPeakDataFromSparky(theLines);
    }
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        }
    }

    public void fromACDLabFile(final String theInputFilePath) {
        List<String> theLines = this.__readLines(theInputFilePath);
        this.setPeak(new Nmr2dCHUnitList());

        this.__removeIndexLine(theLines);
        this.__addPeakDataFromACDLab(theLines);
    }
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            this.setPeak().addPeak(thePeak);
        }
    }

    public void generateMedianPeakList() {
        this.setMedianPeak(new Nmr2dCHUnitList());
        Nmr2dCHUnitList theCopiedPeakList = new Nmr2dCHUnitList(this.getPeak());

        for (Nmr1dUnit theNmr1HPeak : this.getNmr1H()) {
            for (Nmr1dUnit theNmr13CPeak : this.getNmr13C()) {
                this.__generatedMedianPeak(theCopiedPeakList, theNmr1HPeak, theNmr13CPeak);
            }
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    }

    private void __generatedMedianPeak(Nmr2dCHUnitList theCopiedPeakList, Nmr1dUnit theCriterion1HPeak, Nmr1dUnit theCriterion13CPeak) {
        Nmr2dCHUnit theCriterionPeakBasedOnNmr1D = new Nmr2dCHUnit();
        Nmr2dCHUnit theFirstPeakInGroup = new Nmr2dCHUnit();
        Nmr2dCHUnitList theClosePeakSet = new Nmr2dCHUnitList();

        theCriterionPeakBasedOnNmr1D.setPeak(theCriterion13CPeak.getChemicalShift(), theCriterion1HPeak.getChemicalShift());

        theFirstPeakInGroup = this.__getClosestPeak(theCriterionPeakBasedOnNmr1D);
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        return false;
    }

    private Nmr2dCHUnitList __searchPossiblePeakInGroup(Nmr2dCHUnitList theCopiedPeak, Nmr2dCHUnit theFirstPeakInGroup) {
        Nmr2dCHUnitList thePeakSetInSameGroup = new Nmr2dCHUnitList();
        int theIndexOfStartPeak = this.__indexOfSamePeak(theCopiedPeak, theFirstPeakInGroup);
        boolean theJugmentContainingClusterMemberPeak = false;

        theCopiedPeak.remove(theIndexOfStartPeak);
        thePeakSetInSameGroup.addPeak(theFirstPeakInGroup);

        while (!theJugmentContainingClusterMemberPeak) {
            theJugmentContainingClusterMemberPeak = true;

            for (int pi = theCopiedPeak.size() - 1; pi >= 0; pi--) {
                if (this.__isClusterMember(thePeakSetInSameGroup, theCopiedPeak.get(pi))) {
                    thePeakSetInSameGroup.addPeak(theCopiedPeak.get(pi));
                    theCopiedPeak.remove(pi);
                    theJugmentContainingClusterMemberPeak = false;
                }
            }
        }
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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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    }

    private List<CarbonQuery> __generateCarbonQueryListInHydrogenBoundedHeteroAtom(Nmr2dCHUnitList theCriterionPeakList, List<Integer> theNumberOfBoundHydrogenList) {
        List<CarbonQuery> theCarbonQueryList = new ArrayList<>();
        List<Nmr2dCHUnitList> theModifiedGroupByHydrogenShift = new ArrayList<>(this.getGroupByHydrogenShift());
        Nmr2dCHUnitList theModifiedMergedHmbcAndHmqc = new Nmr2dCHUnitList(this.getMergedHmbcAndHmqc());

        this.__removePeaksAndGroupNotBoundedHeteroAtom(theModifiedGroupByHydrogenShift, theModifiedMergedHmbcAndHmqc, theCriterionPeakList);

        for (int pi = theModifiedGroupByHydrogenShift.size() - 1; pi >= 0; pi--) {
            theCarbonQueryList.add(this.__generateCarbonQueryByCriterionPeak(theCriterionPeakList.get(pi), theNumberOfBoundHydrogenList, theModifiedGroupByHydrogenShift));
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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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