872fa77fd778f5ca89b5783181133ae9186f397e,msdk-io/msdk-io-mzml/src/main/java/io/github/msdk/io/mzml/MzMLConverter.java,MzMLConverter,extractIsolations,#Spectrum#,271

Before Change



            for (ParamGroup pg : selectedIonParams) {
                List<CVParam> pgCvParams = pg.getCvParam();
                for (CVParam param : pgCvParams) {
                    String accession = param.getAccession();
                    String value = param.getValue();
                    if ((accession == null) || (value == null))
                        continue;
                    // cvMz is sometimes used is used in mzML 1.0 files
                    if (accession.equals(MzMLCV.cvMz)
                            || accession.equals(MzMLCV.cvPrecursorMz)) {
                        precursorMz = Double.parseDouble(value);
                    }
                    if (accession.equals(MzMLCV.cvChargeState)) {
                        precursorCharge = Integer.parseInt(value);
                    }

                }

            }

            ParamGroup isolationWindowPg = parent.getIsolationWindow();
            if (isolationWindowPg != null) {
                List<CVParam> precCvParams = isolationWindowPg.getCvParam();
                if (precCvParams != null) {
                    for (CVParam param : precCvParams) {
                        String accession = param.getAccession();
                        String value = param.getValue();
                        if ((accession == null) || (value == null))
                            continue;
                        if (accession
                                .equals(MzMLCV.cvIsolationWindowLowerOffset)) {
                            isolationWindowLower = Double.parseDouble(value);
                        }
                        if (accession
                                .equals(MzMLCV.cvIsolationWindowUpperOffset)) {
                            isolationWindowUpper = Double.parseDouble(value);
                        }
                        if (accession.equals(MzMLCV.cvIsolationWindowTarget)) {
                            isolationWindowTarget = Double.parseDouble(value);
                        }
                    }

After Change


                if (!Strings.isNullOrEmpty(cvVal))
                    precursorMz = Double.parseDouble(cvVal);

                cvVal = extractCVValue(pg, MzMLCV.cvChargeState);
                if (!Strings.isNullOrEmpty(cvVal))
                    precursorCharge = Integer.parseInt(cvVal);

            }

            String cvVal = extractCVValue(parent.getIsolationWindow(),
                    MzMLCV.cvIsolationWindowLowerOffset);
            if (!Strings.isNullOrEmpty(cvVal))
                isolationWindowLower = Double.parseDouble(cvVal);

            cvVal = extractCVValue(parent.getIsolationWindow(),
                    MzMLCV.cvIsolationWindowUpperOffset);
            if (!Strings.isNullOrEmpty(cvVal))
                isolationWindowUpper = Double.parseDouble(cvVal);

            cvVal = extractCVValue(parent.getIsolationWindow(),
                    MzMLCV.cvIsolationWindowTarget);
            if (!Strings.isNullOrEmpty(cvVal))
                isolationWindowTarget = Double.parseDouble(cvVal);