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);