added default values to ADAPChromatogramBuilderParameters
@@ -39,8 +39,8 @@ public class ADAPChromatogramBuilderParameters extends SimpleParameterSet {
public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter();
- public static final ScanSelectionParameter scanSelection =
- new ScanSelectionParameter(new ScanSelection(1));
+ public static final ScanSelectionParameter scanSelection = new ScanSelectionParameter(
+ new ScanSelection(1));
public static final IntegerParameter minimumScanSpan = new IntegerParameter(
"Min group size in # of scans",
@@ -50,15 +50,18 @@ public class ADAPChromatogramBuilderParameters extends SimpleParameterSet {
+ "is by studying the raw data and determining what is the typical time span of chromatographic features.",
5, true, 2, null);
- public static final MZToleranceParameter mzTolerance = new MZToleranceParameter();
+ public static final MZToleranceParameter mzTolerance = new MZToleranceParameter(
+ "Scan to scan accuracy (m/z)", "m/z tolerance of the same compound between two scans.\n"
+ + "This does not describe the deviation of the accurate mass (measured) from the exact mass (calculated),\n"
+ + "but the fluctuation of the accurate between two scans.", 0.002, 10);
- public static final StringParameter suffix =
- new StringParameter("Suffix", "This string is added to filename as suffix", "chromatograms");
+ public static final StringParameter suffix = new StringParameter("Suffix",
+ "This string is added to filename as suffix", "chromatograms");
// Owen Edit
public static final DoubleParameter IntensityThresh2 = new DoubleParameter(
"Group intensity threshold",
- "This parameter is the intensity value for wich intensities greater than this value can contribute to the minimumScanSpan count.",
+ "This parameter is the intensity value for which intensities greater than this value can contribute to the minimumScanSpan count.",
MZmineCore.getConfiguration().getIntensityFormat());
public static final DoubleParameter startIntensity = new DoubleParameter("Min highest intensity",
@@ -67,8 +70,9 @@ public class ADAPChromatogramBuilderParameters extends SimpleParameterSet {
// End Owen Edit
public ADAPChromatogramBuilderParameters() {
- super(new Parameter[]{dataFiles, scanSelection, minimumScanSpan, IntensityThresh2,
- startIntensity, mzTolerance, suffix});
+ super(
+ new Parameter[]{dataFiles, scanSelection, minimumScanSpan, IntensityThresh2, startIntensity,
+ mzTolerance, suffix});
}
@Override
