Change minimumScanSpan to IntegerParameter
package net.sf.mzmine.modules.masslistmethods.ADAPchromatogrambuilder;
+import java.awt.Window;
+
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.parameters.Parameter;
import net.sf.mzmine.parameters.dialogs.ParameterSetupDialog;
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
import net.sf.mzmine.parameters.parametertypes.DoubleParameter;
+import net.sf.mzmine.parameters.parametertypes.IntegerParameter;
import net.sf.mzmine.parameters.parametertypes.MassListParameter;
import net.sf.mzmine.parameters.parametertypes.StringParameter;
import net.sf.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
@@ -33,8 +36,6 @@ import net.sf.mzmine.parameters.parametertypes.selectors.ScanSelectionParameter;
import net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;
import net.sf.mzmine.util.ExitCode;
-import java.awt.*;
-
public class ADAPChromatogramBuilderParameters extends SimpleParameterSet {
public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter();
@@ -44,22 +45,19 @@ public class ADAPChromatogramBuilderParameters extends SimpleParameterSet {
public static final MassListParameter massList = new MassListParameter();
- public static final DoubleParameter minimumScanSpan = new DoubleParameter(
+ public static final IntegerParameter minimumScanSpan = new IntegerParameter(
"Min group size in # of scans",
"Minimum scan span over which some peak in the chromatogram must have (continuous) points above the noise level\n"
+ "to be recognized as a chromatogram.\n"
+ "The optimal value depends on the chromatography system setup. The best way to set this parameter\n"
+ "is by studying the raw data and determining what is the typical time span of chromatographic peaks.",
- MZmineCore.getConfiguration().getRTFormat());
-
- public static final DoubleParameter minimumHeight = new DoubleParameter("Min height",
- "Minimum intensity of the highest data point in the chromatogram. If chromatogram height is below this level, it is discarded.",
- MZmineCore.getConfiguration().getIntensityFormat());
+ 5, true, 2, null);
public static final MZToleranceParameter mzTolerance = new MZToleranceParameter();
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",
