Changed NL addDescriptionOfAppliedTask
@@ -79,11 +79,6 @@ public class NeutralLossFilterTask extends AbstractTask {
private PeakList peakList;
private boolean checkRT;
- public enum RatingType {
- HIGHEST, TEMPAVG
- };
-
- RatingType ratingType;
private double dMassLoss;
IIsotope[] el;
@@ -107,7 +102,7 @@ public class NeutralLossFilterTask extends AbstractTask {
suffix = parameters.getParameter(NeutralLossFilterParameters.suffix).getValue();
checkRT = parameters.getParameter(NeutralLossFilterParameters.checkRT).getValue();
- message = "Got paramenters..."; // TODO
+ message = "Got paramenters...";
}
/**
@@ -150,18 +145,13 @@ public class NeutralLossFilterTask extends AbstractTask {
PeakListHandler plh = new PeakListHandler();
plh.setUp(peakList);
- // totalRows = rows.length;
resultPeakList = new SimplePeakList(peakList.getName() + suffix, peakList.getRawDataFiles());
PeakListHandler resultMap = new PeakListHandler();
for (int i = 0; i < totalRows; i++) {
// i will represent the index of the row in peakList
- if (peakList.getRow(i).getPeakIdentities().length > 0
- /* || peakList.getRow(i).getRowCharge() != this.charge */) {
- // logger.info("Charge of row " + i + " is not " + charge + ". Charge of row " +
- // i + " is "
- // + peakList.getRow(i).getRowCharge());
+ if (peakList.getRow(i).getPeakIdentities().length > 0) {
finishedRows++;
continue;
}
@@ -401,7 +391,7 @@ public class NeutralLossFilterTask extends AbstractTask {
* @param row PeakListRow to add the comment to
* @param str comment to be added
*/
- public static void addComment(PeakListRow row, String str) {
+ public static void addComment(PeakListRow row, String str) { // maybe add this to PeakListRow class?
String current = row.getComment();
if (current == null)
row.setComment(str);
@@ -425,6 +415,6 @@ public class NeutralLossFilterTask extends AbstractTask {
// Add task description to peakList
resultPeakList.addDescriptionOfAppliedTask(
- new SimplePeakListAppliedMethod("IsotopePeakScanner", parameters));
+ new SimplePeakListAppliedMethod("NeutralLossFilter", parameters));
}
}
