added some javadoc
@@ -115,8 +115,6 @@ public class IsotopePeakScannerTask extends AbstractTask {
ratingChoice = parameters.getParameter(IsotopePeakScannerParameters.ratingChoices).getValue();
-
-
/*RawDataFile[] raws = peakList.getRawDataFiles();
Scan scan = raws[0].getScan(1);
MassList[] lists = scan.getMassLists();
@@ -351,8 +349,9 @@ public class IsotopePeakScannerTask extends AbstractTask {
if(accurateAvgIntensity)
addComment(parent, " Avg pattern Rating: " + round(candidates.getAvgAvgRatings(), 3));
- comChild = (parent.getID() + "-Parent ID" + " m/z-shift(ppm): " + round(((child.getAverageMZ() - parent.getAverageMZ())
- - diff.get(k))*1E6/child.getAverageMZ(), 2) + " I(c)/I(p): " + round(child.getAverageHeight()/plh.getRowByID(candidates.get(pattern.getHighestDataPointIndex()).getCandID()).getAverageHeight(),2)
+ comChild = (parent.getID() + "-Parent ID" + " m/z-shift(ppm): "
+ + round( ( (child.getAverageMZ() - parent.getAverageMZ() ) - diff.get(k) )/ child.getAverageMZ() * 1E6, 2)
+ + " I(c)/I(p): " + round(child.getAverageHeight()/plh.getRowByID(candidates.get(pattern.getHighestDataPointIndex()).getCandID()).getAverageHeight(),2)
+ " Identity: " + pattern.getDetailedPeakDescription(k)
+ " Rating: " + round(candidates.get(k).getRating(), 3)
+ average);
@@ -511,7 +510,12 @@ public class IsotopePeakScannerTask extends AbstractTask {
return newRow;
}
-
+ /**
+ *
+ * @param pattern IsotopePattern to calculate intensity ratios of
+ * @param index DataPoint index to normalize the intesitys to
+ * @return String of intensity ratios seperated by ":"
+ */
private static String getIntensityRatios(IsotopePattern pattern, int index)
{
DataPoint[] dp = pattern.getDataPoints();
@@ -532,6 +536,11 @@ public class IsotopePeakScannerTask extends AbstractTask {
return bd.doubleValue();
}
+ /**
+ * adds a comment to a PeakListRow without deleting the current comment
+ * @param row PeakListRow to add the comment to
+ * @param str comment to be added
+ */
public static void addComment(PeakListRow row, String str)
{
String current = row.getComment();
