Examples of net.sf.mzmine.data.Scan

net.sf.mzmine.data.Scan
This class represent one spectrum of a raw data file.

      RawDataFile dataFiles[] = MZmineCore.getCurrentProject()
          .getDataFiles();
      for (RawDataFile dataFile : dataFiles) {
        int scanNums[] = dataFile.getScanNumbers();
        for (int scanNum : scanNums) {
          Scan scan = dataFile.getScan(scanNum);
          MassList massLists[] = scan.getMassLists();
          for (MassList massList : massLists) {
            String name = massList.getName();
            if (!currentNames.contains(name))
              currentNames.add(name);
          }

View Full Code Here

   * Returns true if the given data file has mass lists for all MS1 scans
   * 
   */
  public static boolean hasMassLists(RawDataFile dataFile) {
    for (int scanNum : dataFile.getScanNumbers(1)) {
      Scan scan = dataFile.getScan(scanNum);
      if (scan.getMassLists().length == 0)
        return false;
    }
    return true;
  }

View Full Code Here

    RawDataFile dataFile = bestPeak.getDataFile();
    Map<DataPoint, String> msmsAnnotations = null;
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();


    if ((checkMSMS) && (msmsScanNumber > 0)) {
      Scan msmsScan = dataFile.getScan(msmsScanNumber);
      String massListName = msmsParameters.getParameter(
          MSMSScoreParameters.massList).getValue();
      MassList ms2MassList = msmsScan.getMassList(massListName);
      if (ms2MassList == null) {
        setStatus(TaskStatus.ERROR);
        this.errorMessage = "The MS/MS scan #" + msmsScanNumber
            + " in file " + dataFile.getName()
            + " does not have a mass list called '" + massListName

View Full Code Here

        if (isCanceled())
          return;
        PeakListRow row = pp.getRows()[i];
        // TODO search for the peak with the best fragmentation not the
        // most intense peak
        Scan msmsScan = row
            .getBestPeak()
            .getDataFile()
            .getScan(
                row.getBestPeak()
                    .getMostIntenseFragmentScanNumber());

View Full Code Here

          if (isCanceled()) {
            return;
          }


          // Get the scan
          Scan scan = dataFile.getScan(scanNumber);


          // Feed this scan to all gaps
          for (Gap gap : gaps) {
            gap.offerNextScan(scan);
          }

View Full Code Here

          if (isCanceled()) {
            return;
          }


          // Get the scan
          Scan scan = datafile1.getScan(scanNumber);


          // Feed this scan to all gaps
          for (Gap gap : gaps) {
            gap.offerNextScan(scan);
          }

View Full Code Here

    // Update fragment scan
    fragmentScan = ScanUtils.findBestFragmentScan(dataFile,
        dataFile.getDataRTRange(1), rawDataPointsMZRange);


    if (fragmentScan > 0) {
      Scan fragmentScanObject = dataFile.getScan(fragmentScan);
      int precursorCharge = fragmentScanObject.getPrecursorCharge();
      if ((precursorCharge > 0) && (this.charge == 0))
        this.charge = precursorCharge;
    }


  }

View Full Code Here


      if (isCanceled())
        return null;


      // Get next scan
      Scan scan = column.getScan(scanNumber);


      // Find most intense m/z peak
      DataPoint basePeak = ScanUtils.findBasePeak(scan, mzRangeWithTol);


      if (basePeak != null) {
        if (basePeak.getIntensity() > 0)
          dataPointFound = true;
        newPeak.addDatapoint(scan.getScanNumber(), basePeak);
      } else {
        DataPoint fakeDataPoint = new SimpleDataPoint(
            mzRangeWithTol.getAverage(), 0);
        newPeak.addDatapoint(scan.getScanNumber(), fakeDataPoint);
      }


    }


    if (dataPointFound) {

View Full Code Here

      else
        label.setIcon(fileIcon);
    }


    if (embeddedObject instanceof Scan) {
      Scan s = (Scan) embeddedObject;
      label.setIcon(spectrumIcon);
      label.setFont(smallFont);


      // Change the color only if the row is not selected, otherwise we
      // could get blue text on blue background
      if (!sel) {
        if (s.getMSLevel() > 1)
          label.setForeground(Color.red);
        else
          label.setForeground(Color.blue);
      }
    }

View Full Code Here


    fragmentScan = ScanUtils.findBestFragmentScan(dataFile, rtRange,
        mzRange);


    if (fragmentScan > 0) {
      Scan fragmentScanObject = dataFile.getScan(fragmentScan);
      int precursorCharge = fragmentScanObject.getPrecursorCharge();
      if ((precursorCharge > 0) && (this.charge == 0))
        this.charge = precursorCharge;
    }


  }

View Full Code Here

0 1 2 3 4 5 6

TOP

Related Classes of net.sf.mzmine.data.Scan

net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel

net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler

net.sf.mzmine.desktop.impl.projecttree.ProjectTreeRenderer

net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentProcessingTask

net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherParameters

net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherProcessingTask

net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTask

net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTest

net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.Chromatogram

net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderTask

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.