Examples of PSMaps

eu.isas.peptideshaker.myparameters.PSMaps
This class contains all scoring maps from PeptideShaker and will be used to store the information. @author Marc Vaudel

Examples of eu.isas.peptideshaker.myparameters.PSMaps

                new ImageIcon(this.getClass().getResource("/icons/star_grey.png")),
                "Starred", null, null));
        psmTable.getColumn("H").setCellRenderer(new NimbusCheckBoxRenderer());
        psmTable.getColumn("m/z").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, SpectrumFactory.getInstance().getMaxMz(), peptideShakerGUI.getSparklineColor()));
        psmTable.getColumn("Charge").setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL,
                (double) ((PSMaps) peptideShakerGUI.getIdentification().getUrParam(new PSMaps())).getPsmSpecificMap().getMaxCharge(), peptideShakerGUI.getSparklineColor()));
        psmTable.getColumn("RT").setCellRenderer(new JSparklinesIntervalChartTableCellRenderer(PlotOrientation.HORIZONTAL, SpectrumFactory.getInstance().getMinRT(),
                SpectrumFactory.getInstance().getMaxRT(), SpectrumFactory.getInstance().getMaxRT() / 50, peptideShakerGUI.getSparklineColor(), peptideShakerGUI.getSparklineColor()));
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("m/z").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesBarChartTableCellRenderer) psmTable.getColumn("Charge").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth());
        ((JSparklinesIntervalChartTableCellRenderer) psmTable.getColumn("RT").getCellRenderer()).showNumberAndChart(true, TableProperties.getLabelWidth() + 5);

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Examples of eu.isas.peptideshaker.myparameters.PSMaps

//            }
//        }
        waitingHandler.appendReport(report, true, true);
        waitingHandler.appendReportEndLine();
        waitingHandler.appendReportEndLine();
        identification.addUrParam(new PSMaps(matchesValidator.getPsmMap(), matchesValidator.getPeptideMap(), matchesValidator.getProteinMap(), inputMap, ptmScorer.getPsmPTMMap()));
        waitingHandler.setRunFinished();
    }

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Examples of eu.isas.peptideshaker.myparameters.PSMaps

            boolean recalibrate, WaitingHandler waitingHandler) throws IOException, MzMLUnmarshallerException, SQLException, ClassNotFoundException, InterruptedException {


        SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
        SpectrumRecalibrator spectrumRecalibrator = new SpectrumRecalibrator();


        PSMaps psMaps = new PSMaps();
        psMaps = (PSMaps) identification.getUrParam(psMaps);
        PsmSpecificMap psmTargetDecoyMap = psMaps.getPsmSpecificMap();


        int progress = 1;


        for (String fileName : spectrumFactory.getMgfFileNames()) {

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