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Constant Field Values

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org.fhcrc.*

org.fhcrc.cpl.toolbox.TextProvider
public static final java.lang.String TOKEN_INDICATOR "##"

org.fhcrc.cpl.toolbox.commandline.CommandLineModule
public static final java.lang.String MODULE_HELP_AUTOMATIC "MODULE_HELP_AUTOMATIC"
public static final java.lang.String MODULE_USAGE_AUTOMATIC "MODULE_USAGE_AUTOMATIC"
public static final java.lang.String UNNAMED_ARG_SERIES_SEPARATOR "AAAAARGSEPAAAA"

org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition
public static final java.lang.String UNNAMED_PARAMETER_VALUE_ARGUMENT "unnamed_parameter_value_argument"
public static final java.lang.String UNNAMED_PARAMETER_VALUE_SERIES_ARGUMENT "unnamed_parameter_value_series_argument"

org.fhcrc.cpl.toolbox.commandline.arguments.DeltaMassArgumentDefinition
public static final int DELTA_MASS_ABSOLUTE 0
public static final int DELTA_MASS_PPM 1

org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition
public static final int FILE_TYPE_FEATURE 1
public static final int FILE_TYPE_IMAGE 2
public static final int FILE_TYPE_UNKNOWN 0

org.fhcrc.cpl.toolbox.commandline.arguments.StringListArgumentDefinition
public static final java.lang.String DEFAULT_SEPARATOR_STRING ","

org.fhcrc.cpl.toolbox.gui.HtmlGenerator
protected static final java.lang.String HTML_CLOSE_TAG "</html>"
protected static final java.lang.String HTML_OPEN_TAG "<html>"

org.fhcrc.cpl.toolbox.gui.HtmlViewerPanel
public static final int DEFAULT_HEIGHT 800
public static final int DEFAULT_WIDTH 1000

org.fhcrc.cpl.toolbox.gui.InteractiveModuleFrame
protected static final int ARG_HELP_PANEL_HEIGHT 90
protected static final int MAX_FIELDPANE_HEIGHT 600

org.fhcrc.cpl.toolbox.gui.ListenerHelper
protected static final int ACTION 3
protected static final int CHANGE 1
protected static final int COMPONENT 4
protected static final int DOCUMENT 8
protected static final int KEY 7
protected static final int LIST_SELECTION 9
protected static final int MOUSE 5
protected static final int MOUSEMOTION 6
protected static final int PROPERTYCHANGE 2

org.fhcrc.cpl.toolbox.gui.chart.MultiChartDisplayPanel
public static final int DEFAULT_HEIGHT 800
public static final int DEFAULT_WIDTH 800

org.fhcrc.cpl.toolbox.gui.chart.PanelWithChart
public static final int DEFAULT_HEIGHT_FOR_IMAGE_FILE 600
public static final int DEFAULT_WIDTH_FOR_IMAGE_FILE 800

org.fhcrc.cpl.toolbox.gui.chart.PanelWithHeatMap
public static final int DEFAULT_PALETTE 0
public static final int DISTINCT_PALETTE_VALUES 100
public static final int PALETTE_BLUE 2
public static final int PALETTE_BLUE_RED 0
public static final int PALETTE_GRAYSCALE 3
public static final int PALETTE_POSITIVE_WHITE_BLUE_NEGATIVE_BLACK_RED 5
public static final int PALETTE_RED 1
public static final int PALETTE_WHITE_BLUE 4

org.fhcrc.cpl.toolbox.gui.chart.PanelWithHistogram
public static final double BAR_OFFSET 0.13
public static final int DEFAULT_BREAKS 100

org.fhcrc.cpl.toolbox.gui.chart.PanelWithPieChart
public static final int DEFAULT_LABEL_FONT_SIZE 12

org.fhcrc.cpl.toolbox.gui.chart.PanelWithRPairsPlot
public static final int DEFAULT_CHART_DIALOG_HEIGHT 725
public static final int DEFAULT_CHART_DIALOG_WIDTH 710
public static final int DEFAULT_CHART_HEIGHT 700
public static final int DEFAULT_CHART_WIDTH 700

org.fhcrc.cpl.toolbox.gui.chart.PanelWithRPerspectivePlot
public static final java.lang.String DEFAULT_BACKGROUND_COLOR_STRING "white"
public static final int DEFAULT_CHART_DIALOG_HEIGHT 725
public static final int DEFAULT_CHART_DIALOG_WIDTH 710
public static final int DEFAULT_CHART_HEIGHT 700
public static final int DEFAULT_CHART_WIDTH 700
public static final java.lang.String DEFAULT_FOREGROUND_COLOR_STRING "lightgreen"
public static final int DEFAULT_LINE_STYLE 1
public static final int DEFAULT_ROTATION_ANGLE 0
public static final double DEFAULT_SHADE 0.5
public static final int DEFAULT_TILT_ANGLE 30
public static final int LINE_STYLE_DASHED 2
public static final int LINE_STYLE_DOTTED 3
public static final int LINE_STYLE_SOLID 1

org.fhcrc.cpl.toolbox.gui.chart.TabbedMultiChartDisplayPanel
public static final int TABBEDPANE_VERTICAL_SLOP 5

org.fhcrc.cpl.toolbox.gui.widget.SwingWorkerWithProgressBarDialog<T,V>
public static final java.lang.String CURRENT_VALUE_TOKEN "%%CURRENT_VALUE%%"
public static final java.lang.String MAX_VALUE_TOKEN "%%MAX_VALUE%%"
protected static final int PROGRESS_BAR_HEIGHT 50
protected static final int PROGRESS_BAR_WIDTH 250

org.fhcrc.cpl.toolbox.proteomics.MassCalibrationUtilities
public static final double DEFAULT_MAX_LEVERAGE_NUMERATOR_FOR_REGRESSION 4.0
public static final int DEFAULT_MAX_PAIRS_FOR_LEVERAGE_CALC 500000
public static final double DEFAULT_MAX_STUDENTIZED_RESIDUAL_FOR_REGRESSION 2.3
public static final double DEFAULT_THEORETICAL_MASS_WAVELENGTH 1.000476
public static final double THEORETICAL_MASS_DEFECT_INTERCEPT 0.034

org.fhcrc.cpl.toolbox.proteomics.PeptideGenerator
public static final int DIGEST_ALL 2
public static final int DIGEST_TRYPTIC 1
public static final double ELECTRON_MASS 5.485E-4
public static final int H_ION_INDEX 0

org.fhcrc.cpl.toolbox.proteomics.PeptideUtilities
public static final float MOD_MASS_SLOP 0.10000000149011612f

org.fhcrc.cpl.toolbox.proteomics.Protein
public static final java.lang.String SEPARATOR_CHAR "|"
public static final java.lang.String SEPARATOR_PATTERN "\\|"

org.fhcrc.cpl.toolbox.proteomics.ProteomicsRegressionUtilities
public static final int DEFAULT_REGRESSION_MODE 1
public static final int REGRESSION_MODE_SCAN 0
public static final int REGRESSION_MODE_TIME 1

org.fhcrc.cpl.toolbox.proteomics.QuantitationUtilities
public static final float ACRYLAMIDE_LABEL_HEAVYMASS 177.055908203125f
public static final float ACRYLAMIDE_LABEL_LIGHTMASS 174.04580688476562f
public static final float ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE 3.010101318359375f
public static final java.lang.String ALGORITHM_Q3 "Q3"
public static final java.lang.String ALGORITHM_XPRESS "XPRESS"
public static final int LABEL_ACRYLAMIDE 0
public static final java.lang.String LABEL_ACRYLAMIDE_CODE "acrylamide"
public static final java.lang.String LABEL_ACRYLAMIDE_EXPLANATION "Acrylamide (3.0106Da on C)"
public static final int LABEL_LYCINE 1
public static final java.lang.String LABEL_LYCINE_CODE "silac"
public static final java.lang.String LABEL_LYCINE_EXPLANATION "SILAC Lycine labeling (134.115092 on K, i.e. 6Da SILAC)"
public static final float SILAC_LABEL_MASS 134.11509704589844f
public static final float SILAC_LABEL_MASSDIFF_PERRESIDUE 6.020129203796387f

org.fhcrc.cpl.toolbox.proteomics.feature.AnalyzeICAT
public static final float DEFAULT_DELTA_MASS 0.20000000298023224f
public static final int DEFAULT_DELTA_MASS_TYPE 0
public static final float DEFAULT_DELTA_TIME 10.0f
public static final int DELTA_MASS_ABSOLUTE 0
public static final int DELTA_MASS_PPM 1

org.fhcrc.cpl.toolbox.proteomics.feature.Deconvoluter
public static final double DEFAULT_DELTA_MASS 15.0
public static final double DEFAULT_DELTA_TIME 30.0
public static final double DEFAULT_MAX_DELTA_MASS_PPM 40.0
public static final double DEFAULT_MAX_DELTA_TIME 50.0
public static final double DEFAULT_MIN_DELTA_MASS_PPM 5.0
public static final double DEFAULT_MIN_DELTA_TIME 10.0
protected static final double MASS_INCREMENT_PPM 2.0
protected static final double TIME_INCREMENT_SECONDS 5.0

org.fhcrc.cpl.toolbox.proteomics.feature.FeatureClusterer
public static final int DEFAULT_DELTA_MASS_TYPE 0
public static final int DEFAULT_ELUTION_MODE 0
public static final int DEFAULT_MASS_MZ_MODE 1
public static final int DELTA_MASS_TYPE_ABSOLUTE 0
public static final int DELTA_MASS_TYPE_PPM 1
public static final int ELUTION_MODE_SCAN 1
public static final int ELUTION_MODE_TIME 0
public static final int MASS_MZ_MODE_MASS 0
public static final int MASS_MZ_MODE_MZ 1

org.fhcrc.cpl.toolbox.proteomics.feature.FeatureGrouper
public static final int BUCKET_EVALUATION_MODE_ONE_FROM_EACH 0
public static final int BUCKET_EVALUATION_MODE_PEPTIDE_AGREEMENT 1
public static final int CONFLICT_RESOLVER_BEST 1
public static final int CONFLICT_RESOLVER_SUM 0
public static final int DEFAULT_CONFLICT_RESOLVER 0
public static final int DEFAULT_PEPTIDE_AGREEMENT_MATCH_SCORE 1
public static final int DEFAULT_PEPTIDE_AGREEMENT_MISMATCH_PENALTY 1

org.fhcrc.cpl.toolbox.proteomics.feature.FeaturePepXmlWriter
public final int RATIO_MODE_Q3 1
public final int RATIO_MODE_XPRESS 0

org.fhcrc.cpl.toolbox.proteomics.feature.FeatureSet
public static final int DEFAULT_INTENSITY_TYPE 0
public static final int FEATURESET_LOAD_ERROR_BAD_FILE_FORMAT 2
public static final int FEATURESET_LOAD_ERROR_FILE_NOT_FOUND 1
public static final int FEATURESET_LOAD_ERROR_NO_FEATURES_FOUND 3
public static final int FEATURESET_LOAD_ERROR_UNKNOWN 4
public static final int FEATURESET_LOAD_NOT_LOADED -1
public static final int FEATURESET_LOAD_SUCCESS 0
public static final int MAX_INTENSITY 1
public static final int RECALCULATED_INTENSITY 2
public static final int TOTAL_INTENSITY 0

org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum
public static final float HYDROGEN_ION_MASS 1.0072765350341797f

org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.AmtExtraInfoDef
public static final double NO_MATCH_PROBABILITY -999999.0
public static final double NO_OBSERVED_HYDROPHOBICITY -999999.0

org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.FeatureExtraInformationDef
protected static final java.lang.String MULTI_VALUE_LIST_SEPARATOR ";"

org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.IsotopicLabelExtraInfoDef
public static final float NO_RATIO_FOR_FEATURE -1.0f

org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.MS2ExtraInfoDef
public static final float defaultDeltaMass 0.0f
public static final float defaultFDR -1.0f
public static final float defaultFval 0.0f
public static final int defaultNumEnzymaticEnds -1
public static final float defaultPeptideProphet 0.0f
public static final int NO_ENZYMATIC_ENDS_SPECIFIED -1

org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.APMLFeatureFileHandler
public static final java.lang.String APML_CLUSTERS_DESCRIPTION_LABELED_QUANT "labeled_quantitation"
public static final java.lang.String APML_QUALITY_SCORE_ACCMASS "accurate_mass_flag"
public static final java.lang.String APML_QUALITY_SCORE_NAME_KL "KL"
public static final java.lang.String APML_QUALITY_SCORE_SUMSQUARESDIST "sum_squares_dist"
public static final java.lang.String APML_SEARCH_SCORE_NAME_PEPTIDE_PROPHET "PeptideProphet"
public static final java.lang.String APML_SOFTWARE_PARAM_FEATURE_STRATEGY "feature_strategy"
public static final java.lang.String APML_SOFTWARE_PARAM_QUANT_LABEL "quantitation_label"
protected static final float DUMMY_KL_SCORE 2.0f
protected static final int DUMMY_NUM_PEAKS 2
public static final java.lang.String FILE_TYPE_NAME "APML"

org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.BaseFeatureSetFileHandler
public static final java.lang.String FILE_TYPE_NAME ""

org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.HardklorFeatureFileHandler
public static final java.lang.String FILE_TYPE_NAME "HARDKLOR"

org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.NativeTSVFeatureFileHandler
public static final java.lang.String FILE_TYPE_NAME "NATIVE_TSV"

org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.PepXMLFeatureFileHandler
public static final java.lang.String FILE_TYPE_NAME "PEPXML"
public static final int QUANT_ALGORITHM_Q3 0
public static final int QUANT_ALGORITHM_XPRESS 1

org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl
public static final int DEFAULT_ELUTION_MODE 0
public static final int ELUTION_MODE_HYDROPHOBICITY 0
public static final int ELUTION_MODE_SCAN 2
public static final int ELUTION_MODE_TIME 1
public static final int ORDER_BY_ELUTION_CLOSENESS_TO_MASTER_MODE 1
public static final int ORDER_BY_FEATURE_QUALITY_MODE 0

org.fhcrc.cpl.toolbox.proteomics.feature.matching.ClusteringFeatureSetMatcher
protected static final double ABSOLUTE_MASS_BUCKET_INCREMENT 0.05
public static final double DEFAULT_HYDRO_ELUTION_BUCKET_INCREMENT 0.05
protected static final double PPM_MASS_BUCKET_INCREMENT 1.0

org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher
public static final double DEFAULT_DELTA_HYDROPHOBICITY 0.05
public static final float DEFAULT_DELTA_MASS_ABSOLUTE 0.20000000298023224f
public static final float DEFAULT_DELTA_MASS_PPM 5.0f
public static final int DEFAULT_DELTA_MASS_TYPE 1
public static final int DEFAULT_DELTA_SCAN 3
public static final double DEFAULT_DELTA_TIME 20.0
public static final int DELTA_MASS_TYPE_ABSOLUTE 0
public static final int DELTA_MASS_TYPE_PPM 1

org.fhcrc.cpl.toolbox.proteomics.feature.matching.RecursiveFeatureSetMatcher
protected static final double ABSOLUTE_MASS_BUCKET_INCREMENT 0.05
public static final double DEFAULT_HYDRO_ELUTION_BUCKET_INCREMENT 0.01
public static final double DEFAULT_MIN_DELTA_H 0.0050
public static final double DEFAULT_MIN_DELTA_MASS_DA 0.05
public static final double DEFAULT_MIN_DELTA_MASS_PPM 1.0
public static final double DEFAULT_MIN_DELTA_SCAN 5.0
public static final double DEFAULT_MIN_DELTA_TIME 10.0
public static final double DEFAULT_SCAN_ELUTION_BUCKET_INCREMENT 5.0
public static final double DEFAULT_TIME_ELUTION_BUCKET_INCREMENT 10.0
protected static final double PPM_MASS_BUCKET_INCREMENT 2.0

org.fhcrc.cpl.toolbox.proteomics.feature.matching.Window2DFeatureSetMatcher
public static final int DEFAULT_ELUTION_MODE 0
public static final int ELUTION_MODE_HYDROPHOBICITY 0
public static final int ELUTION_MODE_SCAN 2
public static final int ELUTION_MODE_TIME 1
public static final int ELUTION_RANGE_MODE_POINT 0
public static final int ELUTION_RANGE_MODE_RANGE 1

org.fhcrc.cpl.toolbox.proteomics.filehandler.BasePepXmlWriter
public static final java.lang.String PRECURSOR_MASS_TYPE_MONOISOTOPIC "monoisotopic"
public static final java.lang.String SEARCH_ENGINE_XTANDEM_COMET "X! Tandem (comet)"

org.fhcrc.cpl.toolbox.proteomics.filehandler.MzXmlWriter
public static final java.lang.String PRECURSORMZ_ATTR_MSINSPECT_CORRECTED "msInspect_corrected"
public static final double UNSET_INTENSITY_SCALE -1.0
public static final double UNSET_WAVELENGTH_OR_OFFSET 9.99999999E8

org.fhcrc.cpl.toolbox.proteomics.filehandler.PeptideProphetHandler
public static final java.lang.String analysisType "peptideprophet"

org.fhcrc.cpl.toolbox.proteomics.filehandler.Q3AnalysisSummary
public static final java.lang.String analysisType "q3"

org.fhcrc.cpl.toolbox.proteomics.filehandler.Q3Handler
public static final java.lang.String analysisType "q3"

org.fhcrc.cpl.toolbox.proteomics.filehandler.RelativeQuantAnalysisResult
public static final float SENTINEL_NAN -1.0f
public static final float SENTINEL_NEGATIVE_INFINITY -999.0f
public static final float SENTINEL_POSITIVE_INFINITY 999.0f

org.fhcrc.cpl.toolbox.proteomics.filehandler.XPressAnalysisSummary
public static final java.lang.String analysisType "xpress"

org.fhcrc.cpl.toolbox.proteomics.filehandler.XPressHandler
public static final java.lang.String analysisType "xpress"

org.fhcrc.cpl.toolbox.statistics.RegressionUtilities
public static final int DEFAULT_MAX_MILLIS_FOR_ROBUST_REGRESSION 180000
public static final java.lang.String REGRESSION_INTERCEPT_KEY "REGRESSION_INTERCEPT_KEY"
public static final java.lang.String REGRESSION_SIGMA_KEY "REGRESSION_SIGMA_KEY"
public static final java.lang.String REGRESSION_SLOPE_KEY "REGRESSION_SLOPE_KEY"

org.fhcrc.cpl.toolbox.statistics.RInterface
protected static final int DEFAULT_MAX_R_WAIT_MILLIS 5000
protected static final int R_SLEEP_INCREMENT_MILLIS 50

org.fhcrc.cpl.toolbox.statistics.RInterface.RErrorReaderThread
public static final int STATUS_ERROR 1
public static final int STATUS_READING 0

org.fhcrc.cpl.toolbox.statistics.RInterface.RReaderThread
public static final int STATUS_ERROR 1
public static final int STATUS_READING 0

org.fhcrc.cpl.viewer.Application
public static final java.lang.String FAILURE_REPORT_ERRORMESSAGE_TEXT "If you would like help with this issue, please report the problem in detail\nto the msInspect support forum at:\n https://www.labkey.org/Project/msInspect/begin.view\nand attach the failure report file.\n"
public static final java.lang.String FAILURE_REPORT_HEADER_TEXT "#msInspect failure report\n#please report this failure and attach this report on the support forum at https://www.labkey.org/Project/msInspect/begin.view\n"
protected static final java.lang.String LOGFILE_DUMMY_CALLER "//APPLICATION_LOGFILE_DUMMY_CALLER//"

org.fhcrc.cpl.viewer.Localizer
protected static final java.lang.String _fontPrefKeyPrefix "lastFont_"
protected static final java.lang.String _localePrefKey "lastLocale"
protected static final java.lang.String CONTAINER_HEIGHT_SCALE "CONTAINER_HEIGHT_SCALE"
protected static final java.lang.String CONTAINER_WIDTH_SCALE "CONTAINER_WIDTH_SCALE"
public static final java.lang.String DEFAULT_LOCALE_STRING "en"
protected static final java.lang.String FONT_NAME "FONT_NAME"
protected static final java.lang.String FONT_SIZE "FONT_SIZE"
protected static final java.lang.String FONT_STYLE "FONT_STYLE"
protected static final java.lang.String FONT_TEST_STRING "FONT_TEST_STRING"
protected static final java.lang.String LABEL_SCALE "LABEL_SCALE"
protected static final java.lang.String REQUIRES_FONT_CHOICE "REQUIRES_FONT_CHOICE"

org.fhcrc.cpl.viewer.align.Aligner.MassFeaturePairSelector
public static final float DEFAULT_DELTA_MASS 10.0f

org.fhcrc.cpl.viewer.align.Aligner.MassOrMzFeaturePairSelector
public static final float DEFAULT_DELTA_MASS_OR_MZ 10.0f
public static final int DEFAULT_DELTA_MASS_TYPE 1
public static final float DEFAULT_MIN_INTENSITY 100.0f
public static final int MODE_MASS 0
public static final int MODE_MZ 1

org.fhcrc.cpl.viewer.align.Aligner.MzFeaturePairSelector
public static final float DEFAULT_DELTA_MZ 0.10000000149011612f

org.fhcrc.cpl.viewer.align.PeptideArrayAnalyzer
public static final int CONSENSUS_INTENSITY_MODE_FIRST 1
public static final int CONSENSUS_INTENSITY_MODE_MEAN 0
public static final float MAX_Q_VALUE 0.05000000074505806f

org.fhcrc.cpl.viewer.align.SplineAligner
public static final int DEFAULT_DEGREES_OF_FREEDOM 20

org.fhcrc.cpl.viewer.align.commandline.AlignCLM
protected static final int MODE_QUANTILE 1
protected static final int MODE_SPLINE 0

org.fhcrc.cpl.viewer.align.commandline.PeptideArrayAnalyzerCommandLineModule
protected static final int MODE_COMPARE_ALL_INTENSITIES 5
protected static final int MODE_COMPARE_ALL_INTENSITIES_ADD_1 6
protected static final int MODE_COMPARE_INTENSITIES_SAME_PEPTIDE 3
protected static final int MODE_COMPARE_INTENSITIES_SAME_PEPTIDE_ADD_1 7
protected static final int MODE_COMPARE_NON_PEPTIDE_INTENSITIES 8
protected static final int MODE_COUNT_MULTIPLY_OBSERVED_PEPTIDEES 2
protected static final int MODE_CREATE_CONSENSUS_FEATURE_FILE 4
protected static final int MODE_CREATE_FEATURE_FILES_ALL_MATCHED 1
protected static final int MODE_GET_INFO 0

org.fhcrc.cpl.viewer.align.commandline.PeptideArrayCommandLineModule
protected static final int ALIGNMENT_MODE_QUANTILE 1
protected static final int ALIGNMENT_MODE_SPLINE 0

org.fhcrc.cpl.viewer.amt.AmtDatabase
public static final java.lang.String DEFAULT_HYDROPHOBICITY_ALGORITHM_NAME "krokhin"
public static final double DEFAULT_HYDROPHOBICITY_ALGORITHM_VERSION 3.0
public static final double DEFAULT_MODIFICATION_MASS_ROUNDING_FACTOR 1.0
public static final float MODIFICATION_EQUALITY_MASS_TOLERANCE 0.10000000149011612f

org.fhcrc.cpl.viewer.amt.AmtDatabaseBuilder
public static final boolean DEFAULT_IGNORE_UNKNOWN_MODIFICATIONS false
public static final double DEFAULT_MAX_LEVERAGE_NUMERATOR 4.0
public static final double DEFAULT_MAX_STUDENTIZED_RESIDUAL_FOR_INCLUSION 2.0
public static final double DEFAULT_MAX_STUDENTIZED_RESIDUAL_FOR_REGRESSION 2.0
public static final int DEFAULT_MIN_OBSERVATIONS_FOR_ALIGNMENT_REGRESSION 3
public static final int DEFAULT_MIN_PEPTIDES_FOR_ALIGNMENT_REGRESSION 8
public static final float DEFAULT_MS1_MS2_MASS_TOLERANCE_PPM 10.0f
public static final float DEFAULT_MS1_MS2_TIME_TOLERANCE_SECONDS 25.0f

org.fhcrc.cpl.viewer.amt.AmtDatabaseManager
public static final int DEFAULT_MATCHING_DEGREE_FOR_DB_ALIGNMENT 5
public static final int DEFAULT_MIN_OBSERVATIONS_FOR_ALIGNMENT_REGRESSION 3
public static final int DEFAULT_MIN_PEPTIDES_FOR_ALIGNMENT_REGRESSION 30

org.fhcrc.cpl.viewer.amt.AmtDatabaseMatcher
public static final float DEFAULT_2D_MATCH_DELTA_ELUTION 0.15000000596046448f
public static final float DEFAULT_2D_MATCH_DELTA_MASS 10.0f
public static final int DEFAULT_2D_MATCH_DELTA_MASS_TYPE 1
public static final int DEFAULT_DECOY_DB_MASS_ADJUSTMENT_DA 11
public static final double DEFAULT_LEVERAGE_NUMERATOR 6.0
public static final float DEFAULT_MASS_MATCH_DELTA_MASS 5.0f
public static final int DEFAULT_MASS_MATCH_DELTA_MASS_TYPE 1
public static final double DEFAULT_MAX_LEVERAGE_NUMERATOR 12.0
public static final double DEFAULT_MAX_STUDENTIZED_RESIDUAL 3.0
public static final int DEFAULT_NONLINEAR_MAPPING_DEGREE 5
public static final int DEFAULT_QUANTILE_REG_MIN_FEATURES 85
public static final float DEFAULT_SIGNIFICANT_HYDRO_DIFFERENCE 0.4000000059604645f
public static final boolean DEFAULT_USE_MS1_TIMES_FOR_ALIGNMENT true
public static final int MIN_MATCHED_FEATURES_FOR_REGRESSION 8

org.fhcrc.cpl.viewer.amt.AmtFeatureSetMatcherFactory
public static final java.lang.String AMT_PACKAGE "org.fhcrc.cpl.viewer.amt"

org.fhcrc.cpl.viewer.amt.AmtLabeledQuant
public static final double ACRYLAMIDE_MASS_DIFF 3.0101
protected static final double DEFAULT_MASS_SLOP 0.1
public static final float DEFAULT_MAX_SECOND_BEST_PROB_WITHIN_STATE 0.4000000059604645f
public static final float DEFAULT_MIN_PROB_DIFF_WITHIN_STATE 0.10000000149011612f
public static final float DEFAULT_MIN_RATIO_HIGH_PROB 0.699999988079071f
public static final float DEFAULT_MIN_RATIO_LOW_PROB 0.05000000074505806f

org.fhcrc.cpl.viewer.amt.AmtMatchProbabilityAssigner
public static final float DEFAULT_EM_MAX_DELTA_P_FOR_STABLE 0.004999999888241291f
public static final int DEFAULT_EM_MAX_ITERATIONS_STABLE_FOR_CONVERGENCE 1
public static final int DEFAULT_MAX_EM_ITERATIONS 200
public static final float DEFAULT_MAX_SECONDBEST_PROBABILITY 0.5f
public static final int DEFAULT_MIN_EM_ITERATIONS 30
public static final float DEFAULT_MIN_MATCH_PROBABILITY 0.10000000149011612f
public static final float DEFAULT_MIN_SECONDBEST_PROBABILITY_DIFFERENCE 0.10000000149011612f
public static final float KS_CUTOFF_FOR_WARN 0.004999999888241291f
public static final int MAX_R_PROB_ASSIGNMENT_MILLIS 900000
public static final int MAX_TREE_DEPTH 30
public static final int NUM_DECOY_POINTS 30
public static final int NUM_TARGET_POINTS 30
public static final int SCALING_FACTOR 100

org.fhcrc.cpl.viewer.amt.AmtPeptideEntry
protected static final double MEAN_HYDRO_UNCALCULATED_SENTINEL -9.9999999E7

org.fhcrc.cpl.viewer.amt.AmtPeptideEntry.AmtPeptideObservation
public static final int SPECTRAL_COUNT_UNKNOWN -1

org.fhcrc.cpl.viewer.amt.AmtUtilities
public static final java.lang.String HYDROPHOBICITY_ALGORITHM_NAME "krokhin"
public static final double HYDROPHOBICITY_ALGORITHM_VERSION 3.0

org.fhcrc.cpl.viewer.amt.HydrophobicityNormalizer
public static final double KROKHIN_1_MEAN 30.763700485229492
public static final double KROKHIN_1_STDDEV 21.886646343829856
public static final double KROKHIN_3_MEAN 29.575716018676758
public static final double KROKHIN_3_STDDEV 17.596638381015442
public static final double PREDICTNET_1_MEAN 0.337
public static final double PREDICTNET_1_STDDEV 0.21

org.fhcrc.cpl.viewer.amt.PeptideMatcher
public static final int DEFAULT_PEPTIDE_TIME_TOLERANCE_MODE 0
public static final int PEPTIDE_TIME_TOLERANCE_MODE_ADAPTIVE 1
public static final int PEPTIDE_TIME_TOLERANCE_MODE_FIXED 0
public static final int UNOBSERVED_PEPTIDE_GRADIENT_PERCENT_TOLERANCE 5

org.fhcrc.cpl.viewer.amt.ProteinDisplay
public static final int DISPLAY_MATCHED_FEATURES_MODE 0
public static final int DISPLAY_UNMATCHED_MS2_FEATURES_MODE 1
public static final int DISPLAY_UNMATCHED_PROTEIN_PEPTIDES_MODE 2
protected static final java.lang.String NCBIEntrezViewerBaseUrl "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"

org.fhcrc.cpl.viewer.amt.ProteinMatcher
protected static final int MAX_MISSED_CLEAVAGES 1
protected static final int MIN_PEPTIDE_LENGTH 5

org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseCreatorCommandLineModule
protected static final int CREATE_AMTXML_FROM_DIRECTORIES_MODE 0
protected static final int CREATE_AMTXML_FROM_MS2_FEATURES_MODE 1
protected static final int CREATE_AMTXML_FROM_MULTIPLE_AMT_XMLS_MODE 2
protected static final int CREATE_AMTXML_FROM_PROTEIN_TRYPTIC_PEPTIDES_MODE 4
protected static final int CREATE_AMTXML_FROM_RANDOM_PEPTIDES_MODE 3

org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseDiagnosticCommandLineModule
protected static final int MODE_BASIC_INFO 7
protected static final int MODE_COMPARE_CALC_H_TIME 1
protected static final int MODE_COMPARE_OBS_H_CALC_H 0
protected static final int MODE_HIST_HYDRO_STD_DEV 3
protected static final int MODE_HIST_ID_PROBS 12
protected static final int MODE_HIST_MASSES 8
protected static final int MODE_PEPTIDE_DETAILS 10
protected static final int MODE_PLOT_MASS_H 11
protected static final int MODE_PLOT_MASS_VS_OBS_HYDRO 6
protected static final int MODE_PLOT_RUN_H_VS_MEDIAN 9
protected static final int MODE_PLOT_RUN_HYDRO_DIFFS 4
protected static final int MODE_PLOT_T_H_MAPS 2
protected static final int MODE_SAVE_ALL_CHARTS 5

org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseManagerCommandLineModule
protected static final int ADJUST_ACRYLAMIDE_MODE 5
protected static final int ALIGN_ALL_RUNS_MODE 4
protected static final int FILTER_OBSERVATIONS_BY_PPROPHET_MODE 8
protected static final int REMOVE_FASTA_PEPTIDES_MODE 7
protected static final int REMOVE_FEW_OBSERVATIONS_MODE 2
protected static final int REMOVE_OUTLIER_OBSERVATIONS_MODE 0
protected static final int REMOVE_PEPTIDES_WITH_RESIDUE_MODE 6
protected static final int REMOVE_PREDICTED_H_OUTLIERS_MODE 1
protected static final int REMOVE_RUNS_WITHOUT_MASS_MATCHES_MODE 3

org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseMatcherCLM
public static final double DEFAULT_MIN_EMBEDDED_MS2_PEPTIDE_PROPHET 0.9
protected static final int MODE_MATCH_AGAINST_MS1 0
protected static final int MODE_MATCH_AGAINST_MS1_DIR 1

org.fhcrc.cpl.viewer.amt.commandline.CombineAmtMs2FilesCLM
protected static final int FORMAT_FEATURE 1
protected static final int FORMAT_PEPXML 0

org.fhcrc.cpl.viewer.amt.commandline.ProteinRollupCommandLineModule
protected static final int MODE_COLLAPSE_PEPTIDES 3
protected static final int MODE_CREATE_PEPXML_FOR_TABFILE 2
protected static final int MODE_DIGEST_PROTXML 0
protected static final int MODE_ROLLUP_GENES 4
protected static final int MODE_ROLLUP_PEPTIDES_TO_GENES 5
protected static final int MODE_TABFILE 1

org.fhcrc.cpl.viewer.commandline.modules.ConvertFeatureFileCommandLineModule
protected static final int FILE_FORMAT_APML 3
protected static final int FILE_FORMAT_HARDKLOR 4
protected static final int FILE_FORMAT_MSINSPECT 0
protected static final int FILE_FORMAT_MULTI_MSINSPECT 5
protected static final int FILE_FORMAT_PEPXML 1
protected static final int FILE_FORMAT_SPECARRAY 2
protected static final int SPECARRAY_VERSION_1_0 0
protected static final int SPECARRAY_VERSION_1_2_0 1

org.fhcrc.cpl.viewer.commandline.modules.FeatureSetMatcherCommandLineModule
protected static final int MODE_MS1_MS2 0
protected static final int MODE_MS1_MS2_DIR 1

org.fhcrc.cpl.viewer.commandline.modules.FilterFeaturesCommandLineModule
public static final int OUT_FORMAT_MSINSPECT 0
public static final int OUT_FORMAT_PEPXML 1

org.fhcrc.cpl.viewer.commandline.modules.FindPeptidesCommandLineModule
public static final float DEFAULT_MAX_KL 3.0f
public static final int DEFAULT_MIN_PEAKS 2

org.fhcrc.cpl.viewer.commandline.modules.PlotFeatureAttributesCLM
protected static final int CHARGE 6
protected static final float FEATURE_NO_ATTRIBUTE -9999.9326171875f
protected static final int FRACTIONAL_DELTA_MASS 1
protected static final int FVAL 11
protected static final int INTENSITY 2
protected static final int KL 8
protected static final int LIGHTAREA 5
protected static final int MASS 12
protected static final int MODE_BOXPLOT 2
protected static final int MODE_HISTOGRAM 0
protected static final int MODE_SCATTER 1
protected static final int MZ 13
protected static final int NUM_CYSTEINES 14
protected static final int NUM_K_OR_R 15
protected static final int PEAKS 9
protected static final int PEPTIDE_PROPHET 0
protected static final int RATIO 4
protected static final int SEARCHSCORE 10
protected static final int SUMSQUARES_DISTANCE 7
protected static final int TIME 3

org.fhcrc.cpl.viewer.database.HibernateManager
public static final java.lang.String HIBERNATE_CONFIG_FILE_PREF_NAME "hibernateConfigFile"

org.fhcrc.cpl.viewer.feature.FeatureExtractor
public static final int TYPE_1D 1
public static final int TYPE_2D 2

org.fhcrc.cpl.viewer.feature.extraction.AccurateMassAdjuster
public static final int DEFAULT_RESAMPLING_FREQUENCY 36
public static final int DEFAULT_SCAN_WINDOW_SIZE 1

org.fhcrc.cpl.viewer.feature.extraction.DefaultFeatureScorer
public static final int DEFAULT_MAX_PEAKS_PER_FEATURE 10
public static final float SUMSQUARES_MZ_WEIGHT 6.0f
public static final float SUMSQUARES_SCALED_INTENSITY_WEIGHT 4.0f

org.fhcrc.cpl.viewer.feature.extraction.DefaultPeakCombiner
public static final double DEFAULT_MAX_ABS_DISTANCE_BETWEEN_PEAKS 1.0

org.fhcrc.cpl.viewer.feature.extraction.FeatureFinder
public static final int DEFAULT_ACCURATE_MASS_ADJUSTMENT_SCANS 3

org.fhcrc.cpl.viewer.feature.extraction.FeatureFindingBroker
public static final java.lang.String NEW_FEATURE_FINDING_PACKAGE_NAME "org.fhcrc.cpl.viewer.feature.extraction.strategy"
public static final java.lang.String OLD_FEATURE_FINDING_PACKAGE_NAME "org.fhcrc.cpl.viewer.feature"

org.fhcrc.cpl.viewer.feature.extraction.PeakCombiner
public static final int DEFAULT_MAX_CHARGE 6

org.fhcrc.cpl.viewer.feature.extraction.PeakExtractor
public static final boolean DEFAULT_PEAK_RIDGE_WALK_SMOOTHED false

org.fhcrc.cpl.viewer.feature.extraction.SmallMoleculePeakCombiner
public static final double DEFAULT_MAX_ABS_DISTANCE_BETWEEN_PEAKS 1.0
public static final float MAX_ANY_FIRST_PEAK_PROPORTION 0.800000011920929f

org.fhcrc.cpl.viewer.feature.extraction.SpectrumResampler
public static final int DEFAULT_RESAMPLE_FREQ 36

org.fhcrc.cpl.viewer.feature.extraction.WaveletPeakExtractor
public static final int DEFAULT_PEAK_LENGTH_REQUIREMENT 5
public static final float DEFAULT_THRESHOLD_OFFSET_SMOOTHED 0.0f
public static final float DEFAULT_THRESHOLD_OFFSET_WAVELET 1.0f

org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategyModular
protected static final int WINDOW_MARGIN 64

org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategy
public static final int DEFAULT_RESAMPLING_FREQUENCY 36

org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyWindow
public static final int DEFAULT_WINDOW_WIDTH 256

org.fhcrc.cpl.viewer.gui.ChooseCommandDialog
public static final int height 175
public static final int width 300

org.fhcrc.cpl.viewer.gui.ExtractFeatureRangesAction.ExtractFeatureRangesDialog
public static final int ACTION_CANCEL 0
public static final int ACTION_FIND 2
public static final int ACTION_LOAD 1

org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog
public static final int ACTION_CANCEL 0
public static final int ACTION_OK 1

org.fhcrc.cpl.viewer.gui.FeatureSelectionFrame.FeatureSelectionDialog.ColorEditor
protected static final java.lang.String EDIT "edit"

org.fhcrc.cpl.viewer.gui.MSImageComponent
public static final java.lang.String COLORSCHEME_PROPNAME "MSImageComponent.colorScheme"
public static final java.lang.String DEFAULT_COLORSCHEME "Fancy"
public static final float DEFAULT_FEATURE_MZ_TOLERANCE 3.0f
public static final int DEFAULT_FEATURE_SCAN_TOLERANCE 3

org.fhcrc.cpl.viewer.gui.MSImageComponent.MSImagePanel.FeatureSetImagePanelLayer
public static final int DISPLAY_STYLE_PLUS 1
public static final int DISPLAY_STYLE_X 0

org.fhcrc.cpl.viewer.gui.PropertiesPane
public static final int FEATURECHART_MIN_PEAKS 4
public static final float FEATURECHART_MZ_PADDING_DOWN 1.5f
public static final float FEATURECHART_MZ_PADDING_UP 0.5f
public static final int FEATURECHART_SCAN_PADDING 5

org.fhcrc.cpl.viewer.gui.ProteinMatcherFrame
public static final float DEFAULT_MIN_PEPTIDE_PROPHET_SCORE 0.949999988079071f

org.fhcrc.cpl.viewer.gui.WorkbenchFrame
public static final java.lang.String MSINSPECT_WEBSITE_URL "https://proteomics.fhcrc.org/CPL/msinspect.html"
public static final java.lang.String SUPPORT_URL "https://www.labkey.org/Project/msInspect/begin.view"

org.fhcrc.cpl.viewer.ms2.Fractionation2DUtilities
public static final int BY_COLUMN 1
public static final int BY_ROW 0

org.fhcrc.cpl.viewer.ms2.commandline.CalculateFDRCLM
public static final java.lang.String DEFAULT_REV_PROTEIN_PREFIX "rev_"
public static final java.lang.String DEFAULT_SEARCH_SCORE_NAME "expect"
public static final int MIN_FEATURES_FOR_FDR_CALC 50
protected static final int MODE_PPROPHET 0
protected static final int MODE_SEARCH_SCORE 1
protected static final int OUT_FORMAT_APML 2
protected static final int OUT_FORMAT_INPUT 3
protected static final int OUT_FORMAT_MSINSPECT 1
protected static final int OUT_FORMAT_PEPXML 0

org.fhcrc.cpl.viewer.ms2.commandline.ExtractRunsFromPepXmlCommandLineModule
protected static final int FILE_FORMAT_PEPXML 1
protected static final int FILE_FORMAT_TSV 0

org.fhcrc.cpl.viewer.ms2.commandline.FindSearchScoreCutoffForFARCLM
protected static final int MODE_PPROPHET 0
protected static final int MODE_SEARCH_SCORE 1

org.fhcrc.cpl.viewer.ms2.commandline.GuessProteinsFromFastaCLM
protected static final int OUT_FORMAT_MSINSPECT 0
protected static final int OUT_FORMAT_PEPXML 1

org.fhcrc.cpl.viewer.ms2.commandline.PeptideCompareCommandLineModule
public static final float INFINITE_RATIO 20.0f
protected static final int MODE_CALCULATE_RATIOS 8
protected static final int MODE_CREATE_FEATURES_FOR_UNION 1
protected static final int MODE_ID_CLUSTER 11
protected static final int MODE_PLOT_FVAL 6
protected static final int MODE_PLOT_INTENSITIES 3
protected static final int MODE_PLOT_KSCORE_OR_XCORR 7
protected static final int MODE_PLOT_LIGHT_AREAS 10
protected static final int MODE_PLOT_PAIRWISE_RATIOS 13
protected static final int MODE_PLOT_PEPTIDEPROPHET 5
protected static final int MODE_PLOT_RATIOS 9
protected static final int MODE_PLOT_SPECTRAL_COUNTS 12
protected static final int MODE_PLOT_TIMES 2
protected static final int MODE_PLOT_TOTAL_INTENSITIES 4
protected static final int MODE_SHOW_OVERLAP 0
public static final float ZERO_RATIO 0.05000000074505806f

org.fhcrc.cpl.viewer.ms2.commandline.PickTargetedMS2CandidatesCLM
public static final double PROTON_MASS 1.0072766

org.fhcrc.cpl.viewer.ms2.commandline.SpectralCountCLM
protected static final int MODE_GENE 1
protected static final int MODE_PEPTIDE 0
protected static final int MODE_PROTEIN_GROUP 2

org.fhcrc.cpl.viewer.ms2.gui.MS2ScanViewer
public static final int DEFAULT_RESAMPLING_RESOLUTION 50

org.fhcrc.cpl.viewer.quant.QuantEvent
public static final int CURATION_STATUS_BAD 2
public static final int CURATION_STATUS_GOOD 1
public static final int CURATION_STATUS_RATIO_ONEPEAK 3
public static final int CURATION_STATUS_UNKNOWN 0
public static final float MISSING_RATIO -1.0f

org.fhcrc.cpl.viewer.quant.QuantEventAssessor
public static final float ACRYLAMIDE_LABEL_HEAVYMASS 177.055908203125f
public static final float ACRYLAMIDE_LABEL_LIGHTMASS 174.04580688476562f
public static final float ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE 3.010101318359375f
public static final int DEFAULT_NUM_SCANS_AROUND_EVENT 0
public static final float DEFAULT_PEAK_PPM_TOLERANCE 50.0f
public static final float DEFAULT_PEAKBELOW_INTENSITY_RATIO_CUTOFF 0.4000000059604645f
public static final int FLAG_REASON_COELUTING 1
public static final int FLAG_REASON_DISSIMILAR_KL 2
public static final int FLAG_REASON_DISSIMILAR_MS1_RATIO 3
public static final int FLAG_REASON_OK 0
public static final int FLAG_REASON_UNEVALUATED 4
public static final java.lang.String REASON_DUMMY_SEARCH_SCORE_NAME "dummy_flag_desc"
public static final float SILAC_LABEL_MASS 134.11509704589844f
public static final float SILAC_LABEL_MASSDIFF_PERRESIDUE 6.020129203796387f

org.fhcrc.cpl.viewer.quant.commandline.FlagQuantEventsCLM
public static final java.lang.String REASON_DUMMY_SEARCH_SCORE_NAME "dummy_flag_desc"

org.fhcrc.cpl.viewer.quant.commandline.PeptideQuantVisualizationCLM
protected static final java.lang.String DUMMY_PROTEIN_NAME "DUMMY_PROTEIN"

org.fhcrc.cpl.viewer.quant.gui.PanelWithSpectrumChart
public static final int DEFAULT_CONTOUR_PLOT_HEIGHT 1000
public static final int DEFAULT_CONTOUR_PLOT_ROTATION 80
public static final boolean DEFAULT_CONTOUR_PLOT_SHOW_AXES true
public static final int DEFAULT_CONTOUR_PLOT_TILT 20
public static final int DEFAULT_CONTOUR_PLOT_WIDTH 1000
public static final float DEFAULT_PEAK_SEPARATION_MASS 1.0f
public static final float DEFAULT_PEAK_TOLERANCE_PPM 25.0f
public static final int DEFAULT_RESOLUTION 100
public static final int MAX_Q3_PEAKS 5

org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame
protected final int PROTEINTABLE_HISTPANEL_HEIGHT 150
protected final int PROTEINTABLE_SCATTERPLOTPANEL_HEIGHT 100
protected final int STATUSPANEL_HEIGHT 25
protected final int SUMMARYPANEL_HEIGHT 41
protected final int TABLEROW_HEIGHT 17
protected final int TITLEBAR_HEIGHT 55

org.fhcrc.cpl.viewer.quant.gui.ProteinQuantSummaryFrame.ChartBuilderWorker
protected static final java.lang.String expressionForLabel "Processed %%CURRENT_VALUE%% of %%MAX_VALUE%% events"

org.fhcrc.cpl.viewer.quant.gui.ProteinSummarySelectorFrame
protected final int STATUSPANEL_HEIGHT 25
protected final int SUMMARYPANEL_HEIGHT 81
protected final int TABLEROW_HEIGHT 17
protected final int TITLEBAR_HEIGHT 55

org.fhcrc.cpl.viewer.quant.gui.QuantitationVisualizer
public static final float AMINOACID_MODIFICATION_EQUALITY_MASS_TOLERANCE 0.25f
public static final int DEFAULT_IMAGE_HEIGHT_3D 900
public static final int DEFAULT_IMAGE_WIDTH_3D 900
public static final int DEFAULT_MAX_SINGLE_SCANS_TOTAL_IMAGE_HEIGHT 4000
public static final int DEFAULT_SINGLE_SCAN_IMAGE_HEIGHT 100
public static final int DEFAULT_SPECTRUM_IMAGE_HEIGHT 700
public static final int DEFAULT_SPECTRUM_IMAGE_WIDTH 900
protected static final java.lang.String DUMMY_PROTEIN_NAME "DUMMY_PROTEIN"

org.fhcrc.cpl.viewer.test.commandline.FilterFeaturesTest
protected static final java.lang.String sumMinCharge1MaxCharge1MaxKl2 "57f9ae1925ba11d9fd14ba72576bdef8"
protected static final java.lang.String sumMinIntensity15 "b0c7e567a0e499eff74b3a96de775cd4"
protected static final java.lang.String sumMinPeaks3 "4742db6aefc57223907022818a2d75e5"
protected static final java.lang.String sumMinTime1500MaxTime1550 "4430f8e8460f67d640fe3f2f55121f68"
protected static final java.lang.String sumMinTotalIntensity1000 "b0ccdbece4905be3ffa5bdb9be2b35a4"
protected static final java.lang.String sumScanFirst100ScanLast200 "824e427d2eeec3e2b2710f8403f9f616"

org.fhcrc.cpl.viewer.test.commandline.FindPeptidesTest
protected static final java.lang.String sumStart50Count50Accurate "b246515ec84ef03caedcd0b00e2894c8"
protected static final java.lang.String sumStart50Count50NoAccurate "dea54286edac89d5f8da54a20b7bde70"
protected static final java.lang.String sumStrategyCentroidedStart200Count50 "563e9afc2b024294946271ddc55561cb"
protected static final java.lang.String sumStrategyWaveletStart100Count5MinMz700MaxMz800 "e6b19c1790383f60644697501ac9626f"

org.fhcrc.cpl.viewer.test.commandline.PeptideArrayTest
protected static final java.lang.String sumMassPoint1Scan75Normalize "079ca865079c098b85e0f8db04bbcb8c"
protected static final java.lang.String sumMassPoint2Scan50 "479ed449eeabd7902ce05ad1bfb8a507"
protected static final java.lang.String sumMassPoint2Scan50Details "06328c23859683667e62d430360a0ad0"

org.fhcrc.cpl.viewer.util.SharedProperties
public static final java.lang.String AUTO_ZOOM "autoZoom"
public static final java.lang.String CHART_RANGE "chartRange"
public static final java.lang.String FEATURE_RANGES "featureRanges"
public static final java.lang.String FEATURE_SETS "featureSets"
public static final java.lang.String HIGHLIGHT_FEATURES "highlightFeatures"
public static final java.lang.String HIGHLIGHT_FEATURES2 "highlightFeatures2"
public static final java.lang.String HIGHLIGHT_FEATURES3 "highlightFeatures3"
public static final java.lang.String LOCK_Y_AXIS "lockYAxis"
public static final java.lang.String MS_RUN "MSRun"
public static final java.lang.String MS_SCAN "MSScan"
public static final java.lang.String SELECTED "selectedObject"
public static final java.lang.String SELECTED_POINT "selectedPoint"
public static final java.lang.String ZOOM_REGION "zoomRegion"

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