--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Identification_Parameters_specific.par	Tue May 15 14:50:35 2018 -0400
@@ -0,0 +1,739 @@
+{
+  "marshallableParameterType": "identification_parameters",
+  "name": "SEARCHGUI_IdentificationParameters",
+  "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nPrecursor Tolerance: 100.0 ppm.\nCharge: 1-3.\nDB: dataset_118.dat.\n",
+  "defaultDescription": true,
+  "searchParameters": {
+    "precursorAccuracyType": "PPM",
+    "fragmentAccuracyType": "DA",
+    "precursorTolerance": 100.0,
+    "precursorToleranceDalton": 0.5,
+    "fragmentIonMZTolerance": 0.5,
+    "ptmSettings": {
+      "fixedModifications": [
+        "Carbamidomethylation of C"
+      ],
+      "variableModifications": [
+        "Oxidation of M"
+      ],
+      "refinementVariableModifications": [],
+      "refinementFixedModifications": [],
+      "colors": {},
+      "backUp": {
+        "Oxidation of M": {
+          "type": 0,
+          "name": "Oxidation of M",
+          "shortName": "ox",
+          "neutralLosses": [
+            {
+              "composition": {
+                "atomChain": [
+                  {
+                    "atomSymbol": "C",
+                    "isotope": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0
+                  },
+                  {
+                    "atomSymbol": "O",
+                    "isotope": 0
+                  },
+                  {
+                    "atomSymbol": "S",
+                    "isotope": 0
+                  }
+                ],
+                "mass1": -1.0
+              },
+              "name": "CH4OS",
+              "fixed": false
+            }
+          ],
+          "reporterIons": [],
+          "pattern": {
+            "length": 0,
+            "residueTargeted": {
+              "0": [
+                "M"
+              ]
+            }
+          },
+          "atomChainAdded": {
+            "atomChain": [
+              {
+                "atomSymbol": "O",
+                "isotope": 0
+              }
+            ],
+            "mass1": -1.0
+          },
+          "cvTerm": {
+            "ontology": "UNIMOD",
+            "accession": "UNIMOD:35",
+            "name": "Oxidation"
+          }
+        },
+        "Carbamidomethylation of C": {
+          "type": 0,
+          "name": "Carbamidomethylation of C",
+          "shortName": "cmm",
+          "neutralLosses": [],
+          "reporterIons": [],
+          "pattern": {
+            "length": 0,
+            "residueTargeted": {
+              "0": [
+                "C"
+              ]
+            }
+          },
+          "atomChainAdded": {
+            "atomChain": [
+              {
+                "atomSymbol": "C",
+                "isotope": 0
+              },
+              {
+                "atomSymbol": "C",
+                "isotope": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0
+              },
+              {
+                "atomSymbol": "N",
+                "isotope": 0
+              },
+              {
+                "atomSymbol": "O",
+                "isotope": 0
+              }
+            ],
+            "mass1": -1.0
+          },
+          "cvTerm": {
+            "ontology": "UNIMOD",
+            "accession": "UNIMOD:4",
+            "name": "Carbamidomethyl"
+          }
+        }
+      }
+    },
+    "nMissedCleavages": 2,
+    "digestionPreferences": {
+      "cleavagePreference": "enzyme",
+      "enzymes": [
+        {
+          "id": 0,
+          "name": "Trypsin",
+          "aminoAcidBefore": [],
+          "aminoAcidAfter": [],
+          "restrictionBefore": [],
+          "restrictionAfter": [],
+          "aminoAcidBeforeSet": [
+            "R",
+            "K"
+          ],
+          "aminoAcidAfterSet": [],
+          "restrictionBeforeSet": [],
+          "restrictionAfterSet": [
+            "P"
+          ],
+          "isSemiSpecific": false,
+          "isWholeProtein": false,
+          "cvTerm": {
+            "ontology": "PSI-MS",
+            "accession": "MS:1001251",
+            "name": "Trypsin"
+          }
+        }
+      ],
+      "nMissedCleavages": {
+        "Trypsin": 2
+      },
+      "specificity": {
+        "Trypsin": "specific"
+      }
+    },
+    "fastaFile": {
+      "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
+    },
+    "parametersFile": {},
+    "forwardIons": [
+      1
+    ],
+    "rewindIons": [
+      4
+    ],
+    "minChargeSearched": {
+      "sign": 1,
+      "value": 1
+    },
+    "maxChargeSearched": {
+      "sign": 1,
+      "value": 3
+    },
+    "minIsotopicCorrection": 0,
+    "maxIsotopicCorrection": 1,
+    "refMass": 2000.0,
+    "algorithmParameters": {
+      "1": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters",
+        "data": {
+          "maxEValue": 100.0,
+          "hitListLength": 10,
+          "minimalChargeForMultipleChargedFragments": {
+            "sign": 1,
+            "value": 3
+          },
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "removePrecursor": false,
+          "scalePrecursor": true,
+          "estimateCharge": true,
+          "selectedOutput": "OMX",
+          "memoryMappedSequenceLibraries": false,
+          "numberOfItotopicPeaks": 0,
+          "neutronThreshold": 1446.94,
+          "lowIntensityCutOff": 0.0,
+          "highIntensityCutOff": 0.2,
+          "intensityCutOffIncrement": 5.0E-4,
+          "singleChargeWindow": 27,
+          "doubleChargeWindow": 14,
+          "nPeaksInSingleChargeWindow": 2,
+          "nPeaksInDoubleChargeWindow": 2,
+          "maxHitsPerSpectrumPerCharge": 30,
+          "nAnnotatedMostIntensePeaks": 6,
+          "minAnnotatedPeaks": 2,
+          "minPeaks": 4,
+          "cleaveNtermMethionine": true,
+          "maxMzLadders": 128,
+          "maxFragmentCharge": 2,
+          "fractionOfPeaksForChargeEstimation": 0.95,
+          "determineChargePlusOneAlgorithmically": true,
+          "searchPositiveIons": true,
+          "minPrecPerSpectrum": 1,
+          "searchForwardFragmentFirst": false,
+          "searchRewindFragments": true,
+          "maxFragmentPerSeries": 100,
+          "useCorrelationCorrectionScore": true,
+          "consecutiveIonProbability": 0.5,
+          "iterativeSequenceEvalue": 0.0,
+          "iterativeReplaceEvalue": 0.0,
+          "iterativeSpectrumEvalue": 0.01,
+          "noProlineRuleSeries": [],
+          "ptmIndexes": {}
+        }
+      },
+      "2": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters",
+        "data": {
+          "maxEValue": 0.01,
+          "outputResults": "0",
+          "dynamicRange": 100.0,
+          "nPeaks": 50,
+          "minPrecursorMass": 200.0,
+          "minFragmentMz": 200.0,
+          "minPeaksPerSpectrum": 15,
+          "proteinQuickAcetyl": true,
+          "quickPyrolidone": true,
+          "refine": true,
+          "refineSemi": false,
+          "refinePointMutations": false,
+          "refineSpectrumSynthesis": true,
+          "refineUnanticipatedCleavages": true,
+          "refineSnaps": true,
+          "maximumExpectationValueRefinement": 0.01,
+          "potentialModificationsForFullRefinment": false,
+          "skylinePath": "",
+          "outputProteins": true,
+          "outputSequences": false,
+          "outputSpectra": true,
+          "outputHistograms": false,
+          "stpBias": false,
+          "useNoiseSuppression": true,
+          "proteinPtmComplexity": 6.0
+        }
+      },
+      "3": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters",
+        "data": {
+          "hitListLength": 10,
+          "estimateCharge": true,
+          "correctPrecursorMass": false,
+          "discardLowQualitySpectra": true,
+          "fragmentationModel": "CID_IT_TRYP",
+          "generateQuery": false
+        }
+      },
+      "4": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters",
+        "data": {
+          "maxPeptideMass": 4600.0,
+          "maxCombinations": 250,
+          "topPeaks": 8,
+          "topPeaksWindow": 100,
+          "includeWater": true,
+          "includeAmmonia": true,
+          "dependentLosses": true,
+          "fragmentAll": false,
+          "empiricalCorrection": true,
+          "higherCharge": true,
+          "fragmentationMethod": "CID",
+          "maxNumberOfModifications": 5,
+          "minPeptideLengthNoEnzyme": 8,
+          "maxPeptideLengthNoEnzyme": 25,
+          "equalIL": false,
+          "numberOfCandidates": 10,
+          "ptmIndexes": {},
+          "decoyMode": "none"
+        }
+      },
+      "5": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters",
+        "data": {
+          "generateDecoy": false,
+          "instrumentID": "b, y",
+          "maxRank": 10,
+          "monoisotopic": true,
+          "lowMemoryMode": true
+        }
+      },
+      "7": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters",
+        "data": {
+          "searchDecoyDatabase": false,
+          "instrumentID": 3,
+          "fragmentationType": 3,
+          "protocol": 0,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMarches": 10,
+          "additionalOutput": false,
+          "lowerIsotopeErrorRange": -1,
+          "upperIsotopeErrorRange": 2,
+          "numberTolerableTermini": 2,
+          "numberOfPtmsPerPeptide": 2
+        }
+      },
+      "8": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters",
+        "data": {
+          "ticCutoffPercentage": 100.0,
+          "maxPeakCount": 100,
+          "numIntensityClasses": 3,
+          "adjustPrecursorMass": false,
+          "minPrecursorAdjustment": -0.5,
+          "maxPrecursorAdjustment": 1.5,
+          "precursorAdjustmentStep": 0.1,
+          "numChargeStates": 3,
+          "outputSuffix": "",
+          "useChargeStateFromMS": true,
+          "duplicateSpectra": true,
+          "deisotopingMode": 0,
+          "isotopeMzTolerance": 0.25,
+          "complementMzTolerance": 0.1,
+          "tagLength": 4,
+          "maxDynamicMods": 2,
+          "maxTagCount": 10,
+          "intensityScoreWeight": 1.0,
+          "mzFidelityScoreWeight": 1.0,
+          "complementScoreWeight": 1.0,
+          "variablePtms": []
+        }
+      },
+      "10": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters",
+        "data": {
+          "numberOfSpectrumMatches": 10,
+          "maxVariableMods": 10,
+          "requireVariableMods": false,
+          "minPeaks": 10,
+          "minPeakIntensity": 0.0,
+          "removePrecursor": 0,
+          "removePrecursorTolerance": 1.5,
+          "lowerClearMzRange": 0.0,
+          "upperClearMzRange": 0.0,
+          "enzymeType": 2,
+          "isotopeCorrection": 1,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "maxFragmentCharge": 3,
+          "removeMethionine": false,
+          "batchSize": 0,
+          "theoreticalFragmentIonsSumOnly": false,
+          "fragmentBinOffset": 0.0,
+          "useSparseMatrix": true,
+          "selectedOutputFormat": "PepXML",
+          "printExpectScore": true
+        }
+      },
+      "27": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters",
+        "data": {
+          "numberOfPeptides": 10,
+          "lowerPrecursorMass": 300,
+          "upperPrecursorMass": 5000,
+          "acticationType": "HCD"
+        }
+      },
+      "28": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters",
+        "data": {
+          "fastIndexFolderName": "fasta-index",
+          "maxVariablePtmsPerTypePerPeptide": 2,
+          "minPeptideLength": 6,
+          "maxPeptideLength": 30,
+          "minPrecursorMass": 200.0,
+          "maxPrecursorMass": 7200.0,
+          "decoyFormat": "none",
+          "keepTerminalAminoAcids": "NC",
+          "decoySeed": 1,
+          "outputFolderName": "crux-output",
+          "printPeptides": false,
+          "verbosity": 30,
+          "monoisotopicPrecursor": true,
+          "clipNtermMethionine": false,
+          "digestionType": "full-digest",
+          "computeSpScore": false,
+          "numberOfSpectrumMatches": 10,
+          "computeExactPValues": false,
+          "minSpectrumMz": 0.0,
+          "minSpectrumPeaks": 20,
+          "spectrumCharges": "all",
+          "removePrecursor": false,
+          "removePrecursorTolerance": 1.5,
+          "printProgressIndicatorSize": 1000,
+          "useFlankingPeaks": false,
+          "useNeutralLossPeaks": false,
+          "mzBinWidth": 0.02,
+          "mzBinOffset": 0.0,
+          "concatenateTargetDecoy": false,
+          "textOutput": true,
+          "sqtOutput": false,
+          "pepXmlOutput": false,
+          "mzidOutput": false,
+          "pinOutput": false,
+          "removeTempFolders": true
+        }
+      },
+      "13": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMatches": 10,
+          "ticCutoffPercentage": 0.98,
+          "maxDynamicMods": 2,
+          "minTerminiCleavages": 2,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "useSmartPlusThreeModel": true,
+          "computeXCorr": false,
+          "numIntensityClasses": 3,
+          "classSizeMultiplier": 2,
+          "numberOfBatches": 50,
+          "lowerIsotopeCorrection": -1,
+          "upperIsotopeCorrection": 2,
+          "fragmentationRule": "CID",
+          "maxPeakCount": 300,
+          "outputFormat": "mzIdentML"
+        }
+      },
+      "29": {
+        "type": "com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters",
+        "data": {
+          "fragmentationMethod": "HCD",
+          "massAnalyzer": "FT"
+        }
+      }
+    }
+  },
+  "annotationSettings": {
+    "yAxisZoomExcludesBackgroundPeaks": true,
+    "showAllPeaks": false,
+    "intensityThresholdType": "percentile",
+    "intensityLimit": 0.75,
+    "automaticAnnotation": true,
+    "selectedIonsMap": {
+      "TAG_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "REPORTER_ION": [],
+      "RELATED_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18
+      ],
+      "PEPTIDE_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "PRECURSOR_ION": [
+        0
+      ],
+      "IMMONIUM_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
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+        14,
+        15,
+        16,
+        17,
+        18,
+        19,
+        20
+      ]
+    },
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+              "isotope": 0
+            },
+            {
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+            },
+            {
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+              "isotope": 0
+            }
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+          "stringValue1": "H(2)O"
+        },
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+        "aminoAcids": [
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+          "E",
+          "S",
+          "T"
+        ]
+      },
+      {
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+              "isotope": 0
+            },
+            {
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+            },
+            {
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+            },
+            {
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+            }
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+          "stringValue1": "H(3)N"
+        },
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+        "fixed": false,
+        "aminoAcids": [
+          "K",
+          "N",
+          "Q",
+          "R"
+        ]
+      },
+      {
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+            },
+            {
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+            },
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+            },
+            {
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+            }
+          ],
+          "mass1": -1.0
+        },
+        "name": "CH4OS",
+        "fixed": false
+      }
+    ],
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+    "reporterIons": true,
+    "relatedIons": true,
+    "fragmentIonAccuracy": 0.5,
+    "fragmentIonPpm": false,
+    "showForwardIonDeNovoTags": false,
+    "showRewindIonDeNovoTags": false,
+    "deNovoCharge": 1,
+    "highResolutionAnnotation": true,
+    "tiesResolution": "mostAccurateMz"
+  },
+  "sequenceMatchingPreferences": {
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+    "limitX": 0.25,
+    "peptideMapperType": "fm_index"
+  },
+  "peptideVariantsPreferences": {
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+    "nVariants": 0,
+    "nAaDeletions": 0,
+    "nAaInsertions": 0,
+    "nAaSubstitutions": 0,
+    "nAaSwap": 0,
+    "aaSubstitutionMatrix": {
+      "name": "No Substitution",
+      "description": "No substitution",
+      "substitutions": {},
+      "reverseMap": {}
+    }
+  },
+  "genePreferences": {
+    "autoUpdate": false,
+    "useGeneMapping": false
+  },
+  "psmScoringPreferences": {
+    "spectrumMatchingScores": {
+      "8": [
+        1
+      ],
+      "3": [
+        1
+      ],
+      "27": [
+        1
+      ]
+    },
+    "defaultScores": [
+      -1
+    ],
+    "minDecoysInBin": 10
+  },
+  "peptideAssumptionFilter": {
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+    "maxPepLength": 30,
+    "maxMassDeviation": 10.0,
+    "isPpm": true,
+    "unknownPtm": true,
+    "minIsotopes": 0,
+    "maxIsotopes": 1
+  },
+  "ptmScoringPreferences": {
+    "flr": 1.0,
+    "probabilitsticScoreCalculation": true,
+    "selectedProbabilisticScore": "PhosphoRS",
+    "estimateFlr": false,
+    "probabilisticScoreThreshold": 95.0,
+    "probabilisticScoreNeutralLosses": false,
+    "sequenceMatchingPreferences": {
+      "sequenceMatchingType": "aminoAcid",
+      "limitX": 0.25,
+      "peptideMapperType": "fm_index"
+    },
+    "alignNonConfidentPTMs": true
+  },
+  "proteinInferencePreferences": {
+    "proteinSequenceDatabase": {
+      "path": "./searchgui_tinydb1_concatenated_target_decoy.fasta"
+    },
+    "simplifyProteinGroups": true,
+    "simplifyGroupsScore": true,
+    "simplifyGroupsEvidence": true,
+    "simplifyGroupsEnzymaticity": true,
+    "simplifyGroupsUncharacterized": true
+  },
+  "idValidationPreferences": {
+    "defaultProteinFDR": 1.0,
+    "defaultPeptideFDR": 1.0,
+    "defaultPsmFDR": 1.0,
+    "separatePeptides": true,
+    "separatePsms": true,
+    "mergeSmallSubgroups": true,
+    "validationQCPreferences": {
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+      "firstDecoy": true,
+      "confidenceMargin": 1.0
+    }
+  },
+  "fractionSettings": {
+    "proteinConfidenceMwPlots": 95.0,
+    "fractionMolecularWeightRanges": {}
+  }
+}