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minor refactoring
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@dpolasky
dpolasky committed May 27, 2024
1 parent 5a3b4ef commit f4ae208
Showing 1 changed file with 17 additions and 15 deletions.
32 changes: 17 additions & 15 deletions src/edu/umich/andykong/ptmshepherd/PTMShepherd.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,8 @@
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
Expand Down Expand Up @@ -1148,13 +1150,13 @@ private static GlycoParams parseGlycoParams() {

// parse glyco parameters and initialize database and ratio tables
glycoParams.initIsotopeProbs(getParam("prob_isotope"));
glycoParams.massProbScaling = getParam("prob_mass").equals("") ? GlycoAnalysis.DEFAULT_MASS_PROB_SCALING : Double.parseDouble(getParam("prob_mass"));
glycoParams.massProbScaling = getParam("prob_mass").isEmpty() ? GlycoAnalysis.DEFAULT_MASS_PROB_SCALING : Double.parseDouble(getParam("prob_mass"));
glycoParams.randomGenerator = new Random(glycoRandomSeed);
String decoyParam = getParam("decoy_type");
glycoParams.decoyType = decoyParam.length() > 0 ? Integer.parseInt(decoyParam): GlycoAnalysis.DEFAULT_GLYCO_DECOY_TYPE;
glycoParams.glycoPPMtol = getParam("glyco_ppm_tol").equals("") ? GlycoAnalysis.DEFAULT_GLYCO_PPM_TOL : Double.parseDouble(getParam("glyco_ppm_tol"));
glycoParams.decoyType = !decoyParam.isEmpty() ? Integer.parseInt(decoyParam): GlycoAnalysis.DEFAULT_GLYCO_DECOY_TYPE;
glycoParams.glycoPPMtol = getParam("glyco_ppm_tol").isEmpty() ? GlycoAnalysis.DEFAULT_GLYCO_PPM_TOL : Double.parseDouble(getParam("glyco_ppm_tol"));
glycoParams.glycoIsotopes = GlycoParams.parseGlycoIsotopesParam();
glycoParams.nGlycan = getParam("n_glyco").equals("") || Boolean.parseBoolean(getParam("n_glyco")); // default true
glycoParams.nGlycan = getParam("n_glyco").isEmpty() || Boolean.parseBoolean(getParam("n_glyco")); // default true
String glycanDB = getParam("glycodatabase");
Path testPath = Paths.get(glycanDB.replaceAll("['\"]", ""));
if (glycanDB.isEmpty()) {
Expand All @@ -1180,20 +1182,20 @@ private static GlycoParams parseGlycoParams() {
// default method - glycans passed as string parameter
glycoParams.glycoDatabase = glycoParams.parseGlycanDatabaseString(glycanDB);
}
glycoParams.glycoYnorm = getParam("norm_Ys").equals("") || Boolean.parseBoolean(getParam("norm_Ys")); // default to True if not specified
glycoParams.absScoreErrorParam = getParam("glyco_abs_score_base").equals("") ? GlycoAnalysis.DEFAULT_GLYCO_ABS_SCORE_BASE : Double.parseDouble(getParam("glyco_abs_score_base"));
glycoParams.glycoYnorm = getParam("norm_Ys").isEmpty() || Boolean.parseBoolean(getParam("norm_Ys")); // default to True if not specified
glycoParams.absScoreErrorParam = getParam("glyco_abs_score_base").isEmpty() ? GlycoAnalysis.DEFAULT_GLYCO_ABS_SCORE_BASE : Double.parseDouble(getParam("glyco_abs_score_base"));
String glycoFDRParam = getParam("glyco_fdr");
glycoParams.glycoFDR = glycoFDRParam.equals("") ? GlycoAnalysis.DEFAULT_GLYCO_FDR : Double.parseDouble(glycoFDRParam); // default 0.01 if param not provided, otherwise read provided value
glycoParams.printFullParams = !getParam("print_full_glyco_params").equals("") && Boolean.parseBoolean(getParam("print_full_glyco_params")); // default false - for diagnostics
glycoParams.writeGlycansToAssignedMods = getParam("put_glycans_to_assigned_mods").equals("") || Boolean.parseBoolean(getParam("put_glycans_to_assigned_mods")); // default true
glycoParams.removeGlycanDeltaMass = getParam("remove_glycan_delta_mass").equals("") || Boolean.parseBoolean(getParam("remove_glycan_delta_mass")); // default true
glycoParams.printGlycoDecoys = !getParam("print_decoys").equals("") && Boolean.parseBoolean(getParam("print_decoys")); // default false
glycoParams.glycoFDR = glycoFDRParam.isEmpty() ? GlycoAnalysis.DEFAULT_GLYCO_FDR : Double.parseDouble(glycoFDRParam); // default 0.01 if param not provided, otherwise read provided value
glycoParams.printFullParams = !getParam("print_full_glyco_params").isEmpty() && Boolean.parseBoolean(getParam("print_full_glyco_params")); // default false - for diagnostics
glycoParams.writeGlycansToAssignedMods = getParam("put_glycans_to_assigned_mods").isEmpty() || Boolean.parseBoolean(getParam("put_glycans_to_assigned_mods")); // default true
glycoParams.removeGlycanDeltaMass = getParam("remove_glycan_delta_mass").isEmpty() || Boolean.parseBoolean(getParam("remove_glycan_delta_mass")); // default true
glycoParams.printGlycoDecoys = !getParam("print_decoys").isEmpty() && Boolean.parseBoolean(getParam("print_decoys")); // default false
glycoParams.allowedLocalizationResidues = getParam("localization_allowed_res");
glycoParams.numThreads = Integer.parseInt(params.get("threads"));
glycoParams.useGlycanFragmentProbs = !getParam("use_glycan_fragment_probs").equals("") && Boolean.parseBoolean(getParam("use_glycan_fragment_probs")); // default false
glycoParams.useNewFDR = getParam("use_new_glycan_fdr").equals("") || Boolean.parseBoolean(getParam("use_new_glycan_fdr")); // default true
glycoParams.useNonCompFDR = !getParam("use_noncomp_glycan_fdr").equals("") && Boolean.parseBoolean(getParam("use_noncomp_glycan_fdr")); // default false
glycoParams.defaultProp = getParam("glyco_default_propensity").equals("") ? GlycoAnalysis.DEFAULT_GLYCO_PROPENSITY : Double.parseDouble(getParam("glyco_default_propensity"));
glycoParams.useGlycanFragmentProbs = !getParam("use_glycan_fragment_probs").isEmpty() && Boolean.parseBoolean(getParam("use_glycan_fragment_probs")); // default false
glycoParams.useNewFDR = getParam("use_new_glycan_fdr").isEmpty() || Boolean.parseBoolean(getParam("use_new_glycan_fdr")); // default true
glycoParams.useNonCompFDR = !getParam("use_noncomp_glycan_fdr").isEmpty() && Boolean.parseBoolean(getParam("use_noncomp_glycan_fdr")); // default false
glycoParams.defaultProp = getParam("glyco_default_propensity").isEmpty() ? GlycoAnalysis.DEFAULT_GLYCO_PROPENSITY : Double.parseDouble(getParam("glyco_default_propensity"));


return glycoParams;
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