LocalDatabaseSearchParameters.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.modules.identification.ms.localdatabasesearch;

import java.util.Arrays;

import io.github.msdk.util.tolerances.MaximumMzTolerance;
import io.github.msdk.util.tolerances.RTTolerance;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.ParameterValidator;
import io.github.mzmine.parameters.parametertypes.StringParameter;
import io.github.mzmine.parameters.parametertypes.TextAreaParameter;
import io.github.mzmine.parameters.parametertypes.selectors.FeatureTablesParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.RTToleranceParameter;
import javafx.stage.FileChooser.ExtensionFilter;

public class LocalDatabaseSearchParameters extends ParameterSet {

  public static final FeatureTablesParameter featureTables = new FeatureTablesParameter();

  private static final ExtensionFilter filters[] =
      new ExtensionFilter[] {new ExtensionFilter("All supported files", "*.csv", "*.txt"),
          new ExtensionFilter("CSV files", "*.csv"), new ExtensionFilter("TXT files", "*.txt")};

  public static final TextAreaParameter annotations = new TextAreaParameter("Annotations",
      "Annotated features to use for identification. Any line not starting with a number will be ignored.\n"
          + "The following input formats are accepted:\n"
          + "id, m/z, retention time, compound name\n"
          + "id, m/z, retention time, compound name, formula\n"
          + "id, m/z, retention time, compound name, formula, adduct\n\n"
          + "Optional columns are supported but have to be present after the adduct column.",
      "Features", ParameterValidator.createNonEmptyValidator(), Arrays.asList(filters));

  public static final StringParameter separator = new StringParameter("Field separator",
      "Character(s) used to separate fields in the feature list", "Features",
      ParameterValidator.createNonEmptyValidator(), ",");

  public static final MZToleranceParameter mzTolerance = new MZToleranceParameter("m/z tolerance",
      "Maximum allowed difference between two m/z values to be considered same.\n"
          + "The value is specified both as absolute tolerance (in m/z) and relative tolerance (in ppm).\n"
          + "The tolerance range is calculated using maximum of the absolute and relative tolerances.",
      "Algorithm Parameters", ParameterValidator.createNonEmptyValidator(),
      new MaximumMzTolerance(0.001, 5.0));

  public static final RTToleranceParameter rtTolerance = new RTToleranceParameter("RT tolerance",
      "Maximum allowed retention time difference between the peak apex and the retention times in the above feature input list.",
      "Algorithm Parameters", ParameterValidator.createNonEmptyValidator(),
      new RTTolerance(10, true));

  /**
   * Create the parameter set.
   */
  public LocalDatabaseSearchParameters() {
    super(featureTables, annotations, separator, mzTolerance, rtTolerance);
  }

}