ScanSelectionEditor.java

/*
 * Copyright 2006-2015 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.parameters.parametertypes.selectors;

import java.text.NumberFormat;
import java.util.Arrays;
import java.util.List;

import javax.annotation.Nullable;

import org.controlsfx.control.PropertySheet;

import com.google.common.base.Strings;
import com.google.common.collect.Range;

import io.github.msdk.datamodel.msspectra.MsSpectrumType;
import io.github.msdk.datamodel.rawdata.PolarityType;
import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.parameters.Parameter;
import io.github.mzmine.parameters.ParameterEditor;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.ComboParameter;
import io.github.mzmine.parameters.parametertypes.IntegerParameter;
import io.github.mzmine.parameters.parametertypes.StringParameter;
import io.github.mzmine.parameters.parametertypes.ranges.DoubleRangeParameter;
import io.github.mzmine.parameters.parametertypes.ranges.IntegerRangeParameter;
import javafx.geometry.Pos;
import javafx.scene.Node;
import javafx.scene.control.Button;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Control;
import javafx.scene.layout.HBox;
import javafx.scene.text.Text;

public class ScanSelectionEditor extends HBox implements ParameterEditor<ScanSelection> {

  private final Button setButton, clearButton;
  private final Text restrictionsList;

  private Range<Integer> scanNumberRange;
  private Range<Double> scanRTRange;
  private Integer msLevel;
  private PolarityType polarity;
  private MsSpectrumType spectrumType;
  private String scanDefinition;

  public ScanSelectionEditor(PropertySheet.Item parameter) {

    // HBox properties
    setSpacing(10);
    setAlignment(Pos.CENTER_LEFT);

    restrictionsList = new Text();
    updateRestrictionList();

    setButton = new Button("Set filters");
    setButton.setOnAction(e -> {

      final IntegerRangeParameter scanNumParameter = new IntegerRangeParameter("Scan number",
          "Range of included scan numbers", "Category", scanNumberRange);
      final DoubleRangeParameter rtParameter =
          new DoubleRangeParameter("Retention time", "Retention time range", "Category");
      if (scanRTRange != null)
        rtParameter.setValue(scanRTRange);
      final IntegerParameter msLevelParameter =
          new IntegerParameter("MS level", "MS level", "Category", msLevel);
      final StringParameter scanDefinitionParameter = new StringParameter("Scan definition",
          "Include only scans that match this scan definition. You can use wild cards, e.g. *FTMS*",
          "Category", scanDefinition);
      final List<String> polarityTypes = Arrays.asList(new String[] {"Any", "+", "-"});
      final ComboParameter<String> polarityParameter = new ComboParameter<>("Polarity",
          "Include only scans of this polarity", "Category", polarityTypes);
      if ((polarity == PolarityType.POSITIVE) || (polarity == PolarityType.NEGATIVE))
        polarityParameter.setValue(polarity.toString());
      final List<String> spectraTypes =
          Arrays.asList(new String[] {"Any", "Centroided", "Profile", "Thresholded"});
      final ComboParameter<String> spectrumTypeParameter = new ComboParameter<>("Spectrum type",
          "Include only spectra of this type", "Category", spectraTypes);
      if (spectrumType != null) {
        switch (spectrumType) {
          case CENTROIDED:
            spectrumTypeParameter.setValue(spectraTypes.get(1));
            break;
          case PROFILE:
            spectrumTypeParameter.setValue(spectraTypes.get(2));
            break;
          case THRESHOLDED:
            spectrumTypeParameter.setValue(spectraTypes.get(3));
            break;
        }
      }

      ParameterSet paramSet = new ParameterSet(new Parameter[] {scanNumParameter, rtParameter,
          msLevelParameter, scanDefinitionParameter, polarityParameter, spectrumTypeParameter});
      ButtonType exitCode = paramSet.showSetupDialog(null);
      if (exitCode == ButtonType.OK) {
        scanNumberRange = paramSet.getParameter(scanNumParameter).getValue();
        scanRTRange = paramSet.getParameter(rtParameter).getValue();
        msLevel = paramSet.getParameter(msLevelParameter).getValue();
        scanDefinition = paramSet.getParameter(scanDefinitionParameter).getValue();
        final int selectedPolarityIndex = Arrays.asList(polarityTypes)
            .indexOf(paramSet.getParameter(polarityParameter).getValue());
        switch (selectedPolarityIndex) {
          case 1:
            polarity = PolarityType.POSITIVE;
            break;
          case 2:
            polarity = PolarityType.NEGATIVE;
            break;
          default:
            polarity = null;
            break;
        }
        final int selectedSpectraTypeIndex = Arrays.asList(spectraTypes)
            .indexOf(paramSet.getParameter(spectrumTypeParameter).getValue());
        switch (selectedSpectraTypeIndex) {
          case 1:
            spectrumType = MsSpectrumType.CENTROIDED;
            break;
          case 2:
            spectrumType = MsSpectrumType.PROFILE;
            break;
          case 3:
            spectrumType = MsSpectrumType.THRESHOLDED;
            break;
          default:
            spectrumType = null;
            break;
        }

      }
      updateRestrictionList();

    });

    clearButton = new Button("Clear filters");
    clearButton.setOnAction(e -> {
      scanNumberRange = null;
      scanRTRange = null;
      polarity = null;
      spectrumType = null;
      msLevel = null;
      scanDefinition = null;
      updateRestrictionList();

    });

    getChildren().addAll(restrictionsList, setButton, clearButton);

  }

  @Override
  public void setValue(ScanSelection newValue) {
    if (newValue == null)
      return;
    scanNumberRange = newValue.getScanNumberRange();
    scanRTRange = newValue.getScanRTRange();
    polarity = newValue.getPolarity();
    spectrumType = newValue.getSpectrumType();
    msLevel = newValue.getMsLevel();
    scanDefinition = newValue.getScanDefinition();

    updateRestrictionList();
  }

  @Override
  public ScanSelection getValue() {
    return new ScanSelection(scanNumberRange, scanRTRange, polarity, spectrumType, msLevel,
        scanDefinition);
  }

  private void updateRestrictionList() {

    if ((scanNumberRange == null) && (scanRTRange == null) && (polarity == null)
        && (spectrumType == null) && (msLevel == null) && Strings.isNullOrEmpty(scanDefinition)) {
      restrictionsList.setText("All");
      return;
    }

    StringBuilder newText = new StringBuilder();
    boolean textAdded = false;
    if (scanNumberRange != null) {
      textAdded = true;
      newText.append("Scan number: " + scanNumberRange.lowerEndpoint() + " - "
          + scanNumberRange.upperEndpoint());
    }
    if (scanRTRange != null) {
      if (textAdded)
        newText.append("\n");
      textAdded = true;
      NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
      newText.append("Retention time: " + rtFormat.format(scanRTRange.lowerEndpoint()) + " - "
          + rtFormat.format(scanRTRange.upperEndpoint()) + " min.");
    }
    if (msLevel != null) {
      if (textAdded)
        newText.append("\n");
      textAdded = true;
      newText.append("MS level: " + msLevel);
    }
    if (!Strings.isNullOrEmpty(scanDefinition)) {
      if (textAdded)
        newText.append("\n");
      textAdded = true;
      newText.append("Scan definition: " + scanDefinition);
    }
    if (polarity != null) {
      if (textAdded)
        newText.append("\n");
      textAdded = true;
      newText.append("Polarity: " + polarity.toString());
    }
    if (spectrumType != null) {
      if (textAdded)
        newText.append("\n");
      textAdded = true;
      newText.append("Spectrum type: " + spectrumType.toString().toLowerCase());
    }
    restrictionsList.setText(newText.toString());
  }

  @Override
  public Node getEditor() {
    return this;
  }

  @Override
  @Nullable
  public Control getMainControl() {
    return null;
  }
}