/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program 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 3 of the License, or *
* (at your option) any later version. *
* *
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package com.act.lcms.v2;
import com.act.lcms.MS1;
import java.util.Arrays;
import java.util.List;
import java.util.Set;
import java.util.function.Predicate;
import java.util.stream.Collectors;
public class LcmsIonCalculator implements IonCalculator {
List<Ion> getIonsFromMass(Double mass, Predicate<MS1.MetlinIonMass> ionFilter) {
List<Ion> ions = Arrays.asList(MS1.ionDeltas)
.stream()
.filter(ionFilter)
.map(ionDelta -> new LcmsIon(MS1.computeIonMz(mass, ionDelta), ionDelta))
.collect(Collectors.toList());
return ions;
}
public List<Ion> getIons(Isotope isotope) {
return getIonsFromMass(isotope.getIsotopicMass(), x -> true);
}
public List<Ion> getSelectedIons(Isotope isotope, Predicate<MS1.MetlinIonMass> ionFilter) {
return getIonsFromMass(isotope.getIsotopicMass(), ionFilter);
}
public List<Ion> getSelectedIons(Isotope isotope, Set<String> ionNames, MS1.IonMode mode) {
return getIonsFromMass(isotope.getIsotopicMass(), x -> ionNames.contains(x.getName()) && x.getMode() == mode);
}
public List<Ion> getIons(Metabolite metabolite) {
return getIonsFromMass(metabolite.getMonoIsotopicMass(), x -> true);
}
public List<Ion> getSelectedIons(Metabolite metabolite, Predicate<MS1.MetlinIonMass> ionFilter) {
return getIonsFromMass(metabolite.getMonoIsotopicMass(), ionFilter);
}
public List<Ion> getSelectedIons(Metabolite metabolite, Set<String> ionNames, MS1.IonMode mode) {
return getIonsFromMass(metabolite.getMonoIsotopicMass(), x -> ionNames.contains(x.getName()) && x.getMode() == mode);
}
}