HmdbParserEventHandler.java
/*
* Copyright 2021 Dominik Kopczynski, Nils Hoffmann.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.lifstools.jgoslin.parser;
import org.lifstools.jgoslin.domain.Adduct;
import org.lifstools.jgoslin.domain.Cycle;
import org.lifstools.jgoslin.domain.Dictionary;
import org.lifstools.jgoslin.domain.DoubleBonds;
import org.lifstools.jgoslin.domain.Element;
import org.lifstools.jgoslin.domain.FattyAcid;
import org.lifstools.jgoslin.domain.FunctionalGroup;
import org.lifstools.jgoslin.domain.Headgroup;
import org.lifstools.jgoslin.domain.KnownFunctionalGroups;
import org.lifstools.jgoslin.domain.LipidAdduct;
import org.lifstools.jgoslin.domain.LipidException;
import org.lifstools.jgoslin.domain.LipidFaBondType;
import org.lifstools.jgoslin.domain.LipidLevel;
import org.lifstools.jgoslin.domain.LipidParsingException;
import org.lifstools.jgoslin.domain.UnsupportedLipidException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import static java.util.Map.entry;
/**
* Event handler implementation for the {@link HmdbParser}.
*
* @author Dominik Kopczynski
* @author Nils Hoffmann
*/
public class HmdbParserEventHandler extends LipidBaseParserEventHandler {
private int dbPositions;
private String dbCistrans;
private Dictionary furan = null;
/**
* Create a new {@code HmdbParserEventHandler}.
*
* @param knownFunctionalGroups the known functional groups
*/
public HmdbParserEventHandler(KnownFunctionalGroups knownFunctionalGroups) {
super(knownFunctionalGroups);
try {
registeredEvents = Map.ofEntries(
entry("lipid_pre_event", this::resetParser),
entry("lipid_post_event", this::buildLipid),
// set adduct events
entry("adduct_info_pre_event", this::newAdduct),
entry("adduct_pre_event", this::addAdduct),
entry("charge_pre_event", this::addCharge),
entry("charge_sign_pre_event", this::addChargeSign),
entry("fa_hg_pre_event", this::setHeadGroupName),
entry("gl_hg_pre_event", this::setHeadGroupName),
entry("gl_molecular_hg_pre_event", this::setHeadGroupName),
entry("mediator_pre_event", this::mediatorEvent),
entry("gl_mono_hg_pre_event", this::setHeadGroupName),
entry("pl_hg_pre_event", this::setHeadGroupName),
entry("pl_three_hg_pre_event", this::setHeadGroupName),
entry("pl_four_hg_pre_event", this::setHeadGroupName),
entry("sl_hg_pre_event", this::setHeadGroupName),
entry("st_species_hg_pre_event", this::setHeadGroupName),
entry("st_sub1_hg_pre_event", this::setHeadGroupName),
entry("st_sub2_hg_pre_event", this::setHeadGroupName),
entry("ganglioside_names_pre_event", this::setHeadGroupName),
entry("fa_species_pre_event", this::setSpeciesLevel),
entry("gl_molecular_pre_event", this::setMolecularLevel),
entry("unsorted_fa_separator_pre_event", this::setMolecularLevel),
entry("fa2_unsorted_pre_event", this::setMolecularLevel),
entry("fa3_unsorted_pre_event", this::setMolecularLevel),
entry("fa4_unsorted_pre_event", this::setMolecularLevel),
entry("db_single_position_pre_event", this::setIsomericLevel),
entry("db_single_position_post_event", this::addDbPosition),
entry("db_position_number_pre_event", this::addDbPositionNumber),
entry("cistrans_pre_event", this::addCistrans),
entry("lcb_pre_event", this::newLcb),
entry("lcb_post_event", this::cleanLcb),
entry("fa_pre_event", this::newFa),
entry("fa_post_event", this::appendFa),
entry("ether_pre_event", this::addEther),
entry("hydroxyl_pre_event", this::addHydroxyl),
entry("db_count_pre_event", this::addDoubleBonds),
entry("carbon_pre_event", this::addCarbon),
entry("fa_lcb_suffix_type_pre_event", this::addOneHydroxyl),
entry("interlink_fa_pre_event", this::interlinkFa),
entry("lipid_suffix_pre_event", this::lipidSuffix),
entry("methyl_pre_event", this::addMethyl),
entry("furan_fa_pre_event", this::furanFa),
entry("furan_fa_post_event", this::furanFaPost),
entry("furan_fa_mono_pre_event", this::furanFaMono),
entry("furan_fa_di_pre_event", this::furanFaDi),
entry("furan_first_number_pre_event", this::furanFaFirstNumber),
entry("furan_second_number_pre_event", this::furanFaSecondNumber)
);
} catch (Exception e) {
throw new LipidParsingException("Cannot initialize LipidMapsParserEventHandler.");
}
}
@Override
protected void resetParser(TreeNode node) {
content = null;
level = LipidLevel.FULL_STRUCTURE;
headGroup = "";
lcb = null;
adduct = null;
faList.clear();
currentFa = null;
useHeadGroup = false;
dbPositions = 0;
dbCistrans = "";
furan = new Dictionary();
headgroupDecorators.clear();
}
private void setIsomericLevel(TreeNode node) {
dbPositions = 0;
dbCistrans = "";
}
private void addDbPosition(TreeNode node) {
if (currentFa != null) {
currentFa.getDoubleBonds().getDoubleBondPositions().put(dbPositions, dbCistrans);
if (!dbCistrans.equals("E") && !dbCistrans.equals("Z")) {
setLipidLevel(LipidLevel.STRUCTURE_DEFINED);
}
}
}
private void addDbPositionNumber(TreeNode node) {
dbPositions = node.getInt();
}
private void addCistrans(TreeNode node) {
dbCistrans = node.getText();
}
private void setHeadGroupName(TreeNode node) {
headGroup = node.getText();
}
private void setSpeciesLevel(TreeNode node) {
setLipidLevel(LipidLevel.SPECIES);
}
private void setMolecularLevel(TreeNode node) {
setLipidLevel(LipidLevel.MOLECULAR_SPECIES);
}
private void mediatorEvent(TreeNode node) {
useHeadGroup = true;
headGroup = node.getText();
}
private void newFa(TreeNode node) {
currentFa = new FattyAcid("FA", knownFunctionalGroups);
}
private void newLcb(TreeNode node) {
lcb = new FattyAcid("LCB", knownFunctionalGroups);
lcb.setType(LipidFaBondType.LCB_REGULAR);
setLipidLevel(LipidLevel.STRUCTURE_DEFINED);
currentFa = lcb;
}
private void cleanLcb(TreeNode node) {
if (currentFa.getDoubleBonds().getDoubleBondPositions().isEmpty() && currentFa.getDoubleBonds().getNumDoubleBonds() > 0) {
setLipidLevel(LipidLevel.SN_POSITION);
}
currentFa = null;
}
private void appendFa(TreeNode node) {
if (currentFa.getDoubleBonds().getNumDoubleBonds() < 0) {
throw new LipidException("Double bond count does not match with number of double bond positions");
}
if (currentFa.getDoubleBonds().getDoubleBondPositions().isEmpty() && currentFa.getDoubleBonds().getNumDoubleBonds() > 0) {
setLipidLevel(LipidLevel.SN_POSITION);
}
faList.add(currentFa);
currentFa = null;
}
private void buildLipid(TreeNode node) {
if (lcb != null) {
faList.add(0, lcb);
}
Headgroup headgroup = prepareHeadgroupAndChecks();
LipidAdduct lipid = new LipidAdduct(assembleLipid(headgroup), adduct);
content = lipid;
}
private void addEther(TreeNode node) {
String ether = node.getText();
if (ether.equals("O-") || ether.equals("o-")) {
currentFa.setLipidFaBondType(LipidFaBondType.ETHER_PLASMANYL);
} else if (ether.equals("P-")) {
currentFa.setLipidFaBondType(LipidFaBondType.ETHER_PLASMENYL);
} else {
throw new UnsupportedLipidException("Fatty acyl chain of type '" + ether + "' is currently not supported");
}
}
private void addHydroxyl(TreeNode node) {
String old_hydroxyl = node.getText();
int num_h = 0;
if (old_hydroxyl.equals("d")) {
num_h = 2;
} else if (old_hydroxyl.equals("t")) {
num_h = 3;
}
if (spRegularLcb()) {
num_h -= 1;
}
FunctionalGroup functional_group = knownFunctionalGroups.get("OH");
functional_group.setCount(num_h);
if (!currentFa.getFunctionalGroupsInternal().containsKey("OH")) {
currentFa.getFunctionalGroupsInternal().put("OH", new ArrayList<>());
}
currentFa.getFunctionalGroupsInternal().get("OH").add(functional_group);
}
private void addMethyl(TreeNode node) {
FunctionalGroup functional_group = knownFunctionalGroups.get("Me");
functional_group.setPosition(currentFa.getNumCarbon() - (node.getText().equals("i-") ? 1 : 2));
currentFa.setNumCarbon(currentFa.getNumCarbon() - 1);
if (!currentFa.getFunctionalGroupsInternal().containsKey("Me")) {
currentFa.getFunctionalGroupsInternal().put("Me", new ArrayList<>());
}
currentFa.getFunctionalGroupsInternal().get("Me").add(functional_group);
}
private void addOneHydroxyl(TreeNode node) {
if (currentFa.getFunctionalGroupsInternal().containsKey("OH") && currentFa.getFunctionalGroupsInternal().get("OH").get(0).getPosition() == -1) {
currentFa.getFunctionalGroupsInternal().get("OH").get(0).setCount(currentFa.getFunctionalGroupsInternal().get("OH").get(0).getCount() + 1);
} else {
FunctionalGroup functional_group = knownFunctionalGroups.get("OH");
if (!currentFa.getFunctionalGroupsInternal().containsKey("OH")) {
currentFa.getFunctionalGroupsInternal().put("OH", new ArrayList<>());
}
currentFa.getFunctionalGroupsInternal().get("OH").add(functional_group);
}
}
private void addDoubleBonds(TreeNode node) {
currentFa.getDoubleBonds().setNumDoubleBonds(node.getInt());
}
private void addCarbon(TreeNode node) {
currentFa.setNumCarbon(currentFa.getNumCarbon() + node.getInt());
}
private void furanFa(TreeNode node) {
furan = new Dictionary();
}
private void furanFaPost(TreeNode node) {
int l = 4 + (int) furan.get("len_first") + (int) furan.get("len_second");
currentFa.setNumCarbon(l);
int start = 1 + (int) furan.get("len_first");
int end = 3 + start;
DoubleBonds cyclo_db = new DoubleBonds(2);
cyclo_db.getDoubleBondPositions().put(start, "E");
cyclo_db.getDoubleBondPositions().put(2 + start, "E");
HashMap<String, ArrayList<FunctionalGroup>> cyclo_fg = new HashMap<>();
cyclo_fg.put("Me", new ArrayList<>());
if (((String) furan.get("type")).equals("m")) {
FunctionalGroup fg = knownFunctionalGroups.get("Me");
fg.setPosition(1 + start);
cyclo_fg.get("Me").add(fg);
} else if (((String) furan.get("type")).equals("d")) {
FunctionalGroup fg = knownFunctionalGroups.get("Me");
fg.setPosition(1 + start);
cyclo_fg.get("Me").add(fg);
fg = knownFunctionalGroups.get("Me");
fg.setPosition(2 + start);
cyclo_fg.get("Me").add(fg);
}
ArrayList<Element> bridge_chain = new ArrayList<>();
bridge_chain.add(Element.O);
Cycle cycle = new Cycle(end - start + 1 + bridge_chain.size(), start, end, cyclo_db, cyclo_fg, bridge_chain, knownFunctionalGroups);
currentFa.getFunctionalGroupsInternal().put("cy", new ArrayList<>());
currentFa.getFunctionalGroupsInternal().get("cy").add(cycle);
}
private void furanFaMono(TreeNode node) {
furan.put("type", "m");
}
private void furanFaDi(TreeNode node) {
furan.put("type", "d");
}
private void furanFaFirstNumber(TreeNode node) {
furan.put("len_first", node.getInt());
}
private void furanFaSecondNumber(TreeNode node) {
furan.put("len_second", node.getInt());
}
private void interlinkFa(TreeNode node) {
throw new UnsupportedLipidException("Interconnected fatty acyl chains are currently not supported");
}
private void lipidSuffix(TreeNode node) {
//throw new UnsupportedLipidException("Lipids with suffix '" + node.getText() + "' are currently not supported");
}
private void newAdduct(TreeNode node) {
if (adduct == null) adduct = new Adduct("", "");
}
private void addAdduct(TreeNode node) {
adduct.setAdductString(node.getText());
}
private void addCharge(TreeNode node) {
adduct.setCharge(Integer.valueOf(node.getText()));
}
private void addChargeSign(TreeNode node) {
String sign = node.getText();
if (sign.equals("+")) {
adduct.setChargeSign(1);
} else if (sign.equals("-")) {
adduct.setChargeSign(-1);
}
if (adduct.getCharge() == 0) adduct.setCharge(1);
}
}