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Chemical Renderer that uses Molwitch
/*
* NCATS-MOLWITCH-RENDERER
*
* Copyright 2019 NIH/NCATS
*
* 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 gov.nih.ncats.molwitch.renderer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonValue;
import gov.nih.ncats.molwitch.Chemical;
public class RendererOptions {
public enum DrawOptions{
DRAW_BONDS(true, "PROP_KEY_DRAW_BONDS"),
DRAW_SYMBOLS(true, "PROP_KEY_DRAW_SYMBOLS"),
DRAW_CARBON(false, "PROP_KEY_DRAW_CARBON"),
DRAW_IMPLICIT_HYDROGEN(true, "PROP_KEY_DRAW_IMPLICIT_HYDROGEN"),
DRAW_TERMINAL_CARBON(true, "PROP_KEY_DRAW_TERMINAL_CARBON"),
DRAW_STEREO_BONDS(true, "PROP_KEY_DRAW_STEREO_BONDS"),
DRAW_PROPORTIONAL_ATOM_RADIUS(false, "PROP_KEY_DRAW_PROPORTIONAL_ATOM_RADIUS"),
DRAW_PROPORTION_AVERAGE_BOND_LENGTH(true, "PROP_KEY_DRAW_PROPORTION_AVERAGE_BOND_LENGTH"),
DRAW_CENTER_ALL_DOUBLE_BONDS(false, "PROP_KEY_DRAW_CENTER_ALL_DOUBLE_BONDS"),
DRAW_ATOM_COLOR_ON_BONDS(true, "PROP_KEY_DRAW_ATOM_COLOR_ON_BONDS"),
DRAW_CONSTANT_DASH_WIDTH(true, "PROP_KEY_DRAW_CONSTANT_DASH_WIDTH"),
DRAW_STEREO_DASH_AS_WEDGE(true, "PROP_KEY_DRAW_STEREO_DASH_AS_WEDGE"),
/**
* Show wedge bonds as originating from a small circle (of bond length)
* instead of a point (which is the default).
* Allowing this makes wedges more visible in some cases.
*/
DRAW_WEDGE_AS_POINT(true, "PROP_KEY_DRAW_WEDGE_AS_POINT"),
/**
* Should renderer join wedges/single bonds into an extended stylistic form,
* which is often less jarring than the sudden sharp corners from bridgehead/chain wedges in other styles.
*
* when set to {@code false} (default):
* 
*
* when set to {@code true} :
* 
*
*/
DRAW_STEREO_WEDGE_JOIN(false, "PROP_KEY_DRAW_STEREO_WEDGE_JOIN"),
/**
* Show the final dash line on dash-wedges when not connecting to a symbol.
*/
DRAW_STEREO_LAST_DASH_ON_NON_SYMBOLS(true, "PROP_KEY_DRAW_STEREO_LAST_DASH_ON_NON_SYMBOLS"),
DRAW_CENTER_NONRING_DOUBLE_BONDS(false, "PROP_KEY_DRAW_CENTER_NONRING_DOUBLE_BONDS"),
DRAW_GREYSCALE(false, "PROP_KEY_DRAW_GREYSCALE"),
DRAW_STEREO_LABELS(false, "PROP_KEY_DRAW_STEREO_LABELS"),
DRAW_STEREO_GIVEN_BY_MAP(false, "PROP_KEY_DRAW_STEREO_GIVEN_BY_MAP"),
DRAW_HIGHLIGHT_MAPPED(false, "PROP_KEY_DRAW_HIGHLIGHT_MAPPED"),
DRAW_HIGHLIGHT_WITH_HALO(false, "PROP_KEY_DRAW_HIGHLIGHT_WITH_HALO"),
DRAW_HIGHLIGHT_MONOCHROMATIC(true, "PROP_KEY_DRAW_HIGHLIGHT_MONOCHROMATIC"),
DRAW_HIGHLIGHT_SHOW_ATOM(false, "PROP_KEY_DRAW_HIGHLIGHT_SHOW_ATOM"),
DRAW_SHOW_MAPPED(false, "PROP_KEY_DRAW_SHOW_MAPPED"),
DRAW_STEREO_LABELS_AS_ATOMS(false, "PROP_KEY_DRAW_STEREO_LABELS_AS_ATOMS"),
DRAW_STEREO_LABELS_AS_RELATIVE(false, "PROP_KEY_DRAW_STEREO_LABELS_AS_RELATIVE"),
DRAW_STEREO_LABELS_AS_STARRED(false, "PROP_KEY_DRAW_STEREO_LABELS_AS_STARRED"),
DRAW_STEREO_LABELS_PARENTHESES(false, "PROP_KEY_DRAW_STEREO_LABELS_PARENTHESES"),
DRAW_STEREO_FORCE_MONOCHROMATIC(false, "PROP_KEY_DRAW_STEREO_FORCE_MONOCHROMATIC"),
DRAW_SUPERATOMS_AS_LABELS(true, "PROP_KEY_DRAW_SUPERATOMS_AS_LABELS")
;
private final boolean defaultValue;
/**
* This is the name from the old NChemicalRenderer DisplayParams
* that is sometimes used in legacy NCATS API calls
* to override rendering options. This is used
* only in {@link #safeValueOf(String)}
* to maintain backwards compatibility.
*/
private final String legacyName;
private static final Map nameMap;
static {
nameMap = new HashMap<>();
for(DrawOptions opt : values()) {
nameMap.put(opt.name(), opt);
nameMap.put(opt.legacyName, opt);
}
}
DrawOptions(boolean dv, String legacyName){
defaultValue= dv;
this.legacyName = legacyName;
}
/**
* This is a version of {@link #valueOf(String)}
* but if the given String input is not an enum value
* then it will return null instead of throwing an exception.
*
* @param name the value to parse the Draw option name of.
* @return the {@link DrawOptions} for this name or {@code null}.
*/
public static DrawOptions safeValueOf(String name) {
return nameMap.get(name);
}
public boolean defaultValue() {
return defaultValue;
}
}
public enum DrawProperties{
ATOM_LABEL_FONT_FRACTION(2/3D, "DEF_FONT_PERCENT"),
ATOM_LABEL_BOND_GAP_FRACTION(1, "DEF_FONT_GAP_PERCENT"),
BOND_EXPECTED_LENGTH(1, "DEF_BOND_AVG"),
BOND_STROKE_WIDTH_FRACTION(.095D, "DEF_STROKE_PERCENT"),
BOND_DOUBLE_GAP_FRACTION(.30D, "DEF_DBL_BOND_GAP"),
BOND_DOUBLE_LENGTH_FRACTION(2/3D, "DEF_DBL_BOND_DISTANCE"),
BOND_STEREO_WEDGE_ANGLE( Math.PI/12, "DEF_WEDGE_ANG"),
BOND_OVERLAP_SPACING_FRACTION(1.75D, "DEF_SPLIT_RATIO"),
BOND_STEREO_DASH_NUMBER(6, "DEF_NUM_DASH"),
SUBSCRIPT_Y_DISPLACEMENT_FRACTION(0.2f, "SUBSCRIPT_Y_DISPLACEMENT_FRACTION");
private final double defaultValue;
/**
* This is the name from the old NChemicalRenderer DisplayParams
* that is sometimes used in legacy NCATS API calls
* to override renderering options. This is used
* only in {@link #safeValueOf(String)}
* to maintain backwards compatibility.
*/
private final String legacyName;
private static final Map nameMap;
static {
nameMap = new HashMap<>();
for(DrawProperties opt : values()) {
nameMap.put(opt.name(), opt);
nameMap.put(opt.legacyName, opt);
}
}
DrawProperties(double dv, String legacyName){
defaultValue = dv;
this.legacyName = legacyName;
}
/**
* This is a version of {@link #valueOf(String)}
* but if the given String input is not an enum value
* then it will return null instead of throwing an exception.
*
*@param name the value to parse the draw property name of.
*@return the {@link DrawProperties} for this name or {@code null}.
*/
public static DrawProperties safeValueOf(String name) {
return nameMap.get(name);
}
public double defaultValue() {
return defaultValue;
}
}
private final EnumMap drawOptions = new EnumMap<>(DrawOptions.class);
private final EnumMap drawProps = new EnumMap<>(DrawProperties.class);
private ColorPalette colorPalette = new ColorPalette();
private Function bottomCaptionFunction=null;
private Function topCaptionFunction=null;
private List changeListeners = new ArrayList<>();
public RendererOptions() {
_useDefauls();
}
public RendererOptions copy(){
RendererOptions copy = RendererOptions.createFromMap(asNonDefaultMap());
return copy;
}
@JsonCreator
public static RendererOptions createFromMap(Map map){
RendererOptions opts = new RendererOptions();
opts.changeSettings(map);
return opts;
}
@JsonValue
public Map asNonDefaultMap(){
Map map = new HashMap<>();
for(Entry entry: drawProps.entrySet()){
if(!Objects.equals(entry.getValue(), entry.getKey().defaultValue)) {
map.put(entry.getKey().legacyName, entry.getValue());
}
}
for(Entry entry: drawOptions.entrySet()){
if(entry.getKey().defaultValue != entry.getValue().booleanValue()) {
map.put(entry.getKey().legacyName, entry.getValue());
}
}
Map paletteMap = colorPalette.asNonDefaultMap();
if(!paletteMap.isEmpty()){
map.put("colorPalette", paletteMap);
}
return map;
}
public Map asMap(){
Map map = new HashMap<>();
for(Entry entry: drawProps.entrySet()){
map.put(entry.getKey().legacyName, entry.getValue());
}
for(Entry entry: drawOptions.entrySet()){
map.put(entry.getKey().legacyName, entry.getValue());
}
return map;
}
public void addChangeListener(RendererOptionChangeListener listener){
changeListeners.add(Objects.requireNonNull(listener));
}
public ColorPalette getColorPalette(){
return colorPalette;
}
private void fireChangeListeners(){
changeListeners.forEach(l->l.optionChanged(null));
}
public boolean getDrawOption(DrawOptions o) {
return drawOptions.get(o);
}
public RendererOptions setDrawOption(DrawOptions option, boolean value) {
drawOptions.put(option, value);
fireChangeListeners();
return this;
}
public double getDrawPropertyValue(DrawProperties p) {
return drawProps.get(p);
}
public RendererOptions captionBottom(Function captionFunction) {
this.bottomCaptionFunction = captionFunction;
fireChangeListeners();
return this;
}
public RendererOptions captionTop(Function captionFunction) {
this.topCaptionFunction = captionFunction;
fireChangeListeners();
return this;
}
public RendererOptions setDrawPropertyValue(DrawProperties p, double value) {
drawProps.put(p, value);
fireChangeListeners();
return this;
}
public RendererOptions withSubstructureHighlight() {
drawOptions.put(DrawOptions.DRAW_HIGHLIGHT_MAPPED, true);
drawOptions.put(DrawOptions.DRAW_HIGHLIGHT_WITH_HALO, true);
drawOptions.put(DrawOptions.DRAW_HIGHLIGHT_MONOCHROMATIC, true);
fireChangeListeners();
return this;
}
Optional captionBottom(Chemical c){
if(bottomCaptionFunction!=null) {
return Optional.ofNullable(bottomCaptionFunction.apply(c));
}
return Optional.empty();
}
Optional captionTop(Chemical c){
if(topCaptionFunction!=null) {
return Optional.ofNullable(topCaptionFunction.apply(c));
}
return Optional.empty();
}
public static RendererOptions createDefault() {
return new RendererOptions();
}
public static RendererOptions createBallAndStick() {
RendererOptions opts =new RendererOptions();
opts.setDrawOption(DrawOptions.DRAW_BONDS, true);
opts.setDrawOption(DrawOptions.DRAW_SYMBOLS, false);
opts.setDrawOption(DrawOptions.DRAW_CARBON, true);
opts.setDrawOption(DrawOptions.DRAW_CENTER_ALL_DOUBLE_BONDS, true);
opts.setDrawOption(DrawOptions.DRAW_STEREO_BONDS, false);
return opts;
}
public static RendererOptions createINNLike() {
RendererOptions opts =new RendererOptions();
opts.setDrawOption(DrawOptions.DRAW_GREYSCALE, true);
opts.setDrawOption(DrawOptions.DRAW_STEREO_DASH_AS_WEDGE, false);
opts.setDrawPropertyValue(DrawProperties.BOND_STEREO_WEDGE_ANGLE, Math.PI/12);
opts.setDrawPropertyValue(DrawProperties.BOND_STROKE_WIDTH_FRACTION, 0.050D);
opts.setDrawPropertyValue(DrawProperties.BOND_DOUBLE_GAP_FRACTION, .15D);
opts.setDrawPropertyValue(DrawProperties.ATOM_LABEL_FONT_FRACTION,0.5D);
return opts;
}
public static RendererOptions createUSPLike() {
RendererOptions opts = new RendererOptions();
opts.setDrawOption(DrawOptions.DRAW_GREYSCALE, true);
opts.setDrawPropertyValue(DrawProperties.ATOM_LABEL_FONT_FRACTION,0.494D*0.97);
opts.setDrawPropertyValue(DrawProperties.ATOM_LABEL_BOND_GAP_FRACTION,1.02D);
opts.setDrawPropertyValue(DrawProperties.BOND_STROKE_WIDTH_FRACTION,0.04D*0.8);
opts.setDrawPropertyValue(DrawProperties.BOND_DOUBLE_GAP_FRACTION,0.21D*0.95);
opts.setDrawPropertyValue(DrawProperties.BOND_STEREO_WEDGE_ANGLE, Math.PI/25*0.92);
opts.setDrawPropertyValue(DrawProperties.BOND_STEREO_DASH_NUMBER, 8);
opts.setDrawPropertyValue(DrawProperties.SUBSCRIPT_Y_DISPLACEMENT_FRACTION, 0.17);
opts.setDrawOption(DrawOptions.DRAW_WEDGE_AS_POINT, false);
opts.setDrawOption(DrawOptions.DRAW_STEREO_WEDGE_JOIN, true);
opts.setDrawOption(DrawOptions.DRAW_STEREO_LAST_DASH_ON_NON_SYMBOLS, false);
return opts;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((drawOptions == null) ? 0 : drawOptions.hashCode());
result = prime * result + ((drawProps == null) ? 0 : drawProps.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (obj == null) {
return false;
}
if (!(obj instanceof RendererOptions)) {
return false;
}
RendererOptions other = (RendererOptions) obj;
if (drawOptions == null) {
if (other.drawOptions != null) {
return false;
}
} else if (!drawOptions.equals(other.drawOptions)) {
return false;
}
if (drawProps == null) {
if (other.drawProps != null) {
return false;
}
} else if (!drawProps.equals(other.drawProps)) {
return false;
}
return true;
}
private void _useDefauls() {
for(DrawOptions o : DrawOptions.values()) {
drawOptions.put(o, o.defaultValue());
}
for(DrawProperties o : DrawProperties.values()) {
drawProps.put(o, o.defaultValue());
}
colorPalette = new ColorPalette();
}
public RendererOptions resetToDefaults() {
_useDefauls();
fireChangeListeners();
return this;
}
public RendererOptions turnOffStereo() {
setDrawOption(DrawOptions.DRAW_STEREO_LABELS, false);
setDrawOption(DrawOptions.DRAW_STEREO_LABELS_PARENTHESES, false);
fireChangeListeners();
return this;
}
public RendererOptions turnOnStereo() {
setDrawOption(DrawOptions.DRAW_STEREO_LABELS, true);
setDrawOption(DrawOptions.DRAW_STEREO_LABELS_PARENTHESES, true);
fireChangeListeners();
return this;
}
public RendererOptions changeSettings(Map map) {
for(Entry entry: map.entrySet()) {
if("colorPalette".equals(entry.getKey())){
this.colorPalette = ColorPalette.createFromMap((Map)entry.getValue());
continue;
}
DrawOptions opts = DrawOptions.safeValueOf(entry.getKey());
if(opts ==null) {
DrawProperties props = DrawProperties.safeValueOf(entry.getKey());
if(props !=null) {
if(Number.class.isAssignableFrom(entry.getValue().getClass())){
setDrawPropertyValue(props,((Number)entry.getValue()).doubleValue());
}else if(String.class.isAssignableFrom(entry.getValue().getClass())){
setDrawPropertyValue(props,Double.parseDouble((String)entry.getValue()));
}
}
}else {
if(Boolean.class.isAssignableFrom(entry.getValue().getClass())){
setDrawOption(opts, ((Boolean) entry.getValue()).booleanValue());
}else if(String.class.isAssignableFrom(entry.getValue().getClass())){
setDrawOption(opts,Boolean.parseBoolean((String)entry.getValue()));
}
}
}
return this;
}
}