This method initializes map for glyphs and their respective ports.
@param glyphs Glyph list of SBGN model
174432
private void initPortIdToGlyphMap(List<Glyph> glyphs)
    {
        for(Glyph glyph: glyphs)
        {
            for(Port p: glyph.getPort())
            {
                portIDToOwnerGlyph.put(p.getId(), glyph );
            }
            if(glyph.getGlyph().size() > 0)
                initPortIdToGlyphMap(glyph.getGlyph());
        }
    }
54010
public void setChannelMappings(java.util.Collection<AudioChannelMapping> channelMappings) {
        if (channelMappings == null) {
            this.channelMappings = null;
            return;
        }

        this.channelMappings = new java.util.ArrayList<AudioChannelMapping>(channelMappings);
    }
1151026
public void init(Map<String,Object> properties)
    {
        if (properties == null)
            m_properties = new Hashtable<String,Object>();
        else
            m_properties = properties;
        m_vApplication = new Vector<App>();
    }
764539
public void setGeometries(List<Geometry> geometries) {
        this.mGeometries.clear();
        if (geometries != null) {
            this.mGeometries.addAll(geometries);
        }
    }
790826
protected Map<Character, List<Pair<FeaturePattern, FeatureReplacement>>> initMapping() {
		final Map<Character, List<Pair<FeaturePattern, FeatureReplacement>>> map = new TreeMap<>();
		if (!this.ruleReader.initializeConversions(map, this.context) && this.initializer != null) {
			this.initializer.initializeConversions((simpleName, source, target) -> {
				final char c = getKey(simpleName);
				if (c == FeaturePattern.ALL_PATTERN_CHAR) {
					for (int i = 'a'; i <= 'z'; ++i) {
						createMappingEntry(map, (char) i, source, target);
					}
				} else {
					createMappingEntry(map, c, source, target);
				}
			});
		}
		return map;
	}
764152
def _init_glyph(self, plot, mapping, properties):
        
        properties = mpl_to_bokeh(properties)
        properties = dict(properties, **mapping)
        if 'xs' in mapping:
            renderer = plot.patches(**properties)
        else:
            renderer = plot.quad(**properties)
        if self.colorbar and 'color_mapper' in self.handles:
            self._draw_colorbar(plot, self.handles['color_mapper'])
        return renderer, renderer.glyph
899991
private void initializeMapper() {
    if (itemClass == null) {
      itemMapper = CatchAllMapper.getInstance();
    } else {
      try {
        itemMapper = MapperFactory.getInstance().getMapper(itemClass);
      } catch (NoSuitableMapperException exp) {
        itemMapper = CatchAllMapper.getInstance();
      }
    }
  }
952222
public static void loadGlyphsFont(InputStream stream, String keyPrefix) throws IOException {
        try {
            DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
            DocumentBuilder docBuilder = docFactory.newDocumentBuilder();

            docBuilder.setEntityResolver((publicId, systemId) -> {
                // disable dtd entites at runtime
                return new InputSource(new StringReader(""));
            });

            Document doc = docBuilder.parse(stream);
            doc.getDocumentElement().normalize();

            NodeList glyphsList = doc.getElementsByTagName("glyph");
            for (int i = 0; i < glyphsList.getLength(); i++) {
                Node glyph = glyphsList.item(i);
                Node glyphName = glyph.getAttributes().getNamedItem("glyph-name");
                if (glyphName == null) {
                    continue;
                }

                String glyphId = glyphName.getNodeValue();
                SVGGlyphBuilder glyphPane = new SVGGlyphBuilder(i,
                    glyphId,
                    glyph.getAttributes()
                        .getNamedItem("d")
                        .getNodeValue());
                glyphsMap.put(keyPrefix + "." + glyphId, glyphPane);
            }
            stream.close();
        } catch (ParserConfigurationException | SAXException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
1333432
private void init(boolean importFonts) {
		fontMap = new HashMap();
		if(this.rtfParser != null) {
			this.importHeader = this.rtfParser.getImportManager();
		}
		this.setToDefaults();
		if(importFonts) {
			importSystemFonts();
		}
	}
1264872
private void initializeGlucose() {
    this.initializeGlucoseConfig();
    this.watchesBin = new LNGVector<>();
    this.permDiff = new LNGIntVector();
    this.lastDecisionLevel = new LNGIntVector();
    this.lbdQueue = new LNGBoundedLongQueue();
    this.trailQueue = new LNGBoundedIntQueue();
    this.assump = new LNGBooleanVector();
    this.lbdQueue.initSize(sizeLBDQueue);
    this.trailQueue.initSize(sizeTrailQueue);
    this.myflag = 0;
    this.analyzeBtLevel = 0;
    this.analyzeLBD = 0;
    this.analyzeSzWithoutSelectors = 0;
    this.nbclausesbeforereduce = firstReduceDB;
    this.conflicts = 0;
    this.conflictsRestarts = 0;
    this.sumLBD = 0;
    this.curRestart = 1;
  }
1133251
protected void updateDimmed (List<? extends ChatGlyph> glyphs)
    {
        for (ChatGlyph glyph : glyphs) {
            glyph.setDim(_dimmed);
        }
    }
952425
private static HashMap<String, ITypeface> init(@NonNull Context ctx,
                                                   @NonNull HashMap<String, ITypeface> fonts) {
        init(ctx);
        if (fonts == null || fonts.size() == 0) {
            fonts = FONTS;
        }
        return fonts;
    }
403750
public void setMappings(Map<String, String> patternMap) {
		this.mappings = new HashMap<String, String>(patternMap);
		for (String key : mappings.keySet()) {
			String result = mappings.get(key);
			if (result.startsWith(FORWARD)) {
				result = result.substring(FORWARD.length());
			}
			if (result.startsWith(REDIRECT)) {
				result = result.substring(REDIRECT.length());
			}
			mappings.put(key, result);
		}
	}
791092
private void initGraphics() {
        if (Double.compare(getPrefWidth(), 0.0) <= 0 || Double.compare(getPrefHeight(), 0.0) <= 0 ||
            Double.compare(getWidth(), 0.0) <= 0 || Double.compare(getHeight(), 0.0) <= 0) {
            if (getPrefWidth() > 0 && getPrefHeight() > 0) {
                setPrefSize(getPrefWidth(), getPrefHeight());
            } else {
                setPrefSize(PREFERRED_WIDTH, PREFERRED_HEIGHT); // 11x7
            }
        }

        state = State.CONSTANT;

        triangle = new Path();
        triangle.setStroke(null);
        triangle.setFill(state.color);
        triangle.setRotate(state.angle);

        nameText = new Text(getName());
        nameText.setTextOrigin(VPos.TOP);

        valueText = new Text(String.format(locale, formatString, getValue()));
        valueText.setTextOrigin(VPos.TOP);

        separator = new Line();

        pane = new Pane(triangle, nameText, valueText, separator);
        pane.setBackground(new Background(new BackgroundFill(Color.TRANSPARENT, CornerRadii.EMPTY, Insets.EMPTY)));

        getChildren().setAll(pane);
    }
978641
private void initLabels() {

        m_addressLabel.setText(Messages.get().key(Messages.GUI_LOCATION_ADDRESS_0));
        m_longitudeLabel.setText(Messages.get().key(Messages.GUI_LOCATION_LONGITUDE_0));
        m_latitudeLabel.setText(Messages.get().key(Messages.GUI_LOCATION_LATITUDE_0));
        m_sizeLabel.setText(Messages.get().key(Messages.GUI_LOCATION_SIZE_0));
        m_zoomLabel.setText(Messages.get().key(Messages.GUI_LOCATION_ZOOM_0));
        m_typeLabel.setText(Messages.get().key(Messages.GUI_LOCATION_TYPE_0));
        m_modeLabel.setText(Messages.get().key(Messages.GUI_LOCATION_MODE_0));

        m_okButton.setText(Messages.get().key(Messages.GUI_OK_0));
        m_okButton.setUseMinWidth(true);
        m_okButton.setButtonStyle(ButtonStyle.TEXT, ButtonColor.BLUE);
        m_cancelButton.setText(Messages.get().key(Messages.GUI_CANCEL_0));
        m_cancelButton.setUseMinWidth(true);
        m_cancelButton.setButtonStyle(ButtonStyle.TEXT, ButtonColor.BLUE);
    }
815839
def _init_glyph(self, plot, mapping, properties):
        
        plot_method = properties.pop('plot_method', None)
        properties = mpl_to_bokeh(properties)
        data = dict(properties, **mapping)
        if self._has_holes:
            plot_method = 'multi_polygons'
        elif plot_method is None:
            plot_method = self._plot_methods.get('single')
        renderer = getattr(plot, plot_method)(**data)
        if self.colorbar:
            for k, v in list(self.handles.items()):
                if not k.endswith('color_mapper'):
                    continue
                self._draw_colorbar(plot, v, k[:-12])
        return renderer, renderer.glyph
713825
public void setBulletPoints(java.util.Collection<String> bulletPoints) {
        if (bulletPoints == null) {
            this.bulletPoints = null;
            return;
        }

        this.bulletPoints = new java.util.ArrayList<String>(bulletPoints);
    }