package jalview.viewmodel.seqfeatures; import jalview.schemes.GraduatedColor; import java.util.Arrays; import java.util.Hashtable; import java.util.Iterator; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; public class FeatureRendererSettings implements Cloneable { String[] renderOrder; Map featureGroups; Map featureColours; float transparency; Map featureOrder; public FeatureRendererSettings(String[] renderOrder, Hashtable featureGroups, Hashtable featureColours, float transparency, Hashtable featureOrder) { super(); this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length); this.featureGroups = new ConcurrentHashMap(featureGroups); this.featureColours = new ConcurrentHashMap(featureColours); this.transparency = transparency; this.featureOrder = new ConcurrentHashMap(featureOrder); } /** * create an independent instance of the feature renderer settings * * @param fr */ public FeatureRendererSettings( jalview.viewmodel.seqfeatures.FeatureRendererModel fr) { renderOrder = null; featureGroups = new ConcurrentHashMap(); featureColours = new ConcurrentHashMap(); featureOrder = new ConcurrentHashMap(); if (fr.renderOrder != null) { this.renderOrder = new String[fr.renderOrder.length]; System.arraycopy(fr.renderOrder, 0, renderOrder, 0, fr.renderOrder.length); } if (fr.featureGroups != null) { this.featureGroups = new ConcurrentHashMap(fr.featureGroups); } if (fr.featureColours != null) { this.featureColours = new ConcurrentHashMap(fr.featureColours); } Iterator en = fr.featureColours.keySet().iterator(); while (en.hasNext()) { Object next = en.next(); Object val = featureColours.get(next); if (val instanceof GraduatedColor) { featureColours.put(next, new GraduatedColor((GraduatedColor) val)); } } this.transparency = fr.transparency; if (fr.featureOrder != null) { this.featureOrder = new ConcurrentHashMap(fr.featureOrder); } } }