public String getFeatureValuesFilePath(CompoundPropertySet cps) {
   String enc =
       (clusteringData != null && cps.isSensitiveTo3D())
           ? (getEncodedSettings(clusteringData.getThreeDBuilder()) + ".")
           : "";
   return Settings.destinationFile(dataset, enc + cps.getNameIncludingParams());
 }
 public String getSmartsMatchesFilePath(
     MatchEngine matchEngine, List<ListedFragmentProperty> fragments) {
   String allSmartsStrings = "";
   for (ListedFragmentProperty fragment : fragments) allSmartsStrings += fragment.getSmarts();
   String enc = StringUtil.getMD5(matchEngine + allSmartsStrings);
   return Settings.destinationFile(dataset, enc + ".matches.csv");
 }
 public String getAlignResultsPerClusterFilePath(int clusterIndex, String params) {
   return Settings.destinationFile(
       dataset,
       getEncodedSettingsIncludingFeatures(clusteringData.getDatasetClusterer())
           + "."
           + StringUtil.getMD5(clusterIndex + params)
           + ".cluster");
 }
 public String getEmbeddingResultsFilePath(String extension) {
   if (clusteringData.getThreeDEmbedder() == null) throw new IllegalStateException();
   return Settings.destinationFile(
       dataset,
       getEncodedSettingsIncludingFeatures(clusteringData.getThreeDEmbedder())
           + ".embed."
           + extension);
 }
 public String getAlignSDFilePath() {
   if (clusteringData.getDatasetClusterer() == null || clusteringData.getThreeDAligner() == null)
     throw new IllegalStateException();
   return Settings.destinationFile(
       dataset,
       getEncodedSettingsIncludingFeatures(
               clusteringData.getDatasetClusterer(), clusteringData.getThreeDAligner())
           + ".align.sdf");
 }
 public String get3DBuilderSDFilePath(ThreeDBuilder builder) {
   if (clusteringData != null
       && clusteringData.getThreeDBuilder() != null
       && clusteringData.getThreeDBuilder() != builder)
     throw new IllegalStateException(
         "set appropriate builder, already set "
             + clusteringData.getThreeDBuilder()
             + " != "
             + builder);
   return Settings.destinationFile(dataset, getEncodedSettings(builder) + ".3d.sdf");
 }
 public String getClusterAssignmentFilePath() {
   if (clusteringData.getDatasetClusterer() == null) throw new IllegalStateException();
   return Settings.destinationFile(
       dataset,
       getEncodedSettingsIncludingFeatures(clusteringData.getDatasetClusterer()) + ".cluster");
 }
 public String getFeatureTableFilePath(String extension) {
   return Settings.destinationFile(
       dataset, getEncodedSettingsIncludingFeatures() + ".features." + extension);
 }
 public String getAppDomainValuesFilePath(AppDomainComputer app, String param) {
   return Settings.destinationFile(
       dataset, getEncodedSettingsIncludingFeatures(app) + "." + param);
 }