diff --git a/Changes b/Changes
index 22f4a94..d8c8592 100644
--- a/Changes
+++ b/Changes
@@ -20,7 +20,9 @@
           fixed a lot of wrong tests for WithinSpans,
 	  renamed KorapFilter to /collection/CollectionBuilder,
 	  renamed SpanMatchModify to SpanFocus,
-	  changed KoralQuery root prefix to "koral" (diewald)
+	  changed KoralQuery root prefix to "koral",
+	  renamed different kinds of "queries" throughout classes,
+	  renamed KorapSearch#run to KorapSearch#apply (diewald)
         - [feature] Improved deserialization of SpanSubSpanQueries
           (margaretha)
 	- [feature] Introducing the potential need for resorting queries
diff --git a/src/main/java/de/ids_mannheim/korap/KorapCollection.java b/src/main/java/de/ids_mannheim/korap/KorapCollection.java
index 120580a..257e245 100644
--- a/src/main/java/de/ids_mannheim/korap/KorapCollection.java
+++ b/src/main/java/de/ids_mannheim/korap/KorapCollection.java
@@ -91,7 +91,7 @@
             
             // Deserialize from recent collections
             if (json.has("collection")) {
-                this.fromJSON(json.get("collection"));
+                this.fromJson(json.get("collection"));
             }
 	    
             // Legacy collection serialization
@@ -102,7 +102,7 @@
                     "Collections are deprecated in favour of a single collection"
                 );
                 for (JsonNode collection : json.get("collections")) {
-                    this.fromJSONLegacy(collection);
+                    this.fromJsonLegacy(collection);
                 };
             };
         }
@@ -135,14 +135,16 @@
      * @param jsonString The "collection" part of a KoralQuery.
      * @throws QueryException
      */
-    public void fromJSON (String jsonString) throws QueryException {
+    public KorapCollection fromJson (String jsonString) throws QueryException {
         ObjectMapper mapper = new ObjectMapper();
         try {
-            this.fromJSON((JsonNode) mapper.readTree(jsonString));
+            this.fromJson((JsonNode) mapper.readTree(jsonString));
         }
         catch (Exception e) {
             this.addError(621, "Unable to parse JSON", "KorapCollection");
         };
+
+        return this;
     };
 
 
@@ -153,19 +155,20 @@
      *        as a {@link JsonNode} object.
      * @throws QueryException
      */
-    public void fromJSON (JsonNode json) throws QueryException {
-        this.filter(this._fromJSON(json));
+    public KorapCollection fromJson (JsonNode json) throws QueryException {
+        this.filter(this._fromJson(json));
+        return this;
     };
 
 
     // Create a boolean filter from JSON
-    private BooleanFilter _fromJSON (JsonNode json) throws QueryException {
-        return this._fromJSON(json, "tokens");
+    private BooleanFilter _fromJson (JsonNode json) throws QueryException {
+        return this._fromJson(json, "tokens");
     };
 
 
     // Create a booleanfilter from JSON
-    private BooleanFilter _fromJSON (JsonNode json, String field) throws QueryException {
+    private BooleanFilter _fromJson (JsonNode json, String field) throws QueryException {
         BooleanFilter bfilter = new BooleanFilter();
 
         // TODO: THIS UNFORTUNATELY BREAKS TESTS
@@ -237,10 +240,10 @@
 
             for (JsonNode operand : json.get("operands")) {
                 if (operation.equals("operation:and"))
-                    group.and(this._fromJSON(operand, field));
+                    group.and(this._fromJson(operand, field));
 
                 else if (operation.equals("operation:or"))
-                    group.or(this._fromJSON(operand, field));
+                    group.or(this._fromJson(operand, field));
 
                 else
                     throw new QueryException(613, "Unknown document group operation");
@@ -264,14 +267,15 @@
      * @throws QueryException
      */
     @Deprecated
-    public void fromJSONLegacy (String jsonString) throws QueryException {
+    public KorapCollection fromJsonLegacy (String jsonString) throws QueryException {
         ObjectMapper mapper = new ObjectMapper();
         try {
-            this.fromJSONLegacy((JsonNode) mapper.readValue(jsonString, JsonNode.class));
+            this.fromJsonLegacy((JsonNode) mapper.readValue(jsonString, JsonNode.class));
         }
         catch (Exception e) {
             this.addError(621, "Unable to parse JSON", "KorapCollection");
         };
+        return this;
     };
 
 
@@ -284,14 +288,14 @@
      * @throws QueryException
      */
     @Deprecated
-    public void fromJSONLegacy (JsonNode json) throws QueryException {
+    public KorapCollection fromJsonLegacy (JsonNode json) throws QueryException {
         if (!json.has("@type"))
             throw new QueryException(701, "JSON-LD group has no @type attribute");
 
         if (!json.has("@value"))
             throw new QueryException(851, "Legacy filter need @value fields");
 
-        BooleanFilter bf = this._fromJSONLegacy(json.get("@value"), "tokens");
+        BooleanFilter bf = this._fromJsonLegacy(json.get("@value"), "tokens");
         String type = json.get("@type").asText();
 
         // Filter the collection
@@ -307,12 +311,14 @@
                 log.trace("Add Extend LEGACY");
             this.extend(bf);
         };
+
+        return this;
     };
 
 
     // Create a boolean filter from a Json string
     @Deprecated
-    private BooleanFilter _fromJSONLegacy (JsonNode json, String field)
+    private BooleanFilter _fromJsonLegacy (JsonNode json, String field)
         throws QueryException {
         BooleanFilter bfilter = new BooleanFilter();
 
@@ -380,7 +386,7 @@
                     throw new QueryException(612, "Operation needs at least two operands");
 
                 for (JsonNode operand : operands) {
-                    group.and(this._fromJSONLegacy(operand, field));
+                    group.and(this._fromJsonLegacy(operand, field));
                 };
                 bfilter.and(group);
                 break;
@@ -390,7 +396,7 @@
                     throw new QueryException(612, "Operation needs at least two operands");
 
                 for (JsonNode operand : operands) {
-                    group.or(this._fromJSONLegacy(operand, field));
+                    group.or(this._fromJsonLegacy(operand, field));
                 };
                 bfilter.and(group);
                 break;
diff --git a/src/main/java/de/ids_mannheim/korap/KorapIndex.java b/src/main/java/de/ids_mannheim/korap/KorapIndex.java
index d64fd7f..6f9130b 100644
--- a/src/main/java/de/ids_mannheim/korap/KorapIndex.java
+++ b/src/main/java/de/ids_mannheim/korap/KorapIndex.java
@@ -1146,7 +1146,7 @@
         collection.setIndex(this);
 
         // Get the spanquery from the KorapSearch object
-        SpanQuery query = ks.getQuery();
+        SpanQuery query = ks.getSpanQuery();
 
         // Get the field of textual data and annotations ("tokens")
         String field = query.getField();
@@ -1387,7 +1387,7 @@
         this.termContexts = new HashMap<Term, TermContext>();
 
         // Get span query
-        SpanQuery query = ks.getQuery();
+        SpanQuery query = ks.getSpanQuery();
 
         // Get the field of textual data and annotations
         String field = query.getField();
diff --git a/src/main/java/de/ids_mannheim/korap/KorapResult.java b/src/main/java/de/ids_mannheim/korap/KorapResult.java
index 1cba877..8f4c1dc 100644
--- a/src/main/java/de/ids_mannheim/korap/KorapResult.java
+++ b/src/main/java/de/ids_mannheim/korap/KorapResult.java
@@ -39,7 +39,7 @@
     public static final short ITEMS_PER_PAGE_MAX = 100;
 
     private int startIndex = 0;
-    private String query;
+    private String serialQuery;
 
     private List<KorapMatch> matches;
 
@@ -67,7 +67,7 @@
     /**
      * Construct a new KorapResult object.
      *
-     * @param query Query representation as a string.
+     * @param serialQuery Query representation as a string.
      * @param startIndex Offset position in match array.
      * @param itemsPerPage Number of matches per page.
      * @param context Requested {@link SearchContext}
@@ -82,7 +82,7 @@
         // mapper.disable(SerializationFeature.WRITE_NULL_MAP_VALUES);
 
         this.matches = new ArrayList<>(itemsPerPage);
-        this.query = query;
+        this.serialQuery = query;
         this.startIndex = startIndex;
         this.itemsPerPage =
             (itemsPerPage > ITEMS_PER_PAGE_MAX || itemsPerPage < 1) ?
@@ -187,8 +187,8 @@
      *
      * @return The string representation of the search query.
      */
-    public String getQuery () {
-        return this.query;
+    public String getSerialQuery () {
+        return this.serialQuery;
     };
 
 
@@ -281,8 +281,8 @@
         // TODO: <test>
         if (this.request != null)
             json.put("request", this.request);
-        if (this.query != null)
-            json.put("query", this.query);
+        if (this.serialQuery != null)
+            json.put("serialQuery", this.serialQuery);
         // </test>
 
         return json;
@@ -298,7 +298,7 @@
         StringBuilder sb = new StringBuilder();
 
         sb.append("Search for: ")
-            .append(this.query)
+            .append(this.serialQuery)
             .append("\n");
 
         int i = 1;
diff --git a/src/main/java/de/ids_mannheim/korap/KorapSearch.java b/src/main/java/de/ids_mannheim/korap/KorapSearch.java
index 88100df..1021bb0 100644
--- a/src/main/java/de/ids_mannheim/korap/KorapSearch.java
+++ b/src/main/java/de/ids_mannheim/korap/KorapSearch.java
@@ -15,31 +15,35 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.JsonNode;
 
+/**
+ * Krill is a corpus data retrieval index using Lucene for Look-Ups.
+ * It is the reference implementation for KoralQuery consumption.
+ *
+ * <blockquote><pre>
+ *   // Create a new krill search object passing a KoralQuery string
+ *   Krill krill = new Krill(jsonString);
+ *
+ *   // Run the query on an index
+ *   KrillResult kr = krill.apply(new KrillIndex());
+ * </pre></blockquote>
+ *
+ * @author diewald
+ * @author margaretha
+ */
 /*
- * Todo: Use configuration file
+ * Todo: Use a configuration file
  * Todo: Let this class extend KorapResult!
  *   KorapResult = new KorapSearch(String json).run(KorapIndex ki);
  * Todo: Set timeout default value per config file
  */
 
-/**
- * KorapSearch is the central class for parameterized searches
- * in the index, including the query, the collection,
- * and result parameters. 
- *
- * @author diewald
- *
- */
 public class KorapSearch extends Notifications {
-    private int
-        startIndex = 0,
-        limit = 0;
-    private short
-        count = 25,
-        countMax = 50;
+    private int startIndex = 0, limit = 0;
+    private short count = 25, countMax = 50, itemsPerResource = 0;
     private boolean cutOff = false;
-    private short itemsPerResource = 0;
-    private SpanQuery query;
+
+    private SpanQuery spanQuery;
+
     private KorapCollection collection;
     private KorapIndex index;
 
@@ -47,6 +51,7 @@
     private long timeout = (long) 120_000;
 
     private HashSet<String> fields;
+    private HashSet<Integer> highlights;
 
     private JsonNode request;
 
@@ -58,8 +63,9 @@
     {
         context  = new SearchContext();
 
-        // Lift legacy fields per default
         fields = new HashSet<String>(16);
+
+        // Lift legacy fields per default
         for (String field : new String[]{
                 "ID",
                 "UID",
@@ -76,153 +82,217 @@
                 "tokenization"}) {
             fields.add(field);
         };
+
+        // Classes used for highlights
+        highlights = new HashSet<Integer>(3);
     };
 
-    public KorapSearch (String jsonString) {
-        ObjectMapper mapper = new ObjectMapper();
 
+    /**
+     * Construct a new Krill object.
+     */
+    public KorapSearch () {};
+
+
+    /**
+     * Construct a new Krill object,
+     * consuming a {@link SpanQueryWrapper} object.
+     *
+     * @param query The {@link SpanQueryWrapper} object.
+     */
+    public KorapSearch (SpanQueryWrapper query) {
         try {
-            // Todo - use correct method!
-            this.request = mapper.readTree(jsonString);
-            
-            // "query" value
-            if (this.request.has("query")) {
-                try {
-                    KorapQuery kq = new KorapQuery("tokens");
-                    SpanQueryWrapper qw = kq.fromJson(this.request.get("query"));
-                    
-                    if (qw.isEmpty()) {
-                        
-                        // Unable to process result
-                        this.addError(780, "This query matches everywhere");
-                    }
-                    else {
-                        this.query = qw.toQuery();
-                        if (qw.isOptional())
-                            this.addWarning(781, "Optionality of query is ignored");
-                        if (qw.isNegative())
-                            this.addWarning(782, "Exclusivity of query is ignored");
-                        
-                    };
-                    // Copy notifications from query
-                    this.copyNotificationsFrom(kq);
-                    kq.clearNotifications();
-                }
-                catch (QueryException q) {
-                    this.addError(q.getErrorCode(), q.getMessage());
-                };
-            }
-            else {
-                this.addError(700, "No query given");
-            };
-
-            // <legacycode>
-            if (this.request.has("warning") &&
-                this.request.get("warning").asText().length() > 0) {
-                this.addWarning(
-                    799,
-                    this.request.get("warning").asText()
-                );
-            };
-            // </legacycode>
-
-            // <legacycode>
-            if (this.request.has("warnings")) {
-                JsonNode warnings = this.request.get("warnings");
-                for (JsonNode node : warnings)
-                    if (node.asText().length() > 0)
-                        this.addWarning(799, node.asText());
-            };
-            // </legacycode>
-
-            // Copy notifications from request
-            this.copyNotificationsFrom(this.request);
-	    
-            // virtual collections
-            if (this.request.has("collection") ||
-                // <legacycode>
-                this.request.has("collections")
-                // </legacycode>
-                ) {
-                this.setCollection(new KorapCollection(jsonString));
-            };
-
-            // No errors - go on with parsing
-            if (!this.hasErrors()) {
-                if (this.request.has("meta")) {
-                    JsonNode meta = this.request.get("meta");
-
-                    // Defined count
-                    if (meta.has("count"))
-                        this.setCount(meta.get("count").asInt());
-
-                    // Defined startIndex
-                    if (meta.has("startIndex"))
-                        this.setStartIndex(meta.get("startIndex").asInt());
-
-                    // Defined startPage
-                    if (meta.has("startPage"))
-                        this.setStartPage(meta.get("startPage").asInt());
-
-                    // Defined cutOff
-                    if (meta.has("cutOff"))
-                        this.setCutOff(meta.get("cutOff").asBoolean());
-
-                    // Defined contexts
-                    if (meta.has("context"))
-                        this.context.fromJson(meta.get("context"));
-
-                    // Defined resource count
-                    if (meta.has("timeout"))
-                        this.setTimeOut(meta.get("timeout").asLong());
-
-                    // Defined resource count
-                    if (meta.has("itemsPerResource"))
-                        this.setItemsPerResource(
-                            meta.get("itemsPerResource").asInt()
-                    );
-
-                    // Only lift a limited amount of fields from the metadata
-                    if (meta.has("fields")) {
-                        
-                        // Remove legacy default fields
-                        this.fields.clear();
-
-                        // Add fields
-                        if (meta.get("fields").isArray()) {
-                            for (JsonNode field : (JsonNode) meta.get("fields")) {
-                                this.addField(field.asText());
-                            };
-                        }
-                        else
-                            this.addField(meta.get("fields").asText());
-                    };
-                };
-            };
-        }
-
-        // Unable to parse JSON
-        catch (IOException e) {
-            this.addError(621, "Unable to parse JSON");
-        };
-    };
-
-    // Maybe accept queryWrapperStuff
-    public KorapSearch (SpanQueryWrapper sqwi) {
-        try {
-            this.query = sqwi.toQuery();
+            this.spanQuery = query.toQuery();
         }
         catch (QueryException q) {
             this.addError(q.getErrorCode(), q.getMessage());
         };
     };
     
-    public KorapSearch (SpanQuery sq) {
-        this.query = sq;
+
+    /**
+     * Construct a new Krill object,
+     * consuming a {@link SpanQuery} object.
+     *
+     * @param query The {@link SpanQuery} object.
+     */
+    public KorapSearch (SpanQuery query) {
+        this.spanQuery = query;
     };
 
-    // Empty constructor
-    public KorapSearch () { };
+
+    public KorapSearch (String jsonString) {
+        try {
+            // Parse json string
+            this.fromJson(jsonString);
+        }
+        catch (QueryException qe) {
+            this.addError(qe.getErrorCode(), qe.getMessage());
+        };
+    };
+
+    public KorapSearch (JsonNode json) {
+        try {
+            this.fromJson(json);
+        }
+        catch (QueryException qe) {
+            this.addError(qe.getErrorCode(), qe.getMessage());
+        };
+    };
+
+
+    public KorapSearch fromJson (JsonNode json) throws QueryException {
+        // Parse "query" attribute
+        if (json.has("query")) {
+            try {
+                KorapQuery kq = new KorapQuery("tokens");
+                SpanQueryWrapper qw = kq.fromJson(json.get("query"));
+
+                // Unable to process result
+                if (qw.isEmpty())
+                    this.addError(780, "This query matches everywhere");
+                else {
+                    this.spanQuery = qw.toQuery();
+                    if (qw.isOptional())
+                        this.addWarning(781, "Optionality of query is ignored");
+                    if (qw.isNegative())
+                        this.addWarning(782, "Exclusivity of query is ignored");
+                };
+                // Copy notifications from query
+                this.copyNotificationsFrom(kq);
+                kq.clearNotifications();
+            }
+            catch (QueryException q) {
+                this.addError(q.getErrorCode(), q.getMessage());
+            };
+        }
+        else
+            this.addError(700, "No query given");
+
+        // <legacycode>
+        if (json.has("warning") &&
+            json.get("warning").asText().length() > 0) {
+            this.addWarning(799, json.get("warning").asText());
+        };
+        // </legacycode>
+
+        // <legacycode>
+        if (json.has("warnings")) {
+            JsonNode warnings = json.get("warnings");
+            for (JsonNode node : warnings)
+                if (node.asText().length() > 0)
+                    this.addWarning(799, node.asText());
+        };
+        // </legacycode>
+
+        // Copy notifications from request
+        this.copyNotificationsFrom(json);
+	    
+        // virtual collections
+        if (json.has("collection")) {
+            this.setCollection(
+                new KorapCollection().fromJson(json.get("collection"))
+            );
+        }
+
+        // <legacycode>
+        else if (json.has("collections")) {
+            KorapCollection kc = new KorapCollection();
+            for (JsonNode collection : json.get("collections")) {
+                kc.fromJsonLegacy(collection);
+            };
+
+            this.setCollection(kc);
+        };
+        // </legacycode>
+
+
+        // No errors
+        if (!this.hasErrors()) {
+
+            // Parse meta section
+            if (json.has("meta")) {
+                JsonNode meta = json.get("meta");
+
+                // Defined count
+                if (meta.has("count"))
+                    this.setCount(meta.get("count").asInt());
+
+                // Defined startIndex
+                if (meta.has("startIndex"))
+                    this.setStartIndex(meta.get("startIndex").asInt());
+
+                // Defined startPage
+                if (meta.has("startPage"))
+                    this.setStartPage(meta.get("startPage").asInt());
+
+                // Defined cutOff
+                if (meta.has("cutOff"))
+                    this.setCutOff(meta.get("cutOff").asBoolean());
+
+                // Defined contexts
+                if (meta.has("context"))
+                    this.context.fromJson(meta.get("context"));
+
+                // Defined resource count
+                if (meta.has("timeout"))
+                    this.setTimeOut(meta.get("timeout").asLong());
+
+                // Defined resource count
+                if (meta.has("itemsPerResource"))
+                    this.setItemsPerResource(
+                        meta.get("itemsPerResource").asInt()
+                    );
+
+                // Defined highlights
+                if (meta.has("highlight")) {
+
+                    // Add highlights
+                    if (meta.get("highlight").isArray()) {
+                        for (JsonNode highlight : (JsonNode) meta.get("highlight")) {
+                            this.addHighlight(highlight.asInt());
+                        };
+                    }
+                    else
+                        this.addHighlight(meta.get("highlight").asInt());
+                };
+
+                // Only lift a limited amount of fields from the metadata
+                if (meta.has("fields")) {
+                        
+                    // Remove legacy default fields
+                    this.fields.clear();
+
+                    // Add fields
+                    if (meta.get("fields").isArray()) {
+                        for (JsonNode field : (JsonNode) meta.get("fields")) {
+                            this.addField(field.asText());
+                        };
+                    }
+                    else
+                        this.addField(meta.get("fields").asText());
+                };
+            };
+        };
+        return this;
+    };
+
+
+    public KorapSearch fromJson (String jsonString) throws QueryException {
+        ObjectMapper mapper = new ObjectMapper();
+        try {
+            this.request = mapper.readTree(jsonString);
+            this.fromJson(this.request);
+        }
+
+        // Unable to parse JSON
+        catch (IOException e) {
+            this.addError(621, "Unable to parse JSON");
+        };
+
+        return this;
+    };
+
 
     public long getTimeOut () {
         return this.timeout;
@@ -232,18 +302,18 @@
         this.timeout = timeout;
     };
 
-    public SpanQuery getQuery () {
-        return this.query;
+    public SpanQuery getSpanQuery () {
+        return this.spanQuery;
     };
 
     public JsonNode getRequest () {
         return this.request;
     };
 
-    public KorapSearch setQuery (SpanQueryWrapper sqwi) {
+    public KorapSearch setSpanQuery (SpanQueryWrapper sqwi) {
         // this.copyNotifications(sqwi);
         try {
-            this.query = sqwi.toQuery();
+            this.spanQuery = sqwi.toQuery();
         }
         catch (QueryException q) {
             this.addError(q.getErrorCode(), q.getMessage());
@@ -251,8 +321,8 @@
         return this;
     };
 
-    public KorapSearch setQuery (SpanQuery sq) {
-        this.query = sq;
+    public KorapSearch setSpanQuery (SpanQuery sq) {
+        this.spanQuery = sq;
         return this;
     };
 
@@ -335,21 +405,44 @@
         return this.itemsPerResource;
     };
 
-    // Add field to set of fields
+
+    // Get set of fields
+    /**
+     * Get the fields as a set
+     */
+    public HashSet<String> getFields () {
+        return this.fields;
+    };
+
+
+    /**
+     * Add a field to the set of fields to retrieve.
+     *
+     * @param field The field to retrieve.
+     * @return The {@link KorapSearch} object for chaining.
+     */
     public KorapSearch addField (String field) {
         this.fields.add(field);
         return this;
     };
 
-    // Get set of fields
-    public HashSet<String> getFields () {
-        return this.fields;
+
+    /**
+     * Add class numbers to highlight in KWIC view.
+     *
+     * @param classNumber The number of a class to highlight.
+     * @return The {@link KorapSearch} object for chaining.
+     */
+    public KorapSearch addHighlight (int classNumber) {
+        this.highlights.add(classNumber);
+        return this;
     };
 
+
     public KorapSearch setCollection (KorapCollection kc) {
         this.collection = kc;
         
-        // Copy messages from the collection
+        // Move messages from the collection
         this.copyNotificationsFrom(kc);
         kc.clearNotifications();
         return this;
@@ -361,8 +454,12 @@
         return this.collection;
     };
 
-    public KorapResult run (KorapIndex ki) {
-        if (this.query == null) {
+
+    /**
+     * Apply the KoralQuery to an index.
+     */
+    public KorapResult apply (KorapIndex ki) {
+        if (this.spanQuery == null) {
             KorapResult kr = new KorapResult();
             kr.setRequest(this.request);
 
diff --git a/src/main/java/de/ids_mannheim/korap/node/Resource.java b/src/main/java/de/ids_mannheim/korap/node/Resource.java
index f7043e7..bc70cd1 100644
--- a/src/main/java/de/ids_mannheim/korap/node/Resource.java
+++ b/src/main/java/de/ids_mannheim/korap/node/Resource.java
@@ -234,7 +234,7 @@
 		// Only return the first match per text
 		ks.setItemsPerResource(1);
 
-		return ks.run(index).toJsonString();
+		return ks.apply(index).toJsonString();
 	    };
 	    KorapResult kr = new KorapResult();
 	    kr.setNode(KorapNode.getName());
@@ -329,7 +329,7 @@
 
 	// Search index
         if (index != null) {
-            KorapResult kr = new KorapSearch(json).run(index);
+            KorapResult kr = new KorapSearch(json).apply(index);
 	    kr.setNode(KorapNode.getName());
 	    return kr.toJsonString();
 	};
diff --git a/src/test/java/de/ids_mannheim/korap/benchmark/TestBenchmarkSpans.java b/src/test/java/de/ids_mannheim/korap/benchmark/TestBenchmarkSpans.java
index 17dea33..ce3e202 100644
--- a/src/test/java/de/ids_mannheim/korap/benchmark/TestBenchmarkSpans.java
+++ b/src/test/java/de/ids_mannheim/korap/benchmark/TestBenchmarkSpans.java
@@ -46,7 +46,7 @@
 
         t1 = System.nanoTime();
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
         };
         t2 = System.nanoTime();
 
@@ -99,7 +99,7 @@
         t1 = System.nanoTime();
         double length = 0;
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
             length += kr.toJsonString().length();
         };
         t2 = System.nanoTime();
@@ -141,7 +141,7 @@
         t1 = System.nanoTime();
         double length = 0;
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
         };
         t2 = System.nanoTime();
 
@@ -182,7 +182,7 @@
 
         t1 = System.nanoTime();
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
         };
         t2 = System.nanoTime();
 
@@ -197,7 +197,7 @@
         
         t1 = System.nanoTime();
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
         };
         t2 = System.nanoTime();
 
@@ -212,7 +212,7 @@
 
         t1 = System.nanoTime();
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
         };
         t2 = System.nanoTime();
 
@@ -329,7 +329,7 @@
 
         t1 = System.nanoTime();
         for (int i = 1; i <= rounds; i++) {
-            kr = new KorapSearch(json).run(ki);
+            kr = new KorapSearch(json).apply(ki);
         };
         t2 = System.nanoTime();
 
diff --git a/src/test/java/de/ids_mannheim/korap/highlight/TestHighlight.java b/src/test/java/de/ids_mannheim/korap/highlight/TestHighlight.java
index 7e47153..0118e1b 100644
--- a/src/test/java/de/ids_mannheim/korap/highlight/TestHighlight.java
+++ b/src/test/java/de/ids_mannheim/korap/highlight/TestHighlight.java
@@ -282,8 +282,8 @@
         String json = getString(getClass().getResource("/queries/bugs/greater_highlights_15.jsonld").getFile());
 	
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
-        assertEquals(kr.getQuery(),"{15: tokens:s:Alphabet}");
+        KorapResult kr = ks.apply(ki);
+        assertEquals(kr.getSerialQuery(),"{15: tokens:s:Alphabet}");
         assertEquals(kr.getTotalResults(),7);
         assertEquals(kr.getStartIndex(),0);
         assertEquals(kr.getMatch(0).getSnippetBrackets(),"... 2. Herkunft Die aus dem proto-semitischen [{15:Alphabet}] stammende Urform des Buchstaben ist wahrscheinlich ...");
@@ -293,8 +293,8 @@
 
         // 16
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
-        assertEquals(kr.getQuery(),"{16: tokens:s:Alphabet}");
+        kr = ks.apply(ki);
+        assertEquals(kr.getSerialQuery(),"{16: tokens:s:Alphabet}");
         assertEquals(kr.getTotalResults(),7);
         assertEquals(kr.getStartIndex(),0);
         assertEquals(kr.getMatch(0).getSnippetBrackets(),"... 2. Herkunft Die aus dem proto-semitischen [{16:Alphabet}] stammende Urform des Buchstaben ist wahrscheinlich ...");
@@ -304,8 +304,8 @@
         json = getString(getClass().getResource("/queries/bugs/greater_highlights_127.jsonld").getFile());
 	
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
-        assertEquals(kr.getQuery(),"{127: tokens:s:Alphabet}");
+        kr = ks.apply(ki);
+        assertEquals(kr.getSerialQuery(),"{127: tokens:s:Alphabet}");
         assertEquals(kr.getTotalResults(),7);
         assertEquals(kr.getStartIndex(),0);
         assertEquals(kr.getMatch(0).getSnippetBrackets(),"... 2. Herkunft Die aus dem proto-semitischen [{127:Alphabet}] stammende Urform des Buchstaben ist wahrscheinlich ...");
@@ -315,8 +315,8 @@
         json = getString(getClass().getResource("/queries/bugs/greater_highlights_255.jsonld").getFile());
 
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
-        assertEquals(kr.getQuery(),"{255: tokens:s:Alphabet}");
+        kr = ks.apply(ki);
+        assertEquals(kr.getSerialQuery(),"{255: tokens:s:Alphabet}");
         assertEquals(kr.getTotalResults(),7);
         assertEquals(kr.getStartIndex(),0);
         assertEquals(kr.getMatch(0).getSnippetBrackets(),"... 2. Herkunft Die aus dem proto-semitischen [Alphabet] stammende Urform des Buchstaben ist wahrscheinlich ...");
@@ -326,7 +326,7 @@
         json = getString(getClass().getResource("/queries/bugs/greater_highlights_300.jsonld").getFile());
 
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(709, kr.getError(0).getCode());
         assertEquals("Valid class numbers exceeded", kr.getError(0).getMessage());
 
diff --git a/src/test/java/de/ids_mannheim/korap/index/TestFieldDocument.java b/src/test/java/de/ids_mannheim/korap/index/TestFieldDocument.java
index df3c6f3..04ea612 100644
--- a/src/test/java/de/ids_mannheim/korap/index/TestFieldDocument.java
+++ b/src/test/java/de/ids_mannheim/korap/index/TestFieldDocument.java
@@ -198,7 +198,7 @@
 	ks.context.left.setCharacter(true).setLength(6);
 	ks.context.right.setToken(true).setLength(6);
 
-	assertEquals("... okal. [Der Buchstabe A hat in {1:deutschen Texten} eine durchschnittliche Häufigkeit von 6,51 %.] Er ist damit der sechsthäufigste Buchstabe ...", ks.run(ki).getMatch(0).getSnippetBrackets());
+	assertEquals("... okal. [Der Buchstabe A hat in {1:deutschen Texten} eine durchschnittliche Häufigkeit von 6,51 %.] Er ist damit der sechsthäufigste Buchstabe ...", ks.apply(ki).getMatch(0).getSnippetBrackets());
     };
 
     @Test
diff --git a/src/test/java/de/ids_mannheim/korap/index/TestMatchIndex.java b/src/test/java/de/ids_mannheim/korap/index/TestMatchIndex.java
index c3ad7c7..90c88f3 100644
--- a/src/test/java/de/ids_mannheim/korap/index/TestMatchIndex.java
+++ b/src/test/java/de/ids_mannheim/korap/index/TestMatchIndex.java
@@ -388,7 +388,7 @@
         );
 
         kr = ki.search(sq, (short) 10);
-        assertEquals(kr.getQuery(), "spanContain({2: <base:s />}, {3: base:s:b})");
+        assertEquals(kr.getSerialQuery(), "spanContain({2: <base:s />}, {3: base:s:b})");
         assertEquals(kr.getMatch(0).getSnippetBrackets(), "a[{2:{3:b}cab}]cabac");
 
         sq = new SpanFocusQuery(
@@ -399,7 +399,7 @@
         );
 
         kr = ki.search(sq, (short) 10);
-        assertEquals(kr.getQuery(), "focus(3: spanContain({2: <base:s />}, {3: base:s:b}))");
+        assertEquals(kr.getSerialQuery(), "focus(3: spanContain({2: <base:s />}, {3: base:s:b}))");
         assertEquals(kr.getMatch(0).getSnippetBrackets(), "a[{3:b}]cabcab ...");
     };
 
@@ -491,7 +491,7 @@
         //        System.err.println(kr.getOverview());
 
 
-        assertEquals(kr.getQuery(), "spanContain(<base:p />, focus(3: spanContain({2: <base:s />}, {3: base:s:a})))");
+        assertEquals(kr.getSerialQuery(), "spanContain(<base:p />, focus(3: spanContain({2: <base:s />}, {3: base:s:a})))");
         assertEquals(12, kr.getTotalResults());
         assertEquals("[a{2:bc{3:a}b}cabac]", kr.getMatch(0).getSnippetBrackets());
         assertEquals("[ab{2:c{3:a}bcab}ac]", kr.getMatch(1).getSnippetBrackets());
diff --git a/src/test/java/de/ids_mannheim/korap/index/TestRealIndex.java b/src/test/java/de/ids_mannheim/korap/index/TestRealIndex.java
index 070665e..7d0fc46 100644
--- a/src/test/java/de/ids_mannheim/korap/index/TestRealIndex.java
+++ b/src/test/java/de/ids_mannheim/korap/index/TestRealIndex.java
@@ -38,7 +38,7 @@
 	KorapQuery kq = new KorapQuery("tokens");
 	ks = new KorapSearch(kq.within(kq.tag("base/s:s"), kq.seq(kq.re("s:.*")).append(kq._(kq.re("s:.*")))).toQuery());
 	ks.setTimeOut(10000);
-	kr = ks.run(ki);
+	kr = ks.apply(ki);
 	System.err.println(kr.toJsonString());
 	assertEquals(8, kr.getTotalResults());
     };
diff --git a/src/test/java/de/ids_mannheim/korap/index/TestRegexWildcardIndex.java b/src/test/java/de/ids_mannheim/korap/index/TestRegexWildcardIndex.java
index ef34315..20273bc 100644
--- a/src/test/java/de/ids_mannheim/korap/index/TestRegexWildcardIndex.java
+++ b/src/test/java/de/ids_mannheim/korap/index/TestRegexWildcardIndex.java
@@ -61,22 +61,22 @@
 	assertEquals("[affe] afffe ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("affe [afffe] baum ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:baum.*").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:baum.*").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... afffe [baum] baumgarten ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... baum [baumgarten] steingarten ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:.....?garten").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:.....?garten").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... baum [baumgarten] steingarten ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... baumgarten [steingarten] franz ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:ha.s").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:ha.s").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... franz [hans] haus ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... hans [haus] efeu ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:.*ff.*").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:.*ff.*").toQuery()));
 	assertEquals((long) 3, kr.getTotalResults());
 	assertEquals("[affe] afffe ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("affe [afffe] baum ...", kr.getMatch(1).getSnippetBrackets());
@@ -118,25 +118,25 @@
 	assertEquals("[affe] afffe ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("affe [afffe] baum ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").wc("s:baum.*").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").wc("s:baum.*").toQuery()));
 	assertEquals((long) 0, kr.getTotalResults());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").wc("s:baum*").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").wc("s:baum*").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... afffe [baum] baumgarten ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... baum [baumgarten] steingarten ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").wc("s:*garten").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").wc("s:*garten").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... baum [baumgarten] steingarten ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... baumgarten [steingarten] franz ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").wc("s:ha?s").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").wc("s:ha?s").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... franz [hans] haus ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... hans [haus] efeu ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").wc("s:?ff?").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").wc("s:?ff?").toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("[affe] afffe ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... efeu [effe]", kr.getMatch(1).getSnippetBrackets());
@@ -177,30 +177,30 @@
 	assertEquals("[AfFe] aFfFE ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("AfFe [aFfFE] Baum ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:Af.*e").toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:Af.*e").toQuery()));
 	assertEquals((long) 1, kr.getTotalResults());
 	assertEquals("[AfFe] aFfFE ...", kr.getMatch(0).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:baum.*", true).toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:baum.*", true).toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... aFfFE [Baum] Baumgarten ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... Baum [Baumgarten] SteinGarten ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:.*garten", true).toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:.*garten", true).toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... Baum [Baumgarten] SteinGarten ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... Baumgarten [SteinGarten] franZ ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:.*garten", false).toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:.*garten", false).toQuery()));
 	assertEquals((long) 1, kr.getTotalResults());
 	assertEquals("... Baum [Baumgarten] SteinGarten ...", kr.getMatch(0).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:ha.s", true).toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:ha.s", true).toQuery()));
 	assertEquals((long) 2, kr.getTotalResults());
 	assertEquals("... franZ [HaNs] Haus ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("... HaNs [Haus] Efeu ...", kr.getMatch(1).getSnippetBrackets());
 
-	kr = ki.search(ks.setQuery(new KorapQuery("base").re("s:.*f*e", true).toQuery()));
+	kr = ki.search(ks.setSpanQuery(new KorapQuery("base").re("s:.*f*e", true).toQuery()));
 	assertEquals((long) 3, kr.getTotalResults());
 	assertEquals("[AfFe] aFfFE ...", kr.getMatch(0).getSnippetBrackets());
 	assertEquals("AfFe [aFfFE] Baum ...", kr.getMatch(1).getSnippetBrackets());
diff --git a/src/test/java/de/ids_mannheim/korap/index/TestWPDIndex.java b/src/test/java/de/ids_mannheim/korap/index/TestWPDIndex.java
index 5d8b5d2..6711653 100644
--- a/src/test/java/de/ids_mannheim/korap/index/TestWPDIndex.java
+++ b/src/test/java/de/ids_mannheim/korap/index/TestWPDIndex.java
@@ -71,18 +71,18 @@
 		// ordered
 		sq = createDistanceQuery("s:Wir", "s:kommen", 1, 1, true,false);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 8);
 
 		// unordered
 		sq = createDistanceQuery("s:Wir", "s:kommen", 1, 1, false,false);				
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 11);
 		
 		sq = createDistanceQuery("s:kommen", "s:Wir", 1, 1, false,false);				
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 11);
 		//System.out.println(kr.getTotalResults());
 		//for (KorapMatch km : kr.getMatches()){
@@ -98,20 +98,20 @@
 
 		SpanQuery q = new SpanTermQuery(new Term("tokens","s:Wir"));
 		ks = new KorapSearch(q);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 1907);
 		
 		SpanDistanceQuery sq;
 		// ordered
 		sq = createDistanceQuery("s:Wir", "s:kommen", 1, 1, true, true);				
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 1899);
 		
 		// unordered
 		sq = createDistanceQuery("s:Wir", "s:kommen", 1, 1, false, true);				
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 1896);	
 	}
 	
@@ -122,13 +122,13 @@
 		SpanDistanceQuery sq = createElementDistanceQuery("s","s:weg", "s:fahren", 
 				0, 1, true, false);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);		
+		kr = ks.apply(ki);		
 		assertEquals(kr.getTotalResults(), 3);
 		
 		// unordered
 		sq = createElementDistanceQuery("s","s:weg", "s:fahren", 0, 1, false,false);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 5);
 		
 		// only 0
@@ -145,7 +145,7 @@
 		// only 1
 		sq = createElementDistanceQuery("s","s:weg", "s:fahren", 1, 1, false,false);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 3);		
 	}
 	
@@ -154,7 +154,7 @@
 	public void testCase4() throws IOException{
 		SpanDistanceQuery sq = createElementDistanceQuery("s","s:weg", "s:fahren", 1, 1, false, true);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 979);
 		//0.8s
 		
@@ -164,7 +164,7 @@
 		KorapCollection kc = new KorapCollection();	
 		kc.filter(bf);
 		ks.setCollection(kc);
-		kr = ks.run(ki);		
+		kr = ks.apply(ki);		
 		assertEquals(1094,kr.getMatch(0).getStartPos());
 		assertEquals(451,kr.getMatch(1).getEndPos());		
 	}
@@ -175,18 +175,18 @@
 		SpanQuery sq;
 		sq = new SpanRepetitionQuery(new SpanTermQuery(new Term("tokens","mate/p:ADJA")),1,2, true);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 4116416);
 		//0.9s
 		
 		sq = new SpanRepetitionQuery(new SpanTermQuery(new Term("tokens","mate/p:ADJA")),1,1, true);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 3879671);
 		
 		sq = new SpanRepetitionQuery(new SpanTermQuery(new Term("tokens","mate/p:ADJA")),2,2, true);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 236745);
 		//0.65s
 	}
@@ -199,14 +199,14 @@
         		new SpanRepetitionQuery(new SpanTermQuery(new Term("tokens","mate/p:ADJA")),2,2, true)
     		);
 		ks = new KorapSearch(sq);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 30223);
 		// 1.1s
 		
 		SpanQuery sq2 = new SpanNextQuery(sq,
 				new SpanTermQuery(new Term("tokens", "tt/p:NN")));
 		ks = new KorapSearch(sq2);
-		kr = ks.run(ki);
+		kr = ks.apply(ki);
 		assertEquals(kr.getTotalResults(), 26607);
 		// 1.1s
 	}
diff --git a/src/test/java/de/ids_mannheim/korap/query/TestTemporaryQueryLimitations.java b/src/test/java/de/ids_mannheim/korap/query/TestTemporaryQueryLimitations.java
index 33a776a..73ada81 100644
--- a/src/test/java/de/ids_mannheim/korap/query/TestTemporaryQueryLimitations.java
+++ b/src/test/java/de/ids_mannheim/korap/query/TestTemporaryQueryLimitations.java
@@ -53,8 +53,8 @@
 	json = getString(getClass().getResource("/queries/bugs/cosmas_classrefcheck.jsonld").getFile());
 	
 	KorapSearch ks = new KorapSearch(json);
-	KorapResult kr = ks.run(ki);
-	assertEquals(kr.getQuery(),"focus(130: {131: spanContain({129: <tokens:s />}, {130: tokens:s:wegen})})");
+	KorapResult kr = ks.apply(ki);
+	assertEquals(kr.getSerialQuery(),"focus(130: {131: spanContain({129: <tokens:s />}, {130: tokens:s:wegen})})");
 	assertEquals(kr.getTotalResults(),0);
 	assertEquals(kr.getStartIndex(),0);
 
diff --git a/src/test/java/de/ids_mannheim/korap/search/TestKorapResult.java b/src/test/java/de/ids_mannheim/korap/search/TestKorapResult.java
index f07b184..80776b5 100644
--- a/src/test/java/de/ids_mannheim/korap/search/TestKorapResult.java
+++ b/src/test/java/de/ids_mannheim/korap/search/TestKorapResult.java
@@ -62,7 +62,7 @@
 	ObjectMapper mapper = new ObjectMapper();
 	JsonNode res = mapper.readTree(kr.toJsonString());
 	assertEquals(7, res.at("/totalResults").asInt());
-	assertEquals("spanOr([{1: base:s:a}, {2: base:s:b}])", res.at("/query").asText());
+	assertEquals("spanOr([{1: base:s:a}, {2: base:s:b}])", res.at("/serialQuery").asText());
 	assertEquals(0, res.at("/startIndex").asInt());
 	assertEquals(25, res.at("/itemsPerPage").asInt());
 	assertEquals("token", res.at("/context/left/0").asText());
@@ -112,7 +112,7 @@
 	String json = getString(getClass().getResource("/queries/bugs/optionality_warning.jsonld").getFile());
 	KorapSearch ks = new KorapSearch(json);
 
-	KorapResult kr = ks.run(ki);
+	KorapResult kr = ks.apply(ki);
 	assertEquals((long) 2, kr.getTotalResults());
 
 	ObjectMapper mapper = new ObjectMapper();
@@ -154,14 +154,14 @@
 
 	String json = getString(getClass().getResource("/queries/bsp-result-check.jsonld").getFile());
 	KorapSearch ks = new KorapSearch(json);
-	KorapResult kr = ks.run(ki);
+	KorapResult kr = ks.apply(ki);
 	assertEquals((long) 7, kr.getTotalResults());
 
 	ObjectMapper mapper = new ObjectMapper();
 	JsonNode res = mapper.readTree(kr.toJsonString());
 
 	assertEquals(7, res.at("/totalResults").asInt());
-	assertEquals("spanOr([tokens:s:a, tokens:s:b])", res.at("/query").asText());
+	assertEquals("spanOr([tokens:s:a, tokens:s:b])", res.at("/serialQuery").asText());
 	assertEquals(5, res.at("/itemsPerPage").asInt());
 	assertEquals(0, res.at("/startIndex").asInt());
 	assertEquals(1, res.at("/request/meta/startPage").asInt());
@@ -228,7 +228,7 @@
 	ObjectMapper mapper = new ObjectMapper();
 	JsonNode res = mapper.readTree(kr.toTokenListJsonString());
 	assertEquals(3, res.at("/totalResults").asInt());
-	assertEquals("spanNext(base:s:a, base:s:b)", res.at("/query").asText());
+	assertEquals("spanNext(base:s:a, base:s:b)", res.at("/serialQuery").asText());
 	assertEquals(0, res.at("/startIndex").asInt());
 	assertEquals(25, res.at("/itemsPerPage").asInt());
 
diff --git a/src/test/java/de/ids_mannheim/korap/search/TestKorapSearch.java b/src/test/java/de/ids_mannheim/korap/search/TestKorapSearch.java
index b5f3dcf..a13f0bc 100644
--- a/src/test/java/de/ids_mannheim/korap/search/TestKorapSearch.java
+++ b/src/test/java/de/ids_mannheim/korap/search/TestKorapSearch.java
@@ -70,7 +70,7 @@
             new KorapQuery("field1").seg("a").with("b")
         );
         // query
-        assertEquals(ks.getQuery().toString(), "spanSegment(field1:a, field1:b)");
+        assertEquals(ks.getSpanQuery().toString(), "spanSegment(field1:a, field1:b)");
     };
 
 
@@ -103,7 +103,7 @@
         ks.setStartIndex(5);
         ks.context.left.setLength(1);
         ks.context.right.setLength(1);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 6);
         assertEquals(
             kr.getMatch(0).getSnippetBrackets(),
@@ -136,7 +136,7 @@
         );
 
         KorapSearch ks = new KorapSearch(json);
-		KorapResult kr = ks.run(ki);
+		KorapResult kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 66);
         assertEquals(5, kr.getItemsPerPage());
         assertEquals(5, kr.getStartIndex());
@@ -178,14 +178,14 @@
         );
 
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 1);
 
         ks = new KorapSearch(json);
         // Ignore the collection part of the query!
         ks.setCollection(new KorapCollection());
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 5);
 
@@ -194,14 +194,14 @@
         );
 
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 1);
 
         json = getString(
             getClass().getResource("/queries/metaquery6.jsonld").getFile()
         );
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 1);
     };
 
@@ -225,7 +225,7 @@
             );
         };
         ki.commit();
-        KorapResult kr = new KorapSearch("{ query").run(ki);
+        KorapResult kr = new KorapSearch("{ query").apply(ki);
         assertEquals(kr.getTotalResults(), 0);
         assertEquals(kr.getError(0).getMessage(), "Unable to parse JSON");
     };
@@ -254,7 +254,7 @@
             getClass().getResource("/queries/bsp-fail1.jsonld").getFile()
         );
 
-        KorapResult kr = new KorapSearch(json).run(ki);
+        KorapResult kr = new KorapSearch(json).apply(ki);
         assertEquals(0, kr.getStartIndex());
         assertEquals(kr.getTotalResults(), 0);
         assertEquals(25, kr.getItemsPerPage());
@@ -284,7 +284,7 @@
             getClass().getResource("/queries/bsp-fail2.jsonld").getFile()
         );
 
-        KorapResult kr = new KorapSearch(json).run(ki);
+        KorapResult kr = new KorapSearch(json).apply(ki);
         assertEquals(50, kr.getItemsPerPage());
         assertEquals(49950, kr.getStartIndex());
         assertEquals(kr.getTotalResults(), 0);
@@ -315,7 +315,7 @@
         );
 
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 10);
         assertEquals("A bzw. a ist der erste Buchstabe des" +
                      " lateinischen [Alphabets] und ein Vokal." +
@@ -325,7 +325,7 @@
 
         ks.setCount(5);
         ks.setStartPage(2);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 10);
         assertEquals(5, kr.getStartIndex());
         assertEquals(5, kr.getItemsPerPage());
@@ -334,7 +334,7 @@
             getClass().getResource("/queries/bsp-context-2.jsonld").getFile()
         );
 
-        kr = new KorapSearch(json).run(ki);
+        kr = new KorapSearch(json).apply(ki);
         assertEquals(kr.getTotalResults(), -1);
         assertEquals("... lls seit den Griechen beibehalten worden." +
                      " 3. Bedeutungen in der Biologie steht A für"+
@@ -374,7 +374,7 @@
         );
 
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 10);
         assertEquals(5, kr.getStartIndex());
         assertEquals(5, kr.getItemsPerPage());
@@ -383,7 +383,7 @@
             getClass().getResource("/queries/bsp-cutoff.jsonld").getFile()
         );
         ks = ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), -1);
         assertEquals(2, kr.getStartIndex());
         assertEquals(2, kr.getItemsPerPage());
@@ -422,7 +422,7 @@
         );
 
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 10);
         assertEquals(0, kr.getStartIndex());
         assertEquals(20, kr.getItemsPerPage());
@@ -437,7 +437,7 @@
         ks = new KorapSearch(json);
         ks.setItemsPerResource(1);
 
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals("WPD_AAA.00001", kr.getMatch(0).getDocID());
         assertEquals("WPD_AAA.00002", kr.getMatch(1).getDocID());
@@ -450,7 +450,7 @@
         ks = new KorapSearch(json);
         ks.setItemsPerResource(2);
 
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals("WPD_AAA.00001", kr.getMatch(0).getDocID());
         assertEquals("WPD_AAA.00001", kr.getMatch(1).getDocID());
@@ -467,7 +467,7 @@
         ks.setStartIndex(1);
         ks.setCount(1);
 
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 	
         assertEquals("WPD_AAA.00002", kr.getMatch(0).getDocID());
 
@@ -517,7 +517,7 @@
         kc.setIndex(ki);
         ks.setCollection(kc);
 
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 2);
         assertEquals(0, kr.getStartIndex());
@@ -604,7 +604,7 @@
             seg("mate/m:case:nom").
             with("mate/m:number:pl")
         );
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 148);
         assertEquals(0, kr.getStartIndex());
@@ -695,7 +695,7 @@
             seg("mate/m:case:nom").
             with("mate/m:number:sg")
         );
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 6);
         assertEquals(0, kr.getStartIndex());
@@ -731,9 +731,9 @@
             )
         );
 
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(
-            kr.getQuery(),
+            kr.getSerialQuery(),
             "focus(1: spanContain(<tokens:base/s:s />, {1: tokens:s:Leben}))"
         );
         assertEquals(
@@ -750,9 +750,9 @@
             )
         );
 
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(
-            kr.getQuery(),
+            kr.getSerialQuery(),
             "focus(129: spanContain(<tokens:base/s:s />, {129: tokens:s:Leben}))"
         );
         assertEquals(
@@ -762,9 +762,9 @@
         );
 
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
         assertEquals(
-            kr.getQuery(),
+            kr.getSerialQuery(),
             "focus(129: spanElementDistance({129: tokens:s:Namen}, " +
             "{129: tokens:s:Leben}, [(base/s:s[0:1], notOrdered, notExcluded)]))"
         );
@@ -807,9 +807,9 @@
         );
 	
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(
-            kr.getQuery(),
+            kr.getSerialQuery(),
             "{4: spanNext({1: spanNext({2: tokens:s:ins}, "+
             "{3: tokens:s:Leben})}, tokens:s:gerufen)}"
         );
@@ -852,7 +852,7 @@
         );
 	
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
 
         ObjectMapper mapper = new ObjectMapper();
         JsonNode res = mapper.readTree(kr.toTokenListJsonString());
@@ -861,7 +861,7 @@
         assertEquals(
             "{4: spanNext({1: spanNext({2: tokens:s:ins}, " +
             "{3: tokens:s:Leben})}, tokens:s:gerufen)}",
-            res.at("/query").asText());
+            res.at("/serialQuery").asText());
         assertEquals(0, res.at("/startIndex").asInt());
         assertEquals(25, res.at("/itemsPerPage").asInt());
 
@@ -918,10 +918,10 @@
         ks.setCollection(kc);
         assertEquals(1, kc.numberOf("documents"));
 
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         
         assertEquals(
-            kr.getQuery(),
+            kr.getSerialQuery(),
             "spanOr([SpanMultiTermQueryWrapper(tokens:/tt/p:N.*/), " +
             "spanNext(spanRepetition(SpanMultiTermQueryWrapper"+
             "(tokens:/tt/p:A.*/){1,3}), " +
@@ -986,7 +986,7 @@
         );
 	
         KorapSearch ks = new KorapSearch(json);
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(kr.getTotalResults(), 276);
         assertEquals(0, kr.getStartIndex());
         assertEquals(10, kr.getItemsPerPage());
@@ -998,7 +998,7 @@
         );
 	
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 147);
         assertEquals("WPD_AAA.00001", kr.getMatch(0).getDocID());
@@ -1012,7 +1012,7 @@
         );
 	
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 28);
         assertEquals("WPD_AAA.00002", kr.getMatch(0).getDocID());
@@ -1026,7 +1026,7 @@
         );
 	
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals(kr.getTotalResults(), 0);
         assertEquals(0, kr.getStartIndex());
@@ -1039,7 +1039,7 @@
         );
 	
         ks = new KorapSearch(json);
-        kr = ks.run(ki);
+        kr = ks.apply(ki);
 
         assertEquals("filter with QueryWrapperFilter("+
                      "+(ID:WPD_AAA.00003 (+tokens:s:die"+
@@ -1085,7 +1085,7 @@
         sc.left.setLength((short) 10);
         sc.right.setLength((short) 10);
         
-        KorapResult kr = ks.run(ki);
+        KorapResult kr = ks.apply(ki);
         assertEquals(
             kr.getMatch(1).getSnippetBrackets(),
             "... dezimalen [Wert] 65 sowohl ..."
@@ -1101,7 +1101,7 @@
             getFile()
         );
 
-        kr = new KorapSearch(json).run(ki);
+        kr = new KorapSearch(json).apply(ki);
         assertEquals(
             kr.getMatch(0).getSnippetBrackets(),
             "steht a für den dezimalen [Wert] 97 sowohl im ASCII-"+
@@ -1150,7 +1150,7 @@
             getFile()
         );
 
-        KorapResult kr = new KorapSearch(json).run(ki);
+        KorapResult kr = new KorapSearch(json).apply(ki);
 
         assertEquals(
             kr.getError(0).getMessage(),
@@ -1183,7 +1183,7 @@
             getFile()
         );
 	
-		KorapResult kr = new KorapSearch(json).run(ki);				
+		KorapResult kr = new KorapSearch(json).apply(ki);				
 		assertEquals("... Buchstabe des Alphabetes. In Dänemark ist " +
                      "[der alte Digraph Aa durch Å] ersetzt worden, " +
                      "in Eigennamen und Ortsnamen ...",
@@ -1199,7 +1199,7 @@
             getFile()
         );
 	
-		kr = new KorapSearch(json).run(ki);
+		kr = new KorapSearch(json).apply(ki);
 		
 		assertEquals("... Buchstabe des Alphabetes. In Dänemark ist " +
                      "[der alte Digraph Aa durch Å] ersetzt worden, " +
@@ -1229,7 +1229,7 @@
             getFile()
         );
 	
-		kr = new KorapSearch(json).run(ki);
+		kr = new KorapSearch(json).apply(ki);
 		
 		assertEquals("... Buchstabe des Alphabetes. In Dänemark ist " +
                      "[der alte Digraph Aa durch Å] ersetzt worden, " +
@@ -1245,7 +1245,7 @@
             getFile()
         );
 	
-		kr = new KorapSearch(json).run(ki);	
+		kr = new KorapSearch(json).apply(ki);	
 		assertEquals("... Buchstabe des Alphabetes. In Dänemark ist " +
                      "[der alte Digraph Aa durch Å] ersetzt worden, " +
                      "in Eigennamen und Ortsnamen ...",
diff --git a/src/test/java/de/ids_mannheim/korap/search/TestMetaFields.java b/src/test/java/de/ids_mannheim/korap/search/TestMetaFields.java
index 387b2cb..4074176 100644
--- a/src/test/java/de/ids_mannheim/korap/search/TestMetaFields.java
+++ b/src/test/java/de/ids_mannheim/korap/search/TestMetaFields.java
@@ -33,68 +33,69 @@
     @Test
     public void searchMetaFields () throws IOException {
 
-	// Construct index
-	KorapIndex ki = new KorapIndex();
-	// Indexing test files
-	for (String i : new String[] {"00001",
-				      "00002"}) {
-	    ki.addDocFile(
-	        getClass().getResource("/wiki/" + i + ".json.gz").getFile(), true
+        // Construct index
+        KorapIndex ki = new KorapIndex();
+        // Indexing test files
+        for (String i : new String[] {"00001",
+                                      "00002"}) {
+            ki.addDocFile(
+                getClass().getResource("/wiki/" + i + ".json.gz").getFile(), true
             );
-	};
-	ki.commit();
+        };
+        ki.commit();
 
-	String json = getString(
+        String jsonString = getString(
             getClass().getResource("/queries/metas/fields.jsonld").getFile()
         );
 	
-	KorapSearch ks = new KorapSearch(json);
-	KorapResult kr = ks.run(ki);
-	assertEquals((long) 17, kr.getTotalResults());
-	assertEquals(0, kr.getStartIndex());
-	assertEquals(9, kr.getItemsPerPage());
+        KorapSearch ks = new KorapSearch(jsonString);
 
-	ObjectMapper mapper = new ObjectMapper();
-	JsonNode res = mapper.readTree(kr.toJsonString());
-	assertEquals(0, res.at("/matches/0/UID").asInt());
-	assertEquals("WPD", res.at("/matches/0/corpusID").asText());
-	assertEquals("", res.at("/matches/0/docID").asText());
-	assertEquals("", res.at("/matches/0/textSigle").asText());
-	assertEquals("", res.at("/matches/0/ID").asText());
-	assertEquals("", res.at("/matches/0/author").asText());
-	assertEquals("", res.at("/matches/0/title").asText());
-	assertEquals("", res.at("/matches/0/subTitle").asText());
-	assertEquals("", res.at("/matches/0/textClass").asText());
-	assertEquals("", res.at("/matches/0/pubPlace").asText());
-	assertEquals("", res.at("/matches/0/pubDate").asText());
-	assertEquals("", res.at("/matches/0/foundries").asText());
-	assertEquals("", res.at("/matches/0/layerInfo").asText());
-	assertEquals("", res.at("/matches/0/tokenization").asText());
+        KorapResult kr = ks.apply(ki);
+        assertEquals((long) 17, kr.getTotalResults());
+        assertEquals(0, kr.getStartIndex());
+        assertEquals(9, kr.getItemsPerPage());
+        
+        ObjectMapper mapper = new ObjectMapper();
+        JsonNode res = mapper.readTree(kr.toJsonString());
+        assertEquals(0, res.at("/matches/0/UID").asInt());
+        assertEquals("WPD", res.at("/matches/0/corpusID").asText());
+        assertEquals("", res.at("/matches/0/docID").asText());
+        assertEquals("", res.at("/matches/0/textSigle").asText());
+        assertEquals("", res.at("/matches/0/ID").asText());
+        assertEquals("", res.at("/matches/0/author").asText());
+        assertEquals("", res.at("/matches/0/title").asText());
+        assertEquals("", res.at("/matches/0/subTitle").asText());
+        assertEquals("", res.at("/matches/0/textClass").asText());
+        assertEquals("", res.at("/matches/0/pubPlace").asText());
+        assertEquals("", res.at("/matches/0/pubDate").asText());
+        assertEquals("", res.at("/matches/0/foundries").asText());
+        assertEquals("", res.at("/matches/0/layerInfo").asText());
+        assertEquals("", res.at("/matches/0/tokenization").asText());
 
-	json = getString(
+        jsonString = getString(
             getClass().getResource("/queries/metas/fields_2.jsonld").getFile()
         );
-	ks = new KorapSearch(json);
-	kr = ks.run(ki);
-	assertEquals((long) 17, kr.getTotalResults());
-	assertEquals(0, kr.getStartIndex());
-	assertEquals(2, kr.getItemsPerPage());
-	
-	mapper = new ObjectMapper();
-	res = mapper.readTree(kr.toJsonString());
-	assertEquals(0, res.at("/matches/0/UID").asInt());
-	assertEquals("", res.at("/matches/0/corpusID").asText());
-	assertEquals("Ruru,Jens.Ol,Aglarech", res.at("/matches/0/author").asText());
-	assertEquals("A", res.at("/matches/0/title").asText());
-	assertEquals("WPD_AAA.00001", res.at("/matches/0/docID").asText());
-	assertEquals("", res.at("/matches/0/textSigle").asText());
-	assertEquals("match-WPD_AAA.00001-p6-7", res.at("/matches/0/ID").asText());
-	assertEquals("", res.at("/matches/0/subTitle").asText());
-	assertEquals("", res.at("/matches/0/textClass").asText());
-	assertEquals("", res.at("/matches/0/pubPlace").asText());
-	assertEquals("", res.at("/matches/0/pubDate").asText());
-	assertEquals("", res.at("/matches/0/foundries").asText());
-	assertEquals("", res.at("/matches/0/layerInfo").asText());
-	assertEquals("", res.at("/matches/0/tokenization").asText());
+        ks = new KorapSearch(jsonString);
+        kr = ks.apply(ki);
+        assertEquals((long) 17, kr.getTotalResults());
+        assertEquals(0, kr.getStartIndex());
+        assertEquals(2, kr.getItemsPerPage());
+        
+        mapper = new ObjectMapper();
+        res = mapper.readTree(kr.toJsonString());
+        assertEquals(0, res.at("/matches/0/UID").asInt());
+        assertEquals("", res.at("/matches/0/corpusID").asText());
+        assertEquals("Ruru,Jens.Ol,Aglarech", res.at("/matches/0/author").asText());
+        assertEquals("A", res.at("/matches/0/title").asText());
+        assertEquals("WPD_AAA.00001", res.at("/matches/0/docID").asText());
+        assertEquals("", res.at("/matches/0/textSigle").asText());
+        assertEquals("match-WPD_AAA.00001-p6-7", res.at("/matches/0/ID").asText());
+        assertEquals("", res.at("/matches/0/subTitle").asText());
+        assertEquals("", res.at("/matches/0/textClass").asText());
+        assertEquals("", res.at("/matches/0/pubPlace").asText());
+        assertEquals("", res.at("/matches/0/pubDate").asText());
+        assertEquals("", res.at("/matches/0/foundries").asText());
+        assertEquals("", res.at("/matches/0/layerInfo").asText());
+        assertEquals("", res.at("/matches/0/tokenization").asText());
     };
 };