added ability to set more URL variables and fixed bug removing FLGINT…

src/main/java/org/reactome/web/pwp/client/manager/state/State.java

@@ -51,10 +51,12 @@ public interface StateLoadedHandler {
 
     private String flag;
     private boolean flagIncludeInteractors = false;
+    private Map<String, String> extraParams; //to enable extensions of Reactome project to add extra url parameters
 
     public State(Token token, final StateLoadedHandler handler) {
         List<String> toLoad = token.getToLoad();
         final Map<StateKey, String> parameters = token.getParameters();
+        this.extraParams = token.getExtraParams();
         ContentClient.query(toLoad, new ContentClientHandler.ObjectMapLoaded() {
             private String token;
             private String filter;
@@ -131,6 +133,7 @@ public State(State state) {
         this.analysisStatus = state.analysisStatus;
         this.flag = state.flag;
         this.flagIncludeInteractors = state.flagIncludeInteractors;
+        this.extraParams = state.extraParams;
     }
 
     void doConsistencyCheck(final StateLoadedHandler handler) {
@@ -336,12 +339,19 @@ public String toString() {
             }
 //            addDelimiter=true;
         }
+        if(extraParams != null) {
+        	extraParams.forEach((k,v) -> {
+        		token.append("&");
+        		token.append(k);
+        		token.append("=");
+        		token.append(v);
+        	});
+        }
         return token.toString();
     }
 
     /**
      * Returns the path until the loaded diagram (without including it)
-     *
      * @return the path until the loaded diagram (without including it)
      */
     private Path getPrunedPath() {

src/main/java/org/reactome/web/pwp/client/manager/state/StateManager.java

@@ -165,6 +165,7 @@ public void onDetailsTabChanged(DetailsTabChangedEvent event) {
     public void onDiagramObjectsFlagReset(DiagramObjectsFlagResetEvent event) {
         State desiredState = new State(this.currentState);
         desiredState.setFlag(null);
+        desiredState.setFlagIncludeInteractors(false); //want to set this to false regardless to remove it from url on Flag close.
         this.eventBus.fireEventFromSource(new StateChangedEvent(desiredState), this);
     }
 

src/main/java/org/reactome/web/pwp/client/manager/state/token/Token.java

@@ -14,14 +14,16 @@ public class Token {
     public static String DELIMITER;        // Default in Reactome is "&" -> to be set in Browser.java
 
     private Map<StateKey, String> parameters;
+    private Map<String, String> extraParamMap;
     private boolean wellFormed = true;
 
     public Token(String token) throws TokenMalformedException {
         if(DEFAULT_SPECIES_ID==null || DELIMITER==null) throw new RuntimeException("Please initialise DEFAULT_SPECIES_ID and DELIMITER");
         if (token.startsWith("/")) token = token.substring(1);
 //        if(token.isEmpty()) token = StateKey.SPECIES.getDefaultKey() + "=" + DEFAULT_SPECIES_ID;
-
+        
         this.parameters = new HashMap<>();
+        this.extraParamMap = new HashMap<>();
         try {
             @SuppressWarnings("NonJREEmulationClassesInClientCode")
             String[] tokens = token.split(DELIMITER);
@@ -38,7 +40,7 @@ public Token(String token) throws TokenMalformedException {
                         if (key != null) {
                             parameters.put(key, ts[1]);
                         } else {
-                            wellFormed = false;
+                            extraParamMap.put(ts[0], ts[1]);
                         }
                     }
                 }
@@ -61,6 +63,10 @@ public Token(String token) throws TokenMalformedException {
     public Map<StateKey, String> getParameters() {
         return this.parameters;
     }
+
+    public Map<String, String> getExtraParams() {
+    	return extraParamMap;
+    }
 
     public List<String> getToLoad(){
         List<String> rtn = new LinkedList<>();