fix for issue #31 (API parameters consistency): add new Graph::applyP…

…ropertyAlgorithm(const std::string &algorithm, PropertyInterface *result, std::string &errorMessage, DataSet *parameters = nullptr, PluginProgress *progress = nullptr) to be consistent with Graph::applyAlgorithm, and deprecate the previously existing version

library/tulip-core/include/tulip/Graph.h

@@ -257,15 +257,13 @@ class TLP_SCOPE Graph : public Observable {
    * If an error occurs, a message describing the error should be stored in errorMessage.
    *
    * @param algorithm The algorithm to apply.
-   * @param errorMessage A string that will be modified to contain an error message should an error
-   *occur.
-   * @param dataSet The parameters to the algorithm. Defaults to nullptr.
-   * @param progress A PluginProgress to report the progress of the operation, as well as final
-   *state. Defaults to nullptr.
-   * @return bool Whether the algorithm was successfully applied.
+   * @param errorMessage A string that will be modified to contain an error message if an error occurs.
+   * @param parameters The parameters of the algorithm. Defaults to nullptr.
+   * @param progress A PluginProgress to report the progress of the operation, as well as the final state. Defaults to nullptr.
+   * @return bool Whether the algorithm applied successfully or not. If not, check the error message.
    **/
   bool applyAlgorithm(const std::string &algorithm, std::string &errorMessage,
-                      DataSet *dataSet = nullptr, PluginProgress *progress = nullptr);
+                      DataSet *parameters = nullptr, PluginProgress *progress = nullptr);
 
   //=========================================================================
   // Graph hierarchy access and building
@@ -1426,20 +1424,27 @@ class TLP_SCOPE Graph : public Observable {
    * @brief Runs a plugin on the graph, whose result is a property.
    *
    * @param algorithm The name of the plugin to run.
-   * @param result The property in which to put the results. All previous values will be erased.
+   * @param result The property in which to store the computed nodes/edges associated values. All previous values will be erased.
    * @param errorMessage Stores the error message if the plugin fails.
-   * @param progress A means of feedback during the plugin execution. Some plugins support being
-   * stopped or cancelled through this.
    * @param parameters The parameters of the algorithm. Some algorithms use this DataSet to output
+   * @param progress A PluginProgress to report the progress of the operation, as well as the final state. Defaults to nullptr.
    * some additional information.
-   * @return Whether the plugin executed successfully or not. If not, check the error message.
+   * @return Whether the plugin applied successfully or not. If not, check the error message.
    *
    * @see PluginLister::getPluginParameters() to retrieve the list of default parameters for the
-   * pligin.
+   * plugin.
    */
   bool applyPropertyAlgorithm(const std::string &algorithm, PropertyInterface *result,
-                              std::string &errorMessage, PluginProgress *progress = nullptr,
-                              DataSet *parameters = nullptr);
+                              std::string &errorMessage, DataSet *parameters = nullptr, PluginProgress *progress = nullptr);
+
+  /**
+   * @brief Deprecated, use applyPropertyAlgorithm(const std::string &algorithm, PropertyInterface *result, std::string &errorMessage, DataSet *parameters = nullptr, PluginProgress *progress = nullptr) instead
+   */
+  _DEPRECATED bool applyPropertyAlgorithm(const std::string &algorithm, PropertyInterface *result,
+                              std::string &errorMessage, PluginProgress *progress,
+					  DataSet *parameters = nullptr) {
+    return applyPropertyAlgorithm(algorithm, result, errorMessage, parameters, progress);
+  }
 
   // updates management
   /**
@@ -1595,8 +1600,7 @@ class TLP_SCOPE Graph : public Observable {
                               bool delAllEdge = true);
 
   /**
-   * @brief deprecated, use createMetaNode(const std::vector<node>&, bool multiEdges = true, bool
-   * delAllEdge = true) instead
+   * @brief Deprecated, use createMetaNode(const std::vector<node>&, bool multiEdges = true, bool delAllEdge = true) instead
    */
   _DEPRECATED node createMetaNode(const std::set<node> &nodeSet, bool multiEdges = true,
                                   bool delAllEdge = true);

library/tulip-core/src/Graph.cpp

@@ -670,7 +670,7 @@ Iterator<Graph *> *tlp::getRootGraphs() {
 }
 
 bool Graph::applyAlgorithm(const std::string &algorithm, std::string &errorMessage,
-                           DataSet *dataSet, PluginProgress *progress) {
+                           DataSet *parameters, PluginProgress *progress) {
   if (!PluginLister::pluginExists(algorithm)) {
     tlp::warning() << "libtulip: " << __FUNCTION__ << ": algorithm plugin \"" << algorithm
                    << "\" does not exist (or is not loaded)" << endl;
@@ -687,7 +687,7 @@ bool Graph::applyAlgorithm(const std::string &algorithm, std::string &errorMessa
   } else
     tmpProgress = progress;
 
-  AlgorithmContext *context = new AlgorithmContext(this, dataSet, tmpProgress);
+  AlgorithmContext *context = new AlgorithmContext(this, parameters, tmpProgress);
   Algorithm *newAlgo = PluginLister::instance()->getPluginObject<Algorithm>(algorithm, context);
 
   if ((result = newAlgo->check(errorMessage))) {
@@ -707,9 +707,11 @@ bool Graph::applyAlgorithm(const std::string &algorithm, std::string &errorMessa
 }
 
 //=========================================================
-bool tlp::Graph::applyPropertyAlgorithm(const std::string &algorithm, PropertyInterface *prop,
-                                        std::string &errorMessage, tlp::PluginProgress *progress,
-                                        tlp::DataSet *parameters) {
+bool tlp::Graph::applyPropertyAlgorithm(const std::string &algorithm,
+					PropertyInterface *prop,
+                                        std::string &errorMessage, 
+                                        tlp::DataSet *parameters,
+					tlp::PluginProgress *progress) {
   bool result;
   tlp::AlgorithmContext context;
 

plugins/clustering/QuotientClustering.cpp

@@ -168,13 +168,13 @@ class QuotientClustering : public tlp::Algorithm {
         layoutParams.set("Unit edge length", std::max(maxSize[0], maxSize[1]) * 5.0);
         cluster->applyPropertyAlgorithm(layoutName,
                                         cluster->getLocalProperty<LayoutProperty>("viewLayout"),
-                                        errMsg, nullptr, &layoutParams);
+                                        errMsg, &layoutParams);
         double border = std::min(minSize[0], minSize[1]);
         layoutParams.set("x border", border);
         layoutParams.set("y border", border);
         cluster->applyPropertyAlgorithm("Fast Overlap Removal",
                                         cluster->getLocalProperty<LayoutProperty>("viewLayout"),
-                                        errMsg, nullptr, &layoutParams);
+                                        errMsg, &layoutParams);
       }
     }
 
@@ -376,13 +376,13 @@ class QuotientClustering : public tlp::Algorithm {
       layoutParams.set("Unit edge length", std::max(maxSize[0], maxSize[1]) * 2.0);
       quotientGraph->applyPropertyAlgorithm(
           layoutName, quotientGraph->getLocalProperty<LayoutProperty>("viewLayout"), errMsg,
-          nullptr, &layoutParams);
+          &layoutParams);
       double border = std::min(minSize[0], minSize[1]);
       layoutParams.set("x border", border);
       layoutParams.set("y border", border);
       quotientGraph->applyPropertyAlgorithm(
           "Fast Overlap Removal", quotientGraph->getLocalProperty<LayoutProperty>("viewLayout"),
-          errMsg, nullptr, &layoutParams);
+          errMsg, &layoutParams);
     }
 
     // recursive call if needed

plugins/clustering/StrengthClustering.cpp

@@ -206,7 +206,7 @@ bool StrengthClustering::run() {
   string errMsg;
   values = new DoubleProperty(graph);
 
-  if (!graph->applyPropertyAlgorithm("Strength", values, errMsg, pluginProgress))
+  if (!graph->applyPropertyAlgorithm("Strength", values, errMsg, nullptr, pluginProgress))
     return false;
 
   NumericProperty *metric = nullptr;

plugins/import/BibTeX/ImportBibTeX.cpp

@@ -2078,8 +2078,8 @@ class ImportBibTeX : public ImportModule {
         graph->delLocalProperty(fromLabriProp->getName());
 
       string err;
-      return graph->applyPropertyAlgorithm(
-          "FM^3 (OGDF)", graph->getProperty<LayoutProperty>("viewLayout"), err, pluginProgress);
+      return graph->applyPropertyAlgorithm("FM^3 (OGDF)", graph->getProperty<LayoutProperty>("viewLayout"),
+					   err, nullptr, pluginProgress);
     }
 
     return true;

plugins/import/CompleteTree.cpp

@@ -89,10 +89,9 @@ class CompleteTree : public ImportModule {
 
     if (needLayout) {
       // apply Tree Leaf
-      DataSet dSet;
       string errMsg;
       LayoutProperty *layout = graph->getProperty<LayoutProperty>("viewLayout");
-      return graph->applyPropertyAlgorithm("Tree Leaf", layout, errMsg, pluginProgress, &dSet);
+      return graph->applyPropertyAlgorithm("Tree Leaf", layout, errMsg, nullptr, pluginProgress);
     }
 
     return true;

plugins/import/FileSystem.cpp

@@ -244,10 +244,10 @@ class FileSystem : public tlp::ImportModule {
     if (_treeLayout) {
       const std::string algoName = "Bubble Tree";
       tlp::DataSet defaultParameters = getDefaultAlgorithmParameters(algoName, graph);
-      tlp::LayoutProperty *viewLayout = graph->getProperty<tlp::LayoutProperty>("viewLayout");
       std::string errMsg;
-      graph->applyPropertyAlgorithm(algoName, viewLayout, errMsg, pluginProgress,
-                                    &defaultParameters);
+      tlp::LayoutProperty *viewLayout = graph->getProperty<tlp::LayoutProperty>("viewLayout");
+      graph->applyPropertyAlgorithm(algoName, viewLayout, errMsg,
+                                    &defaultParameters, pluginProgress);
     }
 
     return true;

plugins/import/RandomTree.cpp

@@ -127,10 +127,9 @@ class RandomTree : public ImportModule {
 
     if (needLayout) {
       // apply Tree Leaf
-      DataSet dSet;
       string errMsg;
       LayoutProperty *layout = graph->getProperty<LayoutProperty>("viewLayout");
-      return graph->applyPropertyAlgorithm("Tree Leaf", layout, errMsg, pluginProgress, &dSet);
+      return graph->applyPropertyAlgorithm("Tree Leaf", layout, errMsg, nullptr, pluginProgress);
     }
 
     return true;

plugins/import/RandomTreeGeneral.cpp

@@ -149,10 +149,9 @@ class RandomTreeGeneral : public ImportModule {
 
     if (needLayout) {
       // apply Tree Leaf
-      DataSet dSet;
       string errMsg;
       LayoutProperty *layout = graph->getProperty<LayoutProperty>("viewLayout");
-      return graph->applyPropertyAlgorithm("Tree Leaf", layout, errMsg, pluginProgress, &dSet);
+      return graph->applyPropertyAlgorithm("Tree Leaf", layout, errMsg, nullptr, pluginProgress);
     }
 
     return true;

plugins/import/WebImport.cpp

@@ -794,9 +794,8 @@ struct WebImport : public ImportModule {
       pluginProgress->setComment("Layouting extracted graph using FM³...");
       string errMsg;
       // apply FM³
-      DataSet tmp;
       LayoutProperty *layout = graph->getProperty<LayoutProperty>("viewLayout");
-      return graph->applyPropertyAlgorithm("FM^3 (OGDF)", layout, errMsg, pluginProgress, &tmp);
+      return graph->applyPropertyAlgorithm("FM^3 (OGDF)", layout, errMsg, nullptr, pluginProgress);
     }
 
     return true;

plugins/interactor/NeighborhoodHighlighter/NodeNeighborhoodView.cpp

@@ -131,7 +131,7 @@ void NodeNeighborhoodView::getNeighbors(node n, unsigned int dist, bool noRecurs
     BooleanProperty result(graph_component);
     string errorMsg;
     graph_component->applyPropertyAlgorithm(tlp::SelectionAlgorithm::ReachableSubGraphSelection,
-                                            &result, errorMsg, nullptr, &dataSet);
+                                            &result, errorMsg, &dataSet);
 
     graphViewNodes.clear();
     graphViewEdges.clear();

plugins/layout/BubblePack.cpp

@@ -277,7 +277,7 @@ bool BubblePack::run() {
 
     for (unsigned int i = 0; i < components.size(); ++i) {
       Graph *tmp = graph->inducedSubGraph(components[i]);
-      tmp->applyPropertyAlgorithm("Bubble Pack", result, err, pluginProgress, dataSet);
+      tmp->applyPropertyAlgorithm("Bubble Pack", result, err, dataSet, pluginProgress);
     }
 
     // call connected component packing

plugins/layout/BubbleTree.cpp

@@ -334,15 +334,15 @@ bool BubbleTree::run() {
 
     for (unsigned int i = 0; i < components.size(); ++i) {
       Graph *tmp = graph->inducedSubGraph(components[i]);
-      tmp->applyPropertyAlgorithm("Bubble Tree", result, err, pluginProgress, dataSet);
+      tmp->applyPropertyAlgorithm("Bubble Tree", result, err, dataSet, pluginProgress);
     }
 
     // call connected component packing
     LayoutProperty tmpLayout(graph);
     DataSet tmpdataSet;
     tmpdataSet.set("coordinates", result);
-    graph->applyPropertyAlgorithm("Connected Component Packing", &tmpLayout, err, pluginProgress,
-                                  &tmpdataSet);
+    graph->applyPropertyAlgorithm("Connected Component Packing", &tmpLayout,
+				  err, &tmpdataSet, pluginProgress);
     // forget last temporary graph state
     graph->pop();
     *result = tmpLayout;

plugins/layout/GEMLayout.cpp

@@ -359,15 +359,15 @@ bool GEMLayout::run() {
 
     for (size_t i = 0; i < components.size(); ++i) {
       Graph *tmp = graph->inducedSubGraph(components[i]);
-      tmp->applyPropertyAlgorithm("GEM (Frick)", result, err, pluginProgress, dataSet);
+      tmp->applyPropertyAlgorithm("GEM (Frick)", result, err, dataSet, pluginProgress);
     }
 
     // call connected component packing
     LayoutProperty tmpLayout(graph);
     DataSet ds;
     ds.set("coordinates", result);
-    graph->applyPropertyAlgorithm("Connected Component Packing", &tmpLayout, err, pluginProgress,
-                                  &ds);
+    graph->applyPropertyAlgorithm("Connected Component Packing", &tmpLayout,
+				  err, &ds, pluginProgress);
     // forget last temporary graph state
     graph->pop();
     *result = tmpLayout;

plugins/layout/Grip/Grip.cpp

@@ -134,7 +134,8 @@ bool Grip::run() {
     DataSet tmp;
     tmp.set("coordinates", result);
     LayoutProperty layout(graph);
-    graph->applyPropertyAlgorithm("Connected Component Packing", &layout, err, nullptr, &tmp);
+    graph->applyPropertyAlgorithm("Connected Component Packing", &layout,
+				  err, &tmp);
 
     for (const node &n : graph->nodes()) {
       result->setNodeValue(n, layout.getNodeValue(n));

plugins/layout/HierarchicalGraph.cpp

@@ -364,8 +364,8 @@ bool HierarchicalGraph::run() {
 #ifndef NDEBUG
   resultBool =
 #endif
-      mySGraph->applyPropertyAlgorithm("Hierarchical Tree (R-T Extended)", &tmpLayout, erreurMsg,
-                                       nullptr, &tmp);
+      mySGraph->applyPropertyAlgorithm("Hierarchical Tree (R-T Extended)",
+				       &tmpLayout, erreurMsg, &tmp);
 
   if (edgeLength)
     delete edgeLength;

plugins/layout/MixedModel.cpp

@@ -286,8 +286,8 @@ bool MixedModel::run() {
     LayoutProperty layout(graph);
     DataSet tmp;
     tmp.set("coordinates", result);
-    graph->applyPropertyAlgorithm(string("Connected Component Packing"), &layout, err, nullptr,
-                                  &tmp);
+    graph->applyPropertyAlgorithm(string("Connected Component Packing"),
+				  &layout, err, &tmp);
 
     for (const node &n : graph->nodes()) {
       result->setNodeValue(n, layout.getNodeValue(n));

plugins/perspective/GraphPerspective/src/AlgorithmRunnerItem.cpp

@@ -547,7 +547,7 @@ void AlgorithmRunnerItem::afterRun(Graph *g, const tlp::DataSet &dataSet) {
         cs = ColorScalesManager::getLatestColorScale();
 
       data.set<ColorScale>("color scale", cs);
-      g->applyPropertyAlgorithm("Color Mapping", color, errMsg, nullptr, &data);
+      g->applyPropertyAlgorithm("Color Mapping", color, errMsg, &data);
     }
   } else if (pluginLister->pluginExists<GraphTest>(stdName)) {
     bool result = true;

plugins/view/TableView/PropertiesEditor.cpp

@@ -493,7 +493,7 @@ void PropertiesEditor::toLabels(PropertyInterface *prop, bool nodes, bool edges,
   // _graph->push() must be done outside of this method
   // to allow call from TabelView.cpp
   StringProperty *result = _graph->getProperty<StringProperty>("viewLabel");
-  _graph->applyPropertyAlgorithm("To labels", result, msg, nullptr, &data);
+  _graph->applyPropertyAlgorithm("To labels", result, msg, &data);
 }
 
 void PropertiesEditor::checkStateChanged(QModelIndex index, Qt::CheckState state) {

tests/plugins/BasicLayoutTest.cpp

@@ -90,7 +90,7 @@ void BasicLayoutTest::testDendrogram() {
   ds.set("node size", &size);
   LayoutProperty layout(graph);
   string errorMsg;
-  bool result = graph->applyPropertyAlgorithm("Dendrogram", &layout, errorMsg, nullptr, &ds);
+  bool result = graph->applyPropertyAlgorithm("Dendrogram", &layout, errorMsg, &ds);
   CPPUNIT_ASSERT(result);
 }
 //==========================================================
@@ -122,7 +122,7 @@ void BasicLayoutTest::testMixedModel() {
   ds.set("node size", &size);
   LayoutProperty layout(graph);
   string errorMsg;
-  bool result = graph->applyPropertyAlgorithm("Mixed Model", &layout, errorMsg, nullptr, &ds);
+  bool result = graph->applyPropertyAlgorithm("Mixed Model", &layout, errorMsg, &ds);
   CPPUNIT_ASSERT(result);
 }
 //==========================================================
@@ -141,7 +141,7 @@ void BasicLayoutTest::testSquarifiedTreeMap() {
 
   LayoutProperty layout(graph);
   ds.set("metric", &metric);
-  result = graph->applyPropertyAlgorithm("Squarified Tree Map", &layout, errorMsg, nullptr, &ds);
+  result = graph->applyPropertyAlgorithm("Squarified Tree Map", &layout, errorMsg, &ds);
   CPPUNIT_ASSERT(result);
 }
 //==========================================================
@@ -152,7 +152,7 @@ void BasicLayoutTest::testTreeLeaf() {
   ds.set("node size", &size);
   LayoutProperty layout(graph);
   string errorMsg;
-  bool result = graph->applyPropertyAlgorithm("Tree Leaf", &layout, errorMsg, nullptr, &ds);
+  bool result = graph->applyPropertyAlgorithm("Tree Leaf", &layout, errorMsg, &ds);
   CPPUNIT_ASSERT(result);
 }
 //==========================================================
@@ -194,6 +194,6 @@ void BasicLayoutTest::testFastOverlapRemoval() {
   ds.set("layout", &layout);
   string errorMsg;
   bool result =
-      graph->applyPropertyAlgorithm("Fast Overlap Removal", &layout, errorMsg, nullptr, &ds);
+      graph->applyPropertyAlgorithm("Fast Overlap Removal", &layout, errorMsg, &ds);
   CPPUNIT_ASSERT(result);
 }

tests/plugins/BasicPluginsTest.cpp

@@ -317,7 +317,7 @@ void BasicPluginsTest::testMetricColorMapping() {
   DataSet ds;
   ds.set("linear/uniform\nproperty", &metric);
   ColorProperty color(graph);
-  result = graph->applyPropertyAlgorithm("Color Mapping", &color, errorMsg, nullptr, &ds);
+  result = graph->applyPropertyAlgorithm("Color Mapping", &color, errorMsg, &ds, nullptr);
   CPPUNIT_ASSERT(result);
 }
 //==========================================================
@@ -378,7 +378,7 @@ void BasicPluginsTest::testMetricSizeMapping() {
 
   SizeProperty size(graph);
   ds.set("property", &metric);
-  result = graph->applyPropertyAlgorithm("Size Mapping", &size, errorMsg, nullptr, &ds);
+  result = graph->applyPropertyAlgorithm("Size Mapping", &size, errorMsg, &ds, nullptr);
   CPPUNIT_ASSERT(result);
 }
 //==========================================================
@@ -419,7 +419,7 @@ void BasicPluginsTest::testEqualValueClustering() {
 
   PluginProgress *progress = new SimplePluginProgress();
   initializeGraph("Planar Graph");
-  result = graph->applyPropertyAlgorithm("Degree", metric, errorMsg, progress);
+  result = graph->applyPropertyAlgorithm("Degree", metric, errorMsg, nullptr, progress);
   CPPUNIT_ASSERT_MESSAGE(errorMsg, result);
   result = graph->applyAlgorithm(algorithmName, errorMsg, &ds);
   CPPUNIT_ASSERT_MESSAGE(errorMsg, result);