6 files changed, 175 insertions, 60 deletions

diff --git a/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerAdapter.java b/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerAdapter.java
index bc32323d..ae87d8ac 100644
--- a/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerAdapter.java
+++ b/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerAdapter.java
@@ -8,9 +8,10 @@ package tools.refinery.visualization;
 import tools.refinery.store.adapter.ModelAdapter;
 import tools.refinery.store.map.Version;
 import tools.refinery.store.tuple.Tuple;
-import tools.refinery.visualization.internal.FileFormat;
 import tools.refinery.visualization.internal.ModelVisualizerBuilderImpl;
 
+import java.util.Collection;
+
 public interface ModelVisualizerAdapter extends ModelAdapter {
 
         ModelVisualizerStoreAdapter getStoreAdapter();
@@ -18,27 +19,14 @@ public interface ModelVisualizerAdapter extends ModelAdapter {
                 return new ModelVisualizerBuilderImpl();
         }
 
-        public String createDotForCurrentModelState();
-
-        public String createDotForModelState(Version version);
-
-        public boolean saveDot(String dot, String filePath);
-
-        public boolean renderDot(String dot, String filePath);
-
-        public boolean renderDot(String dot, FileFormat format, String filePath);
-
         public void addTransition(Version from, Version to, String action);
 
 
         public void addTransition(Version from, Version to, String action, Tuple  activation);
         public void addState(Version state);
+        public void addState(Version state, Collection<Double> fitness);
+        public void addState(Version state, String label);
         public void addSolution(Version state);
-
-        public boolean saveDesignSpace(String path);
-
-        public boolean renderDesignSpace(String path);
-
-        public boolean renderDesignSpace(String path, FileFormat format);
+        public void visualize();
 
 }
diff --git a/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java b/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java
index 56cc425e..592f5fcf 100644
--- a/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java
+++ b/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerBuilder.java
@@ -6,6 +6,11 @@
 package tools.refinery.visualization;
 
 import tools.refinery.store.adapter.ModelAdapterBuilder;
+import tools.refinery.visualization.internal.FileFormat;
 
 public interface ModelVisualizerBuilder extends ModelAdapterBuilder {
+        ModelVisualizerBuilder withOutputpath(String outputpath);
+        ModelVisualizerBuilder withFormat(FileFormat format);
+        ModelVisualizerBuilder saveDesignSpace();
+        ModelVisualizerBuilder saveStates();
 }
diff --git a/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerStoreAdapter.java b/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerStoreAdapter.java
index 6599d4c3..46663b2a 100644
--- a/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerStoreAdapter.java
+++ b/subprojects/visualization/src/main/java/tools/refinery/visualization/ModelVisualizerStoreAdapter.java
@@ -6,7 +6,17 @@
 package tools.refinery.visualization;
 
 import tools.refinery.store.adapter.ModelStoreAdapter;
-import tools.refinery.store.query.ModelQueryStoreAdapter;
+import tools.refinery.visualization.internal.FileFormat;
+
+import java.util.Set;
 
 public interface ModelVisualizerStoreAdapter extends ModelStoreAdapter {
+
+        String getOutputPath();
+
+        boolean isRenderDesignSpace();
+
+        boolean isRenderStates();
+
+        Set<FileFormat> getFormats();
 }
diff --git a/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizeStoreAdapterImpl.java b/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizeStoreAdapterImpl.java
index b4db2682..04be22d6 100644
--- a/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizeStoreAdapterImpl.java
+++ b/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizeStoreAdapterImpl.java
@@ -10,11 +10,22 @@ import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.visualization.ModelVisualizerStoreAdapter;
 
+import java.util.Set;
+
 public class ModelVisualizeStoreAdapterImpl implements ModelVisualizerStoreAdapter {
         private final ModelStore store;
+        private final String outputPath;
+        private final boolean renderDesignSpace;
+        private final boolean renderStates;
+        private final Set<FileFormat> formats;
 
-        public ModelVisualizeStoreAdapterImpl(ModelStore store) {
+        public ModelVisualizeStoreAdapterImpl(ModelStore store, String outputPath, Set<FileFormat> formats,
+                                                                                  boolean renderDesignSpace, boolean renderStates) {
                 this.store = store;
+                this.outputPath = outputPath;
+                this.formats = formats;
+                this.renderDesignSpace = renderDesignSpace;
+                this.renderStates = renderStates;
         }
 
         @Override
@@ -26,4 +37,24 @@ public class ModelVisualizeStoreAdapterImpl implements ModelVisualizerStoreAdapt
         public ModelAdapter createModelAdapter(Model model) {
                 return new ModelVisualizerAdapterImpl(model, this);
         }
+
+        @Override
+        public String getOutputPath() {
+                return outputPath;
+        }
+
+        @Override
+        public boolean isRenderDesignSpace() {
+                return renderDesignSpace;
+        }
+
+        @Override
+        public boolean isRenderStates() {
+                return renderStates;
+        }
+
+        @Override
+        public Set<FileFormat> getFormats() {
+                return formats;
+        }
 }
diff --git a/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java b/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java
index 06cc8113..531969b4 100644
--- a/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java
+++ b/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerAdapterImpl.java
@@ -21,38 +21,52 @@ import java.util.stream.Collectors;
 public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
         private final Model model;
         private final ModelVisualizerStoreAdapter storeAdapter;
-        private final Map<AnySymbol, Interpretation<?>> interpretations;
+        private final Map<AnySymbol, Interpretation<?>> allInterpretations;
         private final StringBuilder designSpaceBuilder = new StringBuilder();
         private final Map<Version, Integer> states = new HashMap<>();
         private int transitionCounter = 0;
         private Integer numberOfStates = 0;
-        private static final Map<Object, String> truthValueToDot = new HashMap<>()
-        {{
-                put(TruthValue.TRUE, "1");
-                put(TruthValue.FALSE, "0");
-                put(TruthValue.UNKNOWN, "½");
-                put(TruthValue.ERROR, "E");
-                put(true, "1");
-                put(false, "0");
-        }};
+        private final String outputPath;
+        private final Set<FileFormat> formats;
+        private final boolean renderDesignSpace;
+        private final boolean renderStates;
+
+        private static final Map<Object, String> truthValueToDot = Map.of(
+                        TruthValue.TRUE, "1",
+                        TruthValue.FALSE, "0",
+                        TruthValue.UNKNOWN, "½",
+                        TruthValue.ERROR, "E",
+                        true, "1",
+                        false, "0"
+        );
 
         public ModelVisualizerAdapterImpl(Model model, ModelVisualizerStoreAdapter storeAdapter) {
                 this.model = model;
                 this.storeAdapter = storeAdapter;
-                this.interpretations = new HashMap<>();
+                this.outputPath = storeAdapter.getOutputPath();
+                this.formats = storeAdapter.getFormats();
+                if (formats.isEmpty()) {
+                        formats.add(FileFormat.SVG);
+                }
+                this.renderDesignSpace = storeAdapter.isRenderDesignSpace();
+                this.renderStates = storeAdapter.isRenderStates();
+
+                this.allInterpretations = new HashMap<>();
                 for (var symbol : storeAdapter.getStore().getSymbols()) {
                         var arity = symbol.arity();
                         if (arity < 1 || arity > 2) {
                                 continue;
                         }
                         var interpretation = (Interpretation<?>) model.getInterpretation(symbol);
-                        interpretations.put(symbol, interpretation);
+                        allInterpretations.put(symbol, interpretation);
                 }
                 designSpaceBuilder.append("digraph designSpace {\n");
                 designSpaceBuilder.append("""
+                                nodesep=0
+                                ranksep=5
                                 node[
-                                        style=filled
-                                        fillcolor=white
+                                \tstyle=filled
+                                \tfillcolor=white
                                 ]
                                 """);
         }
@@ -67,8 +81,7 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                 return storeAdapter;
         }
 
-        @Override
-        public String createDotForCurrentModelState() {
+        private String createDotForCurrentModelState() {
 
                 var unaryTupleToInterpretationsMap = new HashMap<Tuple, LinkedHashSet<Interpretation<?>>>();
 
@@ -90,7 +103,7 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                                 ]
                                 """);
 
-                for (var entry : interpretations.entrySet()) {
+                for (var entry : allInterpretations.entrySet()) {
                         var key = entry.getKey();
                         var arity = key.arity();
                         var cursor = entry.getValue().getAll();
@@ -228,8 +241,7 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                 };
         }
 
-        @Override
-        public String createDotForModelState(Version version) {
+        private String createDotForModelState(Version version) {
                 var currentVersion = model.getState();
                 model.restore(version);
                 var graph = createDotForCurrentModelState();
@@ -237,8 +249,7 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                 return graph;
         }
 
-        @Override
-        public boolean saveDot(String dot, String filePath) {
+        private boolean saveDot(String dot, String filePath) {
                 File file = new File(filePath);
                 file.getParentFile().mkdirs();
 
@@ -251,13 +262,11 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                 return true;
         }
 
-        @Override
-        public boolean renderDot(String dot, String filePath) {
+        private boolean renderDot(String dot, String filePath) {
                 return renderDot(dot, FileFormat.SVG, filePath);
         }
 
-        @Override
-        public boolean renderDot(String dot, FileFormat format, String filePath) {
+        private boolean renderDot(String dot, FileFormat format, String filePath) {
                 try {
                         Process process = new ProcessBuilder("dot", "-T" + format.getFormat(), "-o", filePath).start();
 
@@ -303,6 +312,26 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
         }
 
         @Override
+        public void addState(Version state, Collection<Double> fitness) {
+                var labelBuilder = new StringBuilder();
+                for (var f : fitness) {
+                        labelBuilder.append(f).append(", ");
+                }
+                addState(state, labelBuilder.toString());
+        }
+
+        @Override
+        public void addState(Version state, String label) {
+                if (states.containsKey(state)) {
+                        return;
+                }
+                states.put(state, numberOfStates++);
+                designSpaceBuilder.append(states.get(state)).append(" [label = \"").append(states.get(state)).append(" (");
+                designSpaceBuilder.append(label);
+                designSpaceBuilder.append(")\"\n").append("URL=\"./").append(states.get(state)).append(".svg\"]\n");
+        }
+
+        @Override
         public void addSolution(Version state) {
                 addState(state);
                 designSpaceBuilder.append(states.get(state)).append(" [shape = doublecircle]\n");
@@ -313,8 +342,7 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                 return designSpaceBuilder.toString();
         }
 
-        @Override
-        public boolean saveDesignSpace(String path) {
+        private boolean saveDesignSpace(String path) {
                 saveDot(buildDesignSpaceDot(), path + "/designSpace.dot");
                 for (var entry : states.entrySet()) {
                         saveDot(createDotForModelState(entry.getKey()), path + "/" + entry.getValue() + ".dot");
@@ -322,21 +350,38 @@ public class ModelVisualizerAdapterImpl implements ModelVisualizerAdapter {
                 return true;
         }
 
-        @Override
-        public boolean renderDesignSpace(String path) {
-                return renderDesignSpace(path, FileFormat.SVG);
+        private void renderDesignSpace(String path, Set<FileFormat> formats) {
+                File filePath = new File(path);
+                filePath.mkdirs();
+                if (renderStates) {
+                        for (var entry : states.entrySet()) {
+                                var stateId = entry.getValue();
+                                var stateDot = createDotForModelState(entry.getKey());
+                                for (var format : formats) {
+                                        if (format == FileFormat.DOT) {
+                                                saveDot(stateDot, path + "/" + stateId + ".dot");
+                                        }
+                                        else {
+                                                renderDot(stateDot, format, path + "/" + stateId + "." + format.getFormat());
+                                        }
+                                }
+                        }
+                }
+                if (renderDesignSpace) {
+                        var designSpaceDot = buildDesignSpaceDot();
+                        for (var format : formats) {
+                                if (format == FileFormat.DOT) {
+                                        saveDot(designSpaceDot, path + "/designSpace.dot");
+                                }
+                                else {
+                                        renderDot(designSpaceDot, format, path + "/designSpace." + format.getFormat());
+                                }
+                        }
+                }
         }
 
         @Override
-        public boolean renderDesignSpace(String path, FileFormat format) {
-                for (var entry : states.entrySet()) {
-                        var stateId = entry.getValue();
-                        var stateDot = createDotForModelState(entry.getKey());
-                        saveDot(stateDot, path + "/" + stateId + ".dot");
-                        renderDot(stateDot, format, path + "/" + stateId + "." + format.getFormat());
-                }
-                var designSpaceDot = buildDesignSpaceDot();
-                saveDot(designSpaceDot, path + "/designSpace.dot");
-                return renderDot(designSpaceDot, format, path + "/designSpace." + format.getFormat());
+        public void visualize() {
+                renderDesignSpace(outputPath, formats);
         }
 }
diff --git a/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java b/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java
index d19cf2cf..e4d801d8 100644
--- a/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java
+++ b/subprojects/visualization/src/main/java/tools/refinery/visualization/internal/ModelVisualizerBuilderImpl.java
@@ -9,11 +9,47 @@ import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.visualization.ModelVisualizerBuilder;
 
+import java.util.LinkedHashSet;
+import java.util.Set;
+
 public class ModelVisualizerBuilderImpl
                 extends AbstractModelAdapterBuilder<ModelVisualizeStoreAdapterImpl>
                 implements ModelVisualizerBuilder {
+        private String outputPath;
+        private boolean saveDesignSpace = false;
+        private boolean saveStates = false;
+        private Set<FileFormat> formats = new LinkedHashSet<>();
+
         @Override
         protected ModelVisualizeStoreAdapterImpl doBuild(ModelStore store) {
-                return new ModelVisualizeStoreAdapterImpl(store);
+                return new ModelVisualizeStoreAdapterImpl(store, outputPath, formats, saveDesignSpace, saveStates);
+        }
+
+        @Override
+        public ModelVisualizerBuilder withOutputpath(String outputpath) {
+                checkNotConfigured();
+                this.outputPath = outputpath;
+                return this;
+        }
+
+        @Override
+        public ModelVisualizerBuilder withFormat(FileFormat format) {
+                checkNotConfigured();
+                this.formats.add(format);
+                return this;
+        }
+
+        @Override
+        public ModelVisualizerBuilder saveDesignSpace() {
+                checkNotConfigured();
+                this.saveDesignSpace = true;
+                return this;
+        }
+
+        @Override
+        public ModelVisualizerBuilder saveStates() {
+                checkNotConfigured();
+                this.saveStates = true;
+                return this;
         }
 }