added neuronedge to handle horta neuronmodel

build.gradle

@@ -7,7 +7,7 @@ allprojects {
     apply plugin: 'maven-publish'
     apply plugin: 'idea'
     group = 'org.janelia.jacs-model'
-    version = '2.28'
+    version = '2.29.refactor'
 }
 
 subprojects {

jacs-model-core/src/main/java/org/janelia/model/domain/tiledMicroscope/TmGeoAnnotation.java

@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
+import java.util.Map;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 
@@ -40,6 +41,9 @@ public class TmGeoAnnotation {
     @JsonIgnore
     transient private Long neuronId = null;
 
+    @JsonIgnore
+    transient private List<TmNeuronEdge> neuronEdges;
+
     // implementation note: at one point we stored the parent and child objects,
     //  but serializing them for calling remote server routines caused the
     //  whole tree to get walked recursively, overflowing the stack; so
@@ -58,8 +62,10 @@ public TmGeoAnnotation(Long id, Long parentId, Long neuronId, Double x, Double y
         this.radius = radius;
         this.creationDate = creationDate;
         this.modificationDate = modificationDate;
+        this.neuronEdges = new ArrayList<>();
     }
 
+
     @Override
     public String toString() {
         //return String.format("ann id %d", id);
@@ -102,6 +108,10 @@ public void setZ(Double z) {
         updateModificationDate();
     }
 
+    public List<TmNeuronEdge> getNeuronEdges() {
+        return neuronEdges;
+    }
+
     public void addChild(TmGeoAnnotation child) {
         childIds.add(child.getId());
     }

jacs-model-core/src/main/java/org/janelia/model/domain/tiledMicroscope/TmNeuronData.java

@@ -33,13 +33,24 @@ public class TmNeuronData implements Serializable {
     @JsonIgnore
     transient private Map<Long, TmStructuredTextAnnotation> textAnnotationMap;
 
+
     public TmNeuronData() {
     }
 
     public List<Long> getRootAnnotationIds() {
         return rootAnnotationIds;
     }
 
+
+    @JsonIgnore
+    public Collection<TmNeuronEdge> getEdges() {
+        List<TmNeuronEdge> totalEdges = new ArrayList<>();
+        for (TmGeoAnnotation annotation : geoAnnotations) {
+            totalEdges.addAll(annotation.getNeuronEdges());
+        }
+        return totalEdges;
+    }
+
     // maps geo ann ID to geo ann object
     @JsonIgnore
     public Map<Long, TmGeoAnnotation> getGeoAnnotationMap() {

jacs-model-core/src/main/java/org/janelia/model/domain/tiledMicroscope/TmNeuronEdge.java

@@ -0,0 +1,36 @@
+package org.janelia.model.domain.tiledMicroscope;
+
+public class TmNeuronEdge {
+    private final TmGeoAnnotation child;
+    private final TmGeoAnnotation parent;
+
+    TmNeuronEdge(TmGeoAnnotation parent, TmGeoAnnotation child)
+    {
+        this.parent = parent;
+        this.child = child;
+    }
+
+    public TmGeoAnnotation getParentVertex() {
+        return parent;
+    }
+
+    public TmGeoAnnotation getChildVertex() {
+        return child;
+    }
+
+    @Override
+    public boolean equals(Object obj)
+    {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final TmNeuronEdge other = (TmNeuronEdge) obj;
+        if (parent!=other.parent && child!=other.child) {
+            return false;
+        }
+        return true;
+    }
+}

jacs-model-core/src/main/java/org/janelia/model/domain/tiledMicroscope/TmNeuronMetadata.java

@@ -62,6 +62,10 @@ public static TmNeuronMetadata copy(TmNeuronMetadata neuron) {
         return copy;
     }
 
+    public void updateEdges() {
+
+    }
+
     public void merge(TmNeuronMetadata neuron) {
         this.setName(neuron.getName());
         this.setWorkspaceRef(neuron.getWorkspaceRef());
@@ -197,6 +201,14 @@ public void addGeometricAnnotation(TmGeoAnnotation tmGeoAnnotation) {
     }
 
 
+    /**
+     * Pass-through method to TmNeuronData
+     */
+    @JsonIgnore
+    public Collection<TmNeuronEdge> getEdges() {
+        return neuronData.getEdges();
+    }
+
     /**
      * Pass-through method to TmNeuronData
      */