adjusted to recent UG changes concerning synapse types, synapse handl…

…er and distributor

src/main/java/edu/gcsc/vrl/neurobox/NeuroBoxPluginConfigurator.java

@@ -155,7 +155,7 @@ public void register(PluginAPI api)
             vapi.addComponent(Hodgkin_Huxley.class);
             vapi.addComponent(Hodgkin_Huxley_Nernst.class);
             vapi.addComponent(Leakage.class);
-            vapi.addComponent(SynapseHandler.class);
+            vapi.addComponent(SynapseHandler_VRL.class);
 
             // membrane potential mapping
             vapi.addComponent(MembranePotentialMapping.class);

src/main/java/edu/gcsc/vrl/neurobox/SynapseHandler_VRL.java

@@ -0,0 +1,147 @@
+package edu.gcsc.vrl.neurobox;
+
+import edu.gcsc.vrl.ug.api.I_SynapseHandler;
+import edu.gcsc.vrl.ug.api.SynapseHandler;
+import eu.mihosoft.vrl.annotation.ComponentInfo;
+import eu.mihosoft.vrl.annotation.MethodInfo;
+import eu.mihosoft.vrl.annotation.ParamInfo;
+import java.io.Serializable;
+
+/**
+ *
+ * @author mbreit
+ * @date 22-06-2015
+ */
+
+@ComponentInfo(name="Synapse Handler", category="Neuro/cable")
+public class SynapseHandler_VRL implements Serializable
+{
+    private static final long serialVersionUID = 1L;
+
+    private transient I_SynapseHandler synHandler = null;
+
+    /**
+     * @return Hodgkin-Huxley channel object
+     */
+    @MethodInfo(name="create synapse handler", valueName="synapse handler", initializer=true, hide=false, interactive=false)
+    public I_SynapseHandler create()
+    {
+        // construct new synapse handler object
+        synHandler = new SynapseHandler();
+
+        return synHandler;
+    }
+
+
+    @MethodInfo(name="set ALPHA synapse activation timing", interactive=false)
+    public void set_alpha_synapse_activation_timing
+    (
+	/// start time
+        @ParamInfo(name="mean onset [s]", 
+		   style="default", 
+		   options="value=0.01; description=\"default: 10 ms\"") 
+		   Double onset,
+
+	/// duration
+        @ParamInfo(name="mean tau [s]", 
+ 		   style="default", 
+		   options="value=2e-3; description=\"default: 2 ms\"")
+		   Double tau,
+
+	/// peak conductance
+        @ParamInfo(name="mean peak conductance [S]", 
+		   style="default", 
+		   options="value=1.2e-9; description=\"default: 1.2 nS\"")
+		   Double peak_cond,
+
+	/// std deviation of start time
+        @ParamInfo(name="std deviation onset [s]", 
+		   style="default", 
+		   options="value=0.003; description=\"default: 3 ms\"") 
+		   Double onset_dev,
+
+	/// std deviation of duration 
+        @ParamInfo(name="std deviation tau [s]", 
+		   style="default", 
+		   options="value=2e-4; description=\"default: 200 us\"")
+		   Double tau_dev,
+
+	/// std deviation of peak conductance
+        @ParamInfo(name="std deviation peak conductance [S]", 
+		   style="default", 
+		   options="value=1e-10; description=\"default: 100 pS\"")
+		   Double peak_cond_dev
+    )
+    {
+        check_syn_handler();
+        synHandler.set_activation_timing_alpha(onset, tau, peak_cond, onset_dev, tau_dev, peak_cond_dev, true);
+    }
+
+
+    @MethodInfo(name="set EXP2 synapse activation timing", interactive=false)
+    public void set_exp2_synapse_activation_timing
+    (
+	/// average start time
+        @ParamInfo(name="mean onset [s]", 
+		   style="default", 
+		   options="value=0.01; description=\"default: 10 ms\"") 
+		   Double onset_mean,
+
+	/// tau1
+        @ParamInfo(name="mean tau1 [s]", 
+		   style="default",
+		   options="value=7e-4; description=\"0.7-1 ms for AMPA\"") 
+		   Double tau1_mean,
+
+	/// tau2
+        @ParamInfo(name="mean tau2 [s]", 
+		   style="default", 
+		   options="value=5e-3; description=\"5-8 ms for AMPA\"") 
+		   Double tau2_mean,
+
+	/// peak conductance
+        @ParamInfo(name="mean peak conductance [S]", 
+		   style="default", 
+		   options="value=1.2e-9; description=\"default: 1.2 nS\"")
+		   Double peak_cond_mean,
+
+	/// std deviation of start time 
+        @ParamInfo(name="std deviation onset [s]", 
+		   style="default", 
+		   options="value=3e-3; description=\"default: 3 ms\"") 
+		   Double onset_dev,
+
+	/// std deviation of tau1
+        @ParamInfo(name="std deviation tau1 [s]", 
+		   style="default", 
+		   options="value=0.0; description=\"default 0\"") 
+		   Double tau1_dev,
+
+	/// std deviation of tau2
+        @ParamInfo(name="std deviation tau2 [s]", 
+		   style="default", 
+		   options="value=0.0; description=\"default 0\"") 
+		   Double tau2_dev,
+
+	/// std deviation of peak conductance
+        @ParamInfo(name="std deviation peak conductance [S]", 
+		   style="default", 
+		   options="value=1e-10; description=\"default: 100 pS\"")
+		   Double peak_cond_dev
+    )
+    {
+        check_syn_handler();
+        synHandler.set_activation_timing_biexp(onset_mean, tau1_mean, tau2_mean, peak_cond_mean, onset_dev, tau1_dev, tau2_dev, peak_cond_dev, true);
+    }
+
+    @MethodInfo(noGUI=true)
+    private void check_syn_handler()
+    {
+        if (synHandler == null)
+        {
+            eu.mihosoft.vrl.system.VMessage.exception("Usage before initialization: ",
+                "No method can be called on synapse handler object before it has been initialized"
+                + "using the 'create()' method.");
+        }
+    }
+}