Changeset 12113 in project

Timestamp:

10/06/08 09:17:56 (13 years ago)

Author:

Ivan Raikov

Message:

Include support for complex prefixes in the names of transition states.

Location:

release/3/nemo/trunk

Files:

• nemo-core.scm (modified) (1 diff)
• nemo-eggdoc.scm (modified) (2 diffs)
• nemo-nmodl.scm (modified) (6 diffs)

release/3/nemo/trunk/nemo-core.scm

@@ -543 +543 @@
                            (cases nemo:quantity x
                                   (TSCOMP (name initial open transitions power)
-                                          (let ((ss (delete-duplicates (append (map second transitions) 
-                                                                               (map third transitions)))))
-                                            (append ss ax)))
+                                          (let* ((ss1 (delete-duplicates (append (map second transitions) 
+                                                                                 (map third transitions))))
+                                                 (ss2 (map (lambda (x) (list name x))  ss1)))
+                                            (append ss2 ax)))
                                   (else ax))
                            ax)))

release/3/nemo/trunk/nemo-eggdoc.scm

@@ -1 +1 @@
 ;; 
 ;;
-;; nemx documentation for the Chicken Scheme module system.
+;; nemo documentation for the Chicken Scheme module system.
 ;;
 ;;
@@ -75 +75 @@
         (p (symbol-table
             (describe "(INPUT {ID | (ID [AS LOCAL-ID] [FROM NAMESPACE])} ... )"
-                      "declare an imported quantity")
+                      (p "Declares one or several imported quantities. "
+                         
+                         ))
             (describe "(OUTPUT ID)" 
                       "declare that an existing quantity be exported")

release/3/nemo/trunk/nemo-nmodl.scm

@@ -1 +1 @@
 
-;; TODO: * uniquify state names in state complexes
-;;       * check that open states are valid
-;;
+;; TODO: * check that open states are valid
+;;       * include option for generating kinetic eqs
 ;; 
 ;; An extension for translating NeuroML models to NMODL descriptions.
@@ -91 +90 @@
                             expr))
          ((s . es)    (if (symbol? s)  (cons s (map (lambda (x) (rhsexpr x)) es)) expr))
-         (id          id)))
+         (id          (nmodl-name id))))
 
 
@@ -346 +345 @@
 
 (define (state-eqs n initial open transitions power)
-  (let* ((g (make-digraph n (string-append (->string n) " transitions graph")))
+  (let* ((sn  (lambda (x) (string->symbol (s+ n ":" x))))
+         (g   (make-digraph n (string-append (->string n) " transitions graph")))
          (add-node!  (g 'add-node!))
          (add-edge!  (g 'add-edge!))
@@ -356 +356 @@
                            (match (car tlst) 
                                   (('-> s0 s1 rate-expr)
-                                   (loop (cons s0 (cons s1 lst)) (cdr tlst)))
+                                   (loop (cons (sn s0) (cons (sn s1) lst)) (cdr tlst)))
                                   (('-> _)
                                    (nemo:error 'nemo:nmodl-state-eqs ": invalid transition equation " 
@@ -371 +371 @@
       (for-each (lambda (e) 
                   (match e (('-> s0 s1 rate-expr)
-                            (let ((i  (car (alist-ref s0 name->id-map)))
-                                  (j  (car (alist-ref s1 name->id-map)))
+                            (let ((i  (car (alist-ref (sn s0) name->id-map)))
+                                  (j  (car (alist-ref (sn s1) name->id-map)))
                                   (x  (if (eq? s0 (second snode)) snex s0)))
                             (add-edge! (list i j `(* ,x ,rate-expr)))))
@@ -605 +605 @@
            
            (pp indent ,nl (STATE "{"))
-           (for-each (lambda (st) (apply define-state (list indent+ st)))
+           (for-each (lambda (st)
+                       (if (pair? st) 
+                           (apply define-state (list indent+ (->string (second st))))
+                           (apply define-state (list indent+ st))))
                      states)
            (for-each (lambda (st) (apply define-state (list indent+ st)))