12 files changed, 70 insertions, 65 deletions

diff --git a/Makefile.am b/Makefile.am
index 8638119..d54aa2f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,15 +1,26 @@
 ACLOCAL_AMFLAGS = -I ax
 SUBDIRS = src
 
+# Ident formats the source code to conform with GNU style conventions.
 indent :
         indent \
         src/*.c \
-        src/controller/*.c src/controller/*.sqc src/controller/*.h \
+        src/controller/actions/*.c src/controller/actions/*.sqc src/controller/actions/*.h \
+        src/controller/callbacks/*.c src/controller/callbacks/*.h \
         src/db/*.c src/db/*.sqc src/db/*.h \
-        src/model/*.c src/model/*.sqc src/model/*.h \
-        src/model/geometry/*.c src/mode/geometry/*.h \
+        src/model/data/*.c src/model/data/*.sqc src/model/data/*.h \
+        src/model/geometry/*.c src/model/geometry/*.h \
+        src/model/state/*.c src/model/state/*.h \
         src/util/*.c src/util/*.h \
         src/util/amd_performance_monitor/*.c \
         src/util/amd_performance_monitor/*.h \
         src/view/*.c src/view/*.h
 
+# Splint analyzes the code for security vulnerabilities and
+# programming mistakes. It would be great to add a target to run
+# splint here but as of Splint 3.1.2 it does not yet handle C99
+# variable declarations which are used heavily in this project.  This
+# is discussed at
+# http://www.cs.virginia.edu/pipermail/splint-discuss/2009-March/001288.html.
+
+
diff --git a/src/controller/actions/pan.c b/src/controller/actions/pan.c
index 2f856b0..52e5fc1 100644
--- a/src/controller/actions/pan.c
+++ b/src/controller/actions/pan.c
@@ -10,10 +10,10 @@ pan (int x1, int y1, int x2, int y2)
 {
   int dx = x1 - x2;
   int dy = y1 - x2;
-  
+
   if (dx == 0 && dy == 0)
     return;
-  
+
   /*
    * Convert the selection boundary from window coordinates to
    * world coordinates.
@@ -26,9 +26,9 @@ pan (int x1, int y1, int x2, int y2)
   glGetDoublev (GL_PROJECTION_MATRIX, projection);
   GLint viewport[4];
   glGetIntegerv (GL_VIEWPORT, viewport);
-  
+
   check_error (__FILE__, __LINE__);
-  
+
   GLdouble start_position[3];
   gluUnProject (x1,
                 y1,
@@ -36,11 +36,10 @@ pan (int x1, int y1, int x2, int y2)
                 model,
                 projection,
                 viewport,
-                &start_position[0],
-                &start_position[1], &start_position[2]);
-  
+                &start_position[0], &start_position[1], &start_position[2]);
+
   check_error (__FILE__, __LINE__);
-  
+
   GLdouble end_position[3];
   gluUnProject (x2,
                 y2,
@@ -49,13 +48,13 @@ pan (int x1, int y1, int x2, int y2)
                 projection,
                 viewport,
                 &end_position[0], &end_position[1], &end_position[2]);
-  
+
   check_error (__FILE__, __LINE__);
-  
+
   S.pan.trans[0] += end_position[0] - start_position[0];
   S.pan.trans[1] -= end_position[1] - start_position[1];
-  
+
   glutPostRedisplay ();
-  
+
   return;
 }
diff --git a/src/controller/actions/set_ortho.c b/src/controller/actions/set_ortho.c
index ce66f60..e73846c 100644
--- a/src/controller/actions/set_ortho.c
+++ b/src/controller/actions/set_ortho.c
@@ -7,10 +7,7 @@
 void
 set_ortho (void)
 {
-  gluOrtho2D (S.ortho.min_x, 
-              S.ortho.max_x,
-              S.ortho.min_y,
-              S.ortho.max_y);
+  gluOrtho2D (S.ortho.min_x, S.ortho.max_x, S.ortho.min_y, S.ortho.max_y);
 
   return;
 }
diff --git a/src/controller/actions/zoom.c b/src/controller/actions/zoom.c
index 7209e85..53da49b 100644
--- a/src/controller/actions/zoom.c
+++ b/src/controller/actions/zoom.c
@@ -14,7 +14,7 @@ void
 zoom (double x1, double y1, double x2, double y2)
 {
   S.zoom.active = true;
-  
+
   S.zoom.coords[0] = x1;
   S.zoom.coords[1] = x2;
   S.zoom.coords[2] = y1;
@@ -30,7 +30,7 @@ zoom (double x1, double y1, double x2, double y2)
    */
   double width = S.zoom.coords[1] - S.zoom.coords[0];
   double height = S.zoom.coords[3] - S.zoom.coords[2];
-  double difference = fabs(width - height);
+  double difference = fabs (width - height);
 
   if (width > height)
     {
@@ -46,8 +46,8 @@ zoom (double x1, double y1, double x2, double y2)
   GLint viewport[4];
   glGetIntegerv (GL_VIEWPORT, viewport);
   reshape (viewport[2], viewport[3]);
-  
+
   glutPostRedisplay ();
-  
+
   return;
 }
diff --git a/src/controller/callbacks/keyboard.c b/src/controller/callbacks/keyboard.c
index 9e667d8..a74ac7b 100644
--- a/src/controller/callbacks/keyboard.c
+++ b/src/controller/callbacks/keyboard.c
@@ -45,7 +45,7 @@ keyboard (unsigned char key, int x, int y)
        * Reset the view (unzoom, recenter).
        */
       pan_info_init (&S.pan);
-      zoom_info_init (&S.zoom);     
+      zoom_info_init (&S.zoom);
 
       GLint viewport[4];
       glGetIntegerv (GL_VIEWPORT, viewport);
diff --git a/src/controller/callbacks/mouse.c b/src/controller/callbacks/mouse.c
index 34ff290..5f5be43 100644
--- a/src/controller/callbacks/mouse.c
+++ b/src/controller/callbacks/mouse.c
@@ -25,8 +25,8 @@ mouse (int button, int state, int x, int y)
     {
       // Deactive a panning event if one was happening.
       S.pan.active = false;
-      
-      if (S.selection.active && 
+
+      if (S.selection.active &&
           S.selection.purpose == ZOOM &&
           glutGetModifiers () == GLUT_ACTIVE_CTRL)
         {
@@ -35,7 +35,7 @@ mouse (int button, int state, int x, int y)
            */
           if (x == S.selection.x || y == S.selection.y)
             return;
-          
+
           /*
            * Convert the selection boundary from window coordinates to
            * world coordinates.
@@ -48,21 +48,21 @@ mouse (int button, int state, int x, int y)
           glGetDoublev (GL_PROJECTION_MATRIX, projection);
           GLint viewport[4];
           glGetIntegerv (GL_VIEWPORT, viewport);
-          
+
           check_error (__FILE__, __LINE__);
-          
+
           GLdouble start_position[3];
           gluUnProject (x,
-                        viewport[3] -y,
+                        viewport[3] - y,
                         0,
                         model,
                         projection,
                         viewport,
                         &start_position[0],
                         &start_position[1], &start_position[2]);
-          
+
           check_error (__FILE__, __LINE__);
-          
+
           GLdouble end_position[3];
           gluUnProject (S.selection.x,
                         viewport[3] - S.selection.y,
@@ -71,9 +71,9 @@ mouse (int button, int state, int x, int y)
                         projection,
                         viewport,
                         &end_position[0], &end_position[1], &end_position[2]);
-          
+
           check_error (__FILE__, __LINE__);
-          
+
           zoom (fmin (start_position[0], end_position[0]),
                 fmin (start_position[1], end_position[1]),
                 fmax (start_position[0], end_position[0]),
@@ -83,7 +83,7 @@ mouse (int button, int state, int x, int y)
       /*
        * Complete a selection if one was started and not cancelled.
        */
-      if (S.selection.active && 
+      if (S.selection.active &&
           S.selection.purpose == SET &&
           glutGetModifiers () == GLUT_ACTIVE_CTRL)
         {
@@ -161,9 +161,8 @@ mouse (int button, int state, int x, int y)
     }
 
   // Begin selection.
-  if (button == GLUT_LEFT_BUTTON && 
-      state == GLUT_DOWN && 
-      glutGetModifiers () == GLUT_ACTIVE_CTRL)
+  if (button == GLUT_LEFT_BUTTON &&
+      state == GLUT_DOWN && glutGetModifiers () == GLUT_ACTIVE_CTRL)
     {
       S.selection.active = true;
       S.selection.x = x;
@@ -172,8 +171,7 @@ mouse (int button, int state, int x, int y)
 
   // Pan.
   if (button == GLUT_LEFT_BUTTON &&
-      state == GLUT_DOWN &&
-      glutGetModifiers () != GLUT_ACTIVE_CTRL)
+      state == GLUT_DOWN && glutGetModifiers () != GLUT_ACTIVE_CTRL)
     {
       /*
        * Detection of the first point in a panning event.
diff --git a/src/controller/callbacks/mouse_motion.c b/src/controller/callbacks/mouse_motion.c
index 3279773..5cdbac7 100644
--- a/src/controller/callbacks/mouse_motion.c
+++ b/src/controller/callbacks/mouse_motion.c
@@ -14,6 +14,6 @@ mouse_motion (int x, int y)
       S.pan.begin[0] = x;
       S.pan.begin[1] = y;
     }
-  
+
   return;
 }
diff --git a/src/controller/callbacks/mouse_wheel.c b/src/controller/callbacks/mouse_wheel.c
index 9ca73bc..05ce734 100644
--- a/src/controller/callbacks/mouse_wheel.c
+++ b/src/controller/callbacks/mouse_wheel.c
@@ -6,7 +6,7 @@
 
 #define S state0
 
-void 
+void
 mouse_wheel (int button, int dir, int x, int y)
 {
   /*
@@ -14,8 +14,8 @@ mouse_wheel (int button, int dir, int x, int y)
    * start at the position of the mouse.  Calculate a bounding box
    * that will be the selection and zoom to it.
    */
-  double width = fabs(S.ortho.max_x - S.ortho.min_x);
-  double height = fabs(S.ortho.max_y - S.ortho.min_y);
+  double width = fabs (S.ortho.max_x - S.ortho.min_x);
+  double height = fabs (S.ortho.max_y - S.ortho.min_y);
 
   /*
    * Box the smaller of the two dimensions.
@@ -60,7 +60,7 @@ mouse_wheel (int button, int dir, int x, int y)
     }
 
   // Zoom in
-  if (dir > 0) 
+  if (dir > 0)
     {
       zoom (x1 + step, y1 + step, x2 - step, y2 - step);
     }
diff --git a/src/controller/callbacks/reshape.c b/src/controller/callbacks/reshape.c
index fec5443..0414be6 100644
--- a/src/controller/callbacks/reshape.c
+++ b/src/controller/callbacks/reshape.c
@@ -21,23 +21,25 @@ reshape (int w, int h)
     {
       if (w >= h)
         {
-          double scale 
-            = ( ( (S.zoom.coords[1] - S.zoom.coords[0]) * ((double) w / (double) h) )
-                - (S.zoom.coords[1] - S.zoom.coords[0]) )
-            * 0.5;
+          double scale
+            =
+            (((S.zoom.coords[1] -
+               S.zoom.coords[0]) * ((double) w / (double) h)) -
+             (S.zoom.coords[1] - S.zoom.coords[0])) * 0.5;
 
           S.ortho.min_x = S.zoom.coords[0] - scale;
-          S.ortho.max_x = S.zoom.coords[1] + scale; 
+          S.ortho.max_x = S.zoom.coords[1] + scale;
           S.ortho.min_y = S.zoom.coords[2];
           S.ortho.max_y = S.zoom.coords[3];
         }
       else
         {
-          double scale 
-            = ( ( (S.zoom.coords[3] - S.zoom.coords[2]) * ((double) h / (double) w) )
-                - (S.zoom.coords[3] - S.zoom.coords[2]) )
-            * 0.5;
-          
+          double scale
+            =
+            (((S.zoom.coords[3] -
+               S.zoom.coords[2]) * ((double) h / (double) w)) -
+             (S.zoom.coords[3] - S.zoom.coords[2])) * 0.5;
+
           S.ortho.min_x = S.zoom.coords[0];
           S.ortho.max_x = S.zoom.coords[1];
           S.ortho.min_y = S.zoom.coords[2] - scale;
@@ -45,7 +47,7 @@ reshape (int w, int h)
         }
     }
 
-  else 
+  else
     {
       /*
        * This scaling produces an odd effect when the coordinates are
@@ -68,7 +70,7 @@ reshape (int w, int h)
           S.ortho.min_y = S.ortho_min;
           S.ortho.max_y = S.ortho_max;
         }
-    }  
+    }
 
   set_ortho ();
 
diff --git a/src/model/geometry/map_geometry.c b/src/model/geometry/map_geometry.c
index 8bc79a3..c4c8db0 100644
--- a/src/model/geometry/map_geometry.c
+++ b/src/model/geometry/map_geometry.c
@@ -15,10 +15,9 @@ map_geometry (void)
       glLoadName (i);
 
       // Draw the protein geometry.
-      float* v = S.base_vertices_data + (i * 2);
+      float *v = S.base_vertices_data + (i * 2);
       glPushMatrix ();
-      glTranslatef (*v,
-                    *(v+1), 0.0);
+      glTranslatef (*v, *(v + 1), 0.0);
       glColor4fv (S.base_colors_data + (i * 4));
       glCallList (S.list_offset + PROTEIN_GEOMETRY);
       glPopMatrix ();
@@ -27,10 +26,9 @@ map_geometry (void)
       if (S.selection.set[i])
         {
           glPushMatrix ();
-          glTranslatef (*v,
-                        *(v+1), 0.0);
+          glTranslatef (*v, *(v + 1), 0.0);
           glColor4f (0.5, 0.5, 0.5, 1.0);
-          glCallList (S.list_offset + PROTEIN_SELECTED_GEOMETRY);      
+          glCallList (S.list_offset + PROTEIN_SELECTED_GEOMETRY);
           glPopMatrix ();
         }
     }
diff --git a/src/model/state/pan_info_init.h b/src/model/state/pan_info_init.h
index f47b790..0d01659 100644
--- a/src/model/state/pan_info_init.h
+++ b/src/model/state/pan_info_init.h
@@ -3,6 +3,6 @@
 
 #include "pan_info.h"
 
-void pan_info_init (PAN_INFO* p);
+void pan_info_init (PAN_INFO * p);
 
 #endif // PAN_INFO_INIT_H
diff --git a/src/model/state/zoom_info_init.c b/src/model/state/zoom_info_init.c
index aa230d8..662c575 100644
--- a/src/model/state/zoom_info_init.c
+++ b/src/model/state/zoom_info_init.c
@@ -8,6 +8,6 @@ zoom_info_init (ZOOM_INFO * z)
   z->coords[1] = 0.0;
   z->coords[2] = 0.0;
   z->coords[3] = 0.0;
-  
+
   return;
 }