18 files changed, 106 insertions, 47 deletions

diff --git a/src/Makefile.am b/src/Makefile.am
index 6e20122..38626c7 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -12,10 +12,11 @@ exp004viz_SOURCES = \
         controller/set_ortho.c \
         db/dbconnect.c \
         exp004viz.c \
-        model/density_legend_geometry.c \
         model/exp004base.c \
-        model/map_geometry.c \
-        model/protein_geometry.c \
+        model/geometry/density_legend_geometry.c \
+        model/geometry/map_geometry.c \
+        model/geometry/protein_geometry.c \
+        model/geometry/protein_selected_geometry.c \
         model/selection_info_init.c \
         model/zoom_info_init.c \
         util/ati_meminfo.c \
@@ -39,11 +40,12 @@ noinst_HEADERS = \
         controller/selsave.h \
         controller/set_ortho.h \
         db/dbconnect.h \
-        model/density_legend_geometry.h \
         model/exp004base.h \
         model/exp004state.h \
-        model/map_geometry.h \
-        model/protein_geometry.h \
+        model/geometry/density_legend_geometry.h \
+        model/geometry/protein_geometry.h \
+        model/geometry/protein_selected_geometry.h \
+        model/geometry/map_geometry.h \
         model/selection_info.h \
         model/selection_info_init.h \
         model/selection_purposes.h \
diff --git a/src/controller/clear_selection.sqc b/src/controller/clear_selection.sqc
index ec98b4c..b4ff0a3 100644
--- a/src/controller/clear_selection.sqc
+++ b/src/controller/clear_selection.sqc
@@ -1,6 +1,6 @@
 #define GL_GLEXT_PROTOTYPES
 #include "clear_selection.h"
-#include "../model/map_geometry.h"
+#include "../model/geometry/map_geometry.h"
 #include "../view/exp004state0.h"
 #include <GL/glut.h>
 #include "sqlca.h"
diff --git a/src/controller/exp004processhits.c b/src/controller/exp004processhits.c
index 72daa2f..c9ae080 100644
--- a/src/controller/exp004processhits.c
+++ b/src/controller/exp004processhits.c
@@ -1,6 +1,6 @@
 #define GL_GLEXT_PROTOTYPES
 #include "../view/exp004state0.h"
-#include "../model/map_geometry.h"
+#include "../model/geometry/map_geometry.h"
 #include "exp004processhits.h"
 #include "selsave.h"
 
@@ -14,7 +14,7 @@
  * [Angel,2008,pp80-81].
  */
 void
-exp004processhits (const GLint hits, const GLuint* hitlist)
+exp004processhits (const GLint hits, const GLuint * hitlist)
 {
   for (unsigned int i = 0; i < hits; i++)
     {
@@ -24,10 +24,12 @@ exp004processhits (const GLint hits, const GLuint* hitlist)
        * Add the hits to the selection.
        */
       S.selection.set[*hitlist] = true;
+      /*
       S.base_colors_data[*hitlist][0] = SELECT_COLOR_R;
       S.base_colors_data[*hitlist][1] = SELECT_COLOR_G;
       S.base_colors_data[*hitlist][2] = SELECT_COLOR_B;
       S.base_colors_data[*hitlist][3] = SELECT_COLOR_A;
+      */
 
       hitlist++;
     }
diff --git a/src/controller/exp004processhits.h b/src/controller/exp004processhits.h
index b0e088a..0cc9e4b 100644
--- a/src/controller/exp004processhits.h
+++ b/src/controller/exp004processhits.h
@@ -3,6 +3,6 @@
 
 #include <GL/glut.h>
 
-void exp004processhits (const GLint hits, const GLuint *hitlist);
+void exp004processhits (const GLint hits, const GLuint * hitlist);
 
 #endif // EXP004PROCESSHITS_H
diff --git a/src/controller/exp004reshape.c b/src/controller/exp004reshape.c
index 891de08..a127e46 100644
--- a/src/controller/exp004reshape.c
+++ b/src/controller/exp004reshape.c
@@ -1,7 +1,7 @@
 #include "exp004reshape.h"
 #include "set_ortho.h"
 #include "../view/exp004state0.h"
-#include "../model/density_legend_geometry.h"
+#include "../model/geometry/density_legend_geometry.h"
 #include <GL/glut.h>
 
 #define S exp004state0
diff --git a/src/controller/selection_from_db.sqc b/src/controller/selection_from_db.sqc
index 3bde460..755c9c9 100644
--- a/src/controller/selection_from_db.sqc
+++ b/src/controller/selection_from_db.sqc
@@ -1,6 +1,6 @@
 #define GL_GLEXT_PROTOTYPES
 #include "selection_from_db.h"
-#include "../model/map_geometry.h"
+#include "../model/geometry/map_geometry.h"
 #include "../view/exp004state0.h"
 #include "../util/check_error.h"
 #include <GL/glut.h>
diff --git a/src/model/exp004state.h b/src/model/exp004state.h
index 6f9aad7..f6e99c0 100644
--- a/src/model/exp004state.h
+++ b/src/model/exp004state.h
@@ -24,7 +24,8 @@
 #define SELECT_COLOR_A 0.75
 
 typedef enum
-{ PROTEIN_GEOMETRY, DENSITY_LEGEND_GEOMETRY, MAP_GEOMETRY } LISTS;
+{ PROTEIN_GEOMETRY, PROTEIN_SELECTED_GEOMETRY, DENSITY_LEGEND_GEOMETRY,
+    MAP_GEOMETRY } LISTS;
 #define NUM_LISTS 2
 
 /*
diff --git a/src/model/density_legend_geometry.c b/src/model/geometry/density_legend_geometry.c
index 7e30de8..83f34d9 100644
--- a/src/model/density_legend_geometry.c
+++ b/src/model/geometry/density_legend_geometry.c
@@ -1,6 +1,6 @@
 #include "density_legend_geometry.h"
-#include "../view/exp004state0.h"
-#include "../controller/exp004reshape.h"
+#include "../../view/exp004state0.h"
+#include "../../controller/exp004reshape.h"
 #include <GL/glut.h>
 
 #define S exp004state0
diff --git a/src/model/density_legend_geometry.h b/src/model/geometry/density_legend_geometry.h
index 4745ac0..4745ac0 100644
--- a/src/model/density_legend_geometry.h
+++ b/src/model/geometry/density_legend_geometry.h
diff --git a/src/model/geometry/map_geometry.c b/src/model/geometry/map_geometry.c
new file mode 100644
index 0000000..63e409d
--- a/dev/null
+++ b/src/model/geometry/map_geometry.c
@@ -0,0 +1,40 @@
+#include "map_geometry.h"
+#include "../../view/exp004state0.h"
+#include <GL/glut.h>
+
+#define S exp004state0
+
+void
+map_geometry (void)
+{
+  glNewList (S.list_offset + MAP_GEOMETRY, GL_COMPILE);
+  glPolygonMode (GL_FRONT, GL_FILL);
+
+  for (int i = 0; i < ROWS; i++)
+    {
+      glLoadName (i);
+
+      // Draw the protein geometry.
+      glPushMatrix ();
+      glTranslatef (S.base_vertices_data[i][0],
+                    S.base_vertices_data[i][1], 0.0);
+      glColor4fv (S.base_colors_data[i]);
+      glCallList (S.list_offset + PROTEIN_GEOMETRY);
+      glPopMatrix ();
+
+      // If the object is selected, draw the selection geometry.
+      if (S.selection.set[i])
+        {
+          glPushMatrix ();
+          glTranslatef (S.base_vertices_data[i][0],
+                        S.base_vertices_data[i][1], 0.0);
+          glColor4f (0.5, 0.5, 0.5, 1.0);
+          glCallList (S.list_offset + PROTEIN_SELECTED_GEOMETRY);      
+          glPopMatrix ();
+        }
+    }
+
+  glEndList ();
+
+  return;
+}
diff --git a/src/model/map_geometry.h b/src/model/geometry/map_geometry.h
index f5b6701..f5b6701 100644
--- a/src/model/map_geometry.h
+++ b/src/model/geometry/map_geometry.h
diff --git a/src/model/protein_geometry.c b/src/model/geometry/protein_geometry.c
index dc71a4e..30a4350 100644
--- a/src/model/protein_geometry.c
+++ b/src/model/geometry/protein_geometry.c
@@ -1,5 +1,5 @@
 #include "protein_geometry.h"
-#include "../view/exp004state0.h"
+#include "../../view/exp004state0.h"
 #include <GL/glut.h>
 
 #define S exp004state0
diff --git a/src/model/protein_geometry.h b/src/model/geometry/protein_geometry.h
index e9ac0db..e9ac0db 100644
--- a/src/model/protein_geometry.h
+++ b/src/model/geometry/protein_geometry.h
diff --git a/src/model/geometry/protein_selected_geometry.c b/src/model/geometry/protein_selected_geometry.c
new file mode 100644
index 0000000..fb37085
--- a/dev/null
+++ b/src/model/geometry/protein_selected_geometry.c
@@ -0,0 +1,30 @@
+#include "protein_selected_geometry.h"
+#include "../../view/exp004state0.h"
+#include <GL/glut.h>
+
+#define S exp004state0
+
+void
+protein_selected_geometry (void)
+{
+  GLUquadricObj *obj = gluNewQuadric ();
+  gluQuadricDrawStyle (obj, GLU_FILL);
+
+  glNewList (S.list_offset + PROTEIN_SELECTED_GEOMETRY, GL_COMPILE);
+
+  glColor4f (255.0, 255.0, 0.0, 0.8);
+
+  /*
+   * The radius of this disk is relative to the radius of the sphere
+   * used for the protein geometry however this dependency is not captured
+   * in the code.  Perhaps a variable radius for the proteins should be
+   * defined in the state object.
+   */
+  gluDisk (obj, 0.04, 0.05, 20, 20);
+
+  glEndList ();
+
+  gluDeleteQuadric (obj);
+
+  return;
+}
diff --git a/src/model/geometry/protein_selected_geometry.h b/src/model/geometry/protein_selected_geometry.h
new file mode 100644
index 0000000..16cf956
--- a/dev/null
+++ b/src/model/geometry/protein_selected_geometry.h
@@ -0,0 +1,9 @@
+#ifndef PROTEIN_SELECTED_GEOMETRY_H
+#define PROTEIN_SELECTED_GEOMETRY_H
+
+/*
+ * Geometry to use for proteins in the active selection.
+ */
+void protein_selected_geometry (void);
+
+#endif // PROTEIN_SELECTED_GEOMETRY_H
diff --git a/src/model/map_geometry.c b/src/model/map_geometry.c
deleted file mode 100644
index 055eb83..0000000
--- a/src/model/map_geometry.c
+++ b/dev/null
@@ -1,27 +0,0 @@
-#include "map_geometry.h"
-#include "../view/exp004state0.h"
-#include <GL/glut.h>
-
-#define S exp004state0
-
-void
-map_geometry (void)
-{
-  glNewList (S.list_offset + MAP_GEOMETRY, GL_COMPILE);
-  glPolygonMode (GL_FRONT, GL_FILL);
-
-  for (int i = 0; i < ROWS; i++)
-    {
-      glLoadName (i);
-      glPushMatrix ();
-      glTranslatef (S.base_vertices_data[i][0],
-                    S.base_vertices_data[i][1], 0.0);
-      glColor4fv (S.base_colors_data[i]);
-      glCallList (S.list_offset + PROTEIN_GEOMETRY);
-      glPopMatrix ();
-    }
-
-  glEndList ();
-
-  return;
-}
diff --git a/src/model/selection_info_init.c b/src/model/selection_info_init.c
index aea2b07..33b3bb5 100644
--- a/src/model/selection_info_init.c
+++ b/src/model/selection_info_init.c
@@ -3,7 +3,7 @@
 
 void
 selection_info_init (SELECTION_INFO * s)
-{  
+{
   memset (s->set, 0, sizeof (bool) * ROWS);
   s->active = false;
   s->purpose = SET;
diff --git a/src/view/exp004init.c b/src/view/exp004init.c
index 78311e6..30d8d96 100644
--- a/src/view/exp004init.c
+++ b/src/view/exp004init.c
@@ -1,8 +1,9 @@
 #include "exp004init.h"
 #include "exp004state0.h"
-#include "../model/density_legend_geometry.h"
-#include "../model/map_geometry.h"
-#include "../model/protein_geometry.h"
+#include "../model/geometry/density_legend_geometry.h"
+#include "../model/geometry/map_geometry.h"
+#include "../model/geometry/protein_geometry.h"
+#include "../model/geometry/protein_selected_geometry.h"
 #include "../model/selection_info_init.h"
 #include "../model/zoom_info_init.h"
 #include <GL/glut.h>
@@ -18,6 +19,7 @@ exp004init (void)
 
   S.list_offset = glGenLists (NUM_LISTS);
   protein_geometry ();
+  protein_selected_geometry ();
   density_legend_geometry ();
   map_geometry ();