Index: trunk/Ohana/src/addstar/src/build_links.c
===================================================================
--- trunk/Ohana/src/addstar/src/build_links.c	(revision 26398)
+++ trunk/Ohana/src/addstar/src/build_links.c	(revision 26399)
@@ -1,3 +1,26 @@
 # include "addstar.h"
+
+/* 
+
+There are two modes for the measure table: sorted and unsorted. 
+
+In sorted mode, all measures associated with a given average are in a single block.  The block
+is pointed to by average->measureOffset and the range is average->Nmeasure
+
+In unsorted mode, it is not possible to go directly from average to measure without scanning.
+In this case, it is necessary to use the value measure->averef to find the corresponding
+average entry.  
+
+Note that average->measureOffset and measure->averef are only valid for a given load of the
+data: they refer to the sequence number in the data blocks.
+
+next_meas is a list of the equivalent sequence of the measure block as if it were sorted.
+
+to find the sequence of measurements for a given average:
+n_0 = average->measureOffset
+n_1 = next_meas[n_0]
+n_i = next_meas[n_i-1]
+
+*/
 
 /* build the initial links assuming the table is sorted, 
@@ -31,4 +54,110 @@
 }
 
+/* construct measure links which are valid FOR THIS LOAD
+ * - if we have a full load, we will get links which can
+ *   be used by other programs (eg, relphot, etc)
+ * - if we have a partial load, the links are only valid
+ *   for that partial load
+ */ 
+
+int *build_measure_links (Average *average, int Naverage, Measure *measure, int Nmeasure) {
+
+  int i, m, k, Nm, averef;
+  int *next;
+
+  ALLOCATE (next, int, Nmeasure);
+
+  /* reset the Nm, offset values for average */
+  for (i = 0; i < Naverage; i++) {
+    average[i].measureOffset = -1;
+    average[i].Nmeasure     =  0;
+  }
+
+  for (Nm = 0; Nm < Nmeasure; Nm++) {
+    averef = measure[Nm].averef;
+    m = average[averef].measureOffset;  
+    next[Nm] = -1;
+
+    if (m == -1) { /* no links yet for source */
+      average[averef].measureOffset = Nm;
+      average[averef].Nmeasure     = 1;
+      continue;
+    }
+
+    for (k = 0; next[m] != -1; k++) {
+      m = next[m];
+      if (m >= Nmeasure) {
+	fprintf (stderr, "WARNING: m out of bounds (1)\n");
+      }
+    }
+
+    average[averef].Nmeasure = k + 2;
+    next[m] = Nm;
+    if (m >= Nmeasure) {
+      fprintf (stderr, "WARNING: m out of bounds (2)\n");
+    }
+  }
+  return (next);
+}
+
+/* average[].measureOffset, average[].Nmeasure are valid within an addstar run */
+int add_meas_link (Average *average, int *next, int Nmeasure, int NMEASURE) {
+
+  int k, m;
+
+  /* if we have trouble, check validity of next[m] : m < Nmeasure */
+  m = average[0].measureOffset;  
+
+  for (k = 0; k < average[0].Nmeasure - 1; k++)  {
+    m = next[m];
+    if (m >= NMEASURE) {
+      fprintf (stderr, "WARNING: m out of bounds (3)\n");
+    }
+  }
+
+  /* set up references */
+  next[Nmeasure] = -1;
+  if (Nmeasure >= NMEASURE) {
+    fprintf (stderr, "WARNING: Nmeasure out of bounds (1)\n");
+  }
+
+  if (m == -1) {
+    average[0].measureOffset = Nmeasure;
+  } else {
+    next[m] = Nmeasure;
+    if (m >= NMEASURE) {
+      fprintf (stderr, "WARNING: m out of bounds (4)\n");
+    }
+  }
+
+  return (TRUE);
+}
+
+/* Missing does not carry enough information to reconstruct the links
+   we must always save the missing table, if it exists */
+
+Measure *sort_measure (Average *average, int Naverage, Measure *measure, int Nmeasure, int *next) {
+
+  int i, k, n, N;
+  Measure *tmpmeasure;
+
+  /* fix order of Measure (memory intensive, but fast) */
+  N = 0; 
+  ALLOCATE (tmpmeasure, Measure, Nmeasure);
+  for (i = 0; i < Naverage; i++) {
+    n = average[i].measureOffset;
+    average[i].measureOffset = N;
+    for (k = 0; k < average[i].Nmeasure; k++, N++) {
+      if (n == -1) abort();
+      tmpmeasure[N] = measure[n]; 
+      if (measure[n].averef != i) abort();
+      tmpmeasure[N].averef = i;
+      n = next[n];
+    }
+  }
+  free (measure);
+  return (tmpmeasure);
+}
+
 /* build the initial links assuming the table is sorted */
 int *init_missing_links (Average *average, int Naverage, Missing *missing, int Nmissing) {
@@ -57,37 +186,4 @@
 }
 
-/* average[].measureOffset, average[].Nmeasure are valid within an addstar run */
-int add_meas_link (Average *average, int *next, int Nmeasure, int NMEASURE) {
-
-  int k, m;
-
-  /* if we have trouble, check validity of next[m] : m < Nmeasure */
-  m = average[0].measureOffset;  
-
-  for (k = 0; k < average[0].Nmeasure - 1; k++)  {
-    m = next[m];
-    if (m >= NMEASURE) {
-      fprintf (stderr, "WARNING: m out of bounds (3)\n");
-    }
-  }
-
-  /* set up references */
-  next[Nmeasure] = -1;
-  if (Nmeasure >= NMEASURE) {
-    fprintf (stderr, "WARNING: Nmeasure out of bounds (1)\n");
-  }
-
-  if (m == -1) {
-    average[0].measureOffset = Nmeasure;
-  } else {
-    next[m] = Nmeasure;
-    if (m >= NMEASURE) {
-      fprintf (stderr, "WARNING: m out of bounds (4)\n");
-    }
-  }
-
-  return (TRUE);
-}
-
 int add_miss_link (Average *average, int *next, int Nmissing) {
 
@@ -109,75 +205,4 @@
 }
 
-/* construct measure links which are valid FOR THIS LOAD
- * - if we have a full load, we will get links which can
- *   be used by other programs (eg, relphot, etc)
- * - if we have a partial load, the links are only valid
- *   for that partial load
- */ 
-
-int *build_measure_links (Average *average, int Naverage, Measure *measure, int Nmeasure) {
-
-  int i, m, k, Nm, averef;
-  int *next;
-
-  ALLOCATE (next, int, Nmeasure);
-
-  /* reset the Nm, offset values for average */
-  for (i = 0; i < Naverage; i++) {
-    average[i].measureOffset = -1;
-    average[i].Nmeasure     =  0;
-  }
-
-  for (Nm = 0; Nm < Nmeasure; Nm++) {
-    averef = measure[Nm].averef;
-    m = average[averef].measureOffset;  
-    next[Nm] = -1;
-
-    if (m == -1) { /* no links yet for source */
-      average[averef].measureOffset = Nm;
-      average[averef].Nmeasure     = 1;
-      continue;
-    }
-
-    for (k = 0; next[m] != -1; k++) {
-      m = next[m];
-      if (m >= Nmeasure) {
-	fprintf (stderr, "WARNING: m out of bounds (1)\n");
-      }
-    }
-
-    average[averef].Nmeasure = k + 2;
-    next[m] = Nm;
-    if (m >= Nmeasure) {
-      fprintf (stderr, "WARNING: m out of bounds (2)\n");
-    }
-  }
-  return (next);
-}
-
-/* Missing does not carry enough information to reconstruct the links
-   we must always save the missing table, if it exists */
-
-Measure *sort_measure (Average *average, int Naverage, Measure *measure, int Nmeasure, int *next) {
-
-  int i, k, n, N;
-  Measure *tmpmeasure;
-
-  /* fix order of Measure (memory intensive, but fast) */
-  N = 0; 
-  ALLOCATE (tmpmeasure, Measure, Nmeasure);
-  for (i = 0; i < Naverage; i++) {
-    n = average[i].measureOffset;
-    average[i].measureOffset = N;
-    for (k = 0; k < average[i].Nmeasure; k++, N++) {
-      tmpmeasure[N] = measure[n]; 
-      tmpmeasure[N].averef = i;
-      n = next[n];
-    }
-  }
-  free (measure);
-  return (tmpmeasure);
-}
-
 Missing *sort_missing (Average *average, int Naverage, Missing *missing, int Nmissing, int *next) {
 
@@ -199,2 +224,3 @@
   return (tmpmissing);
 }
+