Update docs (and shake out buglets revealed along the way)

7 files changed, 14 insertions, 52 deletions

diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 5f5ff7fa..ae717e55 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -24,7 +24,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
                                  src/geometry.h src/peaks.h src/stream.h \
                                  src/render.h src/index.h src/image.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
-                                 src/index-priv.h src/reax.h src/cell-utils.h \
+                                 src/reax.h src/cell-utils.h \
                                  src/integer_matrix.h src/crystal.h \
                                  src/grainspotter.h src/xds.h
 
diff --git a/libcrystfel/src/index-priv.h b/libcrystfel/src/index-priv.h
deleted file mode 100644
index 6fccee9f..00000000
--- a/libcrystfel/src/index-priv.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * index-priv.h
- *
- * Indexing private data
- *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
- *
- * Authors:
- *   2010,2012 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifndef INDEXPRIV_H
-#define INDEXPRIV_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "index.h"
-
-struct _indexingprivate
-{
-	IndexingMethod indm;
-};
-
-
-#endif	/* INDEXPRIV_H */
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 311dc2ce..bd187cf5 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -48,7 +48,6 @@
 #include "xds.h"
 #include "detector.h"
 #include "index.h"
-#include "index-priv.h"
 #include "reax.h"
 #include "grainspotter.h"
 #include "geometry.h"
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index f8f6e55b..31ee4339 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -64,6 +64,18 @@
  * @INDEXING_DIRAX: Invoke DirAx
  * @INDEXING_MOSFLM: Invoke MOSFLM
  * @INDEXING_REAX: DPS algorithm using known cell parameters
+ * @INDEXING_GRAINSPOTTER: Invoke GrainSpotter
+ * @INDEXING_XDS: Invokve XDS
+ * @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
+ *   axes for agreement with given cell.
+ * @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given
+ *   cell, and permute them if necessary.
+ * @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing
+ *   result.
+ * @INDEXING_USE_LATTICE_TYPE: Use lattice type and centering information to
+ *   guide the indexing process.
+ * @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
+ *   indexingprocess.
  *
  * An enumeration of all the available indexing methods.
  **/
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 6be728fe..f788bae5 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -50,9 +50,6 @@ extern void integrate_reflections(struct image *image,
 extern int peak_sanity_check(struct image *image, Crystal **crystals,
                              int n_cryst);
 
-extern void estimate_resolution(RefList *list, UnitCell *cell,
-                                double *min, double *max);
-
 extern void validate_peaks(struct image *image, double min_snr,
                            int ir_inn, int ir_mid, int ir_out,
                            int use_saturated);
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 3460a4f2..4ecb870b 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -48,7 +48,6 @@
 #include "cell.h"
 #include "cell-utils.h"
 #include "index.h"
-#include "index-priv.h"
 
 
 /* Minimum number of standard deviations above the mean a peak must be in the
diff --git a/libcrystfel/src/symmetry.h b/libcrystfel/src/symmetry.h
index 4a8f98d3..7c80522a 100644
--- a/libcrystfel/src/symmetry.h
+++ b/libcrystfel/src/symmetry.h
@@ -79,6 +79,6 @@ extern int is_centrosymmetric(const SymOpList *s);
 extern const char *symmetry_name(const SymOpList *ops);
 extern void describe_symmetry(const SymOpList *s);
 
-extern void add_symop(SymOpList *s, IntegerMatrix *m);
+extern void add_symop(SymOpList *ops, IntegerMatrix *m);
 
 #endif	/* SYMMETRY_H */