Multiple changes after throughout testing (#308)

- Improved code readability by auto-indenting core functions and reworking 'setup' and 'Examples' functions, including adding necessary files for separation from core functions.
- Renamed functions for clarity and fixed multiple small bugs; changes are compatible with OpenEarthTools but distinct. 

---------

Co-authored-by: Keith Roberts <kroberts@baird.com>

.gitignore

@@ -3,6 +3,7 @@ datasets/
 fort.*
 Examples/*
 !Examples/Example_*
+!Examples/runall.m
 */*.mat
 *.15
 *.14

@ann/ann.m

@@ -1,7 +1,7 @@
 function anno = ann(data)
 %
-% ANN class 
-% 
+% ANN class
+%
 % Usage:
 %   anno = ann(pts)
 %
@@ -15,7 +15,7 @@
 %   ksearch:
 %       k-nn search
 %       [idx dst] = ksearch(anno, pt, k, eps, [asm])
-%       
+%
 %       idx - indices of matching points:  (k)x(#points)
 %       dst - square distance of the points
 %
@@ -42,11 +42,11 @@
 %       anno - active ann object handle
 %       pt   - query point (only one this time, (d)x1 vector)
 %       r    - search radius (_not_ squared)
-%       k    - required k aprox. nearest neighbors. Will return at most k nieghbors 
+%       k    - required k aprox. nearest neighbors. Will return at most k nieghbors
 %              of distance at most r.
 %       eps  - accuracy multiplicative factor
 %       asm  - allow self match flag (optional, default: true)
-%       
+%
 %       note that numel(idx) and numel(dst) = min(k, inr)
 %       inr might be larger than k reflecting how many points are actually
 %       in the search radius.
@@ -86,10 +86,10 @@
 %				algorithm for approximate nearest neighbor searching,''
 %				5th Ann. ACM-SIAM Symposium on Discrete Algorithms,
 %				1994, 573-582.
-% 
-%   This software is provided under the provisions of the 
+%
+%   This software is provided under the provisions of the
 %   Lesser GNU Public License (LGPL).
-%   This software can be used only for research purposes, you should cite 
+%   This software can be used only for research purposes, you should cite
 %   the aforementioned papers in any resulting publication.
 %
 %

@ann/close.m

@@ -5,6 +5,6 @@
 % if isfield(anno,'working_flag') && anno.working_flag
 if anno.working_flag
     annmex(anno.modes.CLOSE, anno.kd_ptr);
-%     anno.kd_ptr = annmex(anno.modes.CLOSE, anno.kd_ptr);
+    % anno.kd_ptr = annmex(anno.modes.CLOSE, anno.kd_ptr);
 end
 anno = [];

@ann/frsearch.m

@@ -1,5 +1,5 @@
 function [idx dst inr] = frsearch(ann, query, r, k, epsl, asm)
-% 
+%
 % kNN FR search
 %   Usage:
 %     [idx dst inr] = frsearch(ann, query, rad, k, asm, eps)
@@ -9,8 +9,8 @@
 %   query - (d)x(N) query points
 %   k - number of nearest nieghbors (if points in ann < k than less than k
 %                                    points are returned)
-%   epsl - epsilon search precision 
-%   asm - allow self match flag, if false points with dst = 0 are ignored 
+%   epsl - epsilon search precision
+%   asm - allow self match flag, if false points with dst = 0 are ignored
 %         (defualt is true)
 %
 if nargin == 5
@@ -27,7 +27,7 @@
 
 [idx dst inr] = annmex(ann.modes.FRSEARCH, ann.kd_ptr, query, k, epsl, r);
 
-if ~asm 
+if ~asm
     if dst(1) == 0
         dst(1) = [];
         idx(1) = [];

@ann/ksearch.m

@@ -1,5 +1,5 @@
 function [idx dst] = ksearch(ann, query, k, epsl, asm)
-% 
+%
 % kNN search
 %   Usage:
 %     [idx dst] = ksearch(ann, query, k, epsl, [asm])
@@ -9,8 +9,8 @@
 %   query - (d)x(N) query points
 %   k - number of nearest nieghbors (if points in ann < k than less than k
 %                                    points are returned)
-%   epsl - epsilon search precision 
-%   asm - allow self match flag, if false points with dst = 0 are ignored 
+%   epsl - epsilon search precision
+%   asm - allow self match flag, if false points with dst = 0 are ignored
 %         (default is true)
 %
 if nargin == 4

@ann/prisearch.m

@@ -1,5 +1,5 @@
 function [idx dst] = prisearch(ann, query, k, epsl, asm)
-% 
+%
 % kNN search
 %   Usage:
 %     [idx dst] = prisearch(ann, query, k, asm, eps)
@@ -9,8 +9,8 @@
 %   query - (d)x(N) query points
 %   k - number of nearest nieghbors (if points in ann < k than less than k
 %                                    points are returned)
-%   epsl - epsilon search precision 
-%   asm - allow self match flag, if false points with dst = 0 are ignored 
+%   epsl - epsilon search precision
+%   asm - allow self match flag, if false points with dst = 0 are ignored
 %         (defualt is true)
 %
 if nargin == 4

@ann/private/get_data_class.m

@@ -1,5 +1,5 @@
 function [ccls cfun] = get_data_class()
-% get class supported by ann 
+% get class supported by ann
 d = annmex();
 ccls = class(d);
 

@ann/private/modes.m

@@ -3,5 +3,5 @@
 m.OPEN = 1;
 m.CLOSE = 2;
 m.KSEARCH = 3;
-m.PRISEARCH=4;
-m.FRSEARCH=5;
+m.PRISEARCH = 4;
+m.FRSEARCH = 5;