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Revision: 7
Committed: Sat Aug 18 14:25:34 2007 UTC (11 years, 9 months ago) by kmr
File size: 6214 byte(s)
Log Message:
README improvements.

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1 This directory contains the code for the user-defined type,
2 BIOSEG, representing contiguous intervals in biological sequence.
3
4 (Most of this documentation is copied from contrib/seg/README.seg in the
5 PostgreSQL source).
6
7
8 FILES
9 =====
10
11 Makefile building instructions for the shared library
12
13 README.bioseg the file you are now reading
14
15 bioseg.c the implementation of this data type in C
16
17 bioseg.sql.in SQL code needed to register this type with PostgreSQL
18 (transformed to bioseg.sql by make)
19
20 INSTALLATION
21 ============
22
23 Change into the contrib directory in PostgreSQL and unpack the bioseg tar
24 file:
25 gzip -d < bioseg-x.y.tar.gz | tar xf -
26
27 To install the type, change to the bioseg directory and run
28
29 make
30 make install
31
32 The user running "make install" may need root access; depending on the
33 configuration of PostgreSQL.
34
35 This only installs the type implementation and documentation. To make the
36 type available in any particular database, do
37
38 psql -d databasename < bioseg.sql
39
40 If you install the type in the template1 database, all subsequently created
41 databases will inherit it.
42
43 To test the new type, after "make install" do
44
45 make installcheck
46
47 If it fails, examine the file regression.diffs to find out the reason (the
48 test code is a direct adaptation of the regression tests from the main
49 source tree).
50
51 If you have a full installation of PostgreSQL, including the pg_config
52 program, bioseg can be unpacked anywhere and built like:
53
54 make USE_PGXS=t
55 make install USE_PGXS=t
56
57 and the type can then be installed in a particular database by any user with:
58
59 psql -d databasename < `pg_config --sharedir`/contrib/bioseg.sql
60
61
62 SYNTAX
63 ======
64
65 The user visible representation of an interval is formed using one or two
66 integers greater than 0 joined by the range operator ('..' or '...').
67 The first integer must be less than or equal to the second.
68
69 11..22 An interval from 10 to 20 inclusive - length 11 (= 22-11+1)
70
71 1...2 The same as 1..2
72
73 50 The same as 50..50
74
75 In a statement, bioseg values have the form:
76 '<start>..<end>'::bioseg
77 or can be created with:
78 bioseg_create(start, end)
79
80 For example:
81 CREATE TABLE test_bioseg (id integer, seg bioseg);
82 insert into test_bioseg values (1, '1000..2000'::bioseg);
83 or, equivalently
84 insert into test_bioseg values (1, bioseg_create(1000, 2000));
85
86
87 USAGE
88 =====
89
90 The following is a list of the available operators. The [a, b] should be
91 replace in a statement with 'a..b'::bioseg or bioseg_create(a, b).
92
93 [a, b] && [c, d] Overlaps
94
95 Returns true if and only if segments [a, b] and [c, d] overlap
96
97 [a, b] << [c, d] Is left of
98
99 The left operand, [a, b], occurs entirely to the left of the
100 right operand, [c, d]. It means, [a, b] << [c, d] is true if b
101 < c and false otherwise
102
103 [a, b] >> [c, d] Is right of
104
105 [a, b] is occurs entirely to the right of [c, d].
106 [a, b] >> [c, d] is true if a > d and false otherwise
107
108 [a, b] &< [c, d] Overlaps or is left of
109
110 This might be better read as "does not extend to right of".
111 It is true when b <= d.
112
113 [a, b] &> [c, d] Overlaps or is right of
114
115 This might be better read as "does not extend to left of".
116 It is true when a >= c.
117
118 [a, b] = [c, d] Same as
119
120 The segments [a, b] and [c, d] are identical, that is, a == b
121 and c == d
122
123 [a, b] @> [c, d] Contains
124
125 The segment [a, b] contains the segment [c, d], that is,
126 a <= c and b >= d
127
128 [a, b] <@ [c, d] Contained in
129
130 The segment [a, b] is contained in [c, d], that is,
131 a >= c and b <= d
132
133 Although the mnemonics of the following operators is questionable, I
134 preserved them to maintain visual consistency with other geometric
135 data types defined in PostgreSQL.
136
137 Other operators:
138
139 [a, b] < [c, d] Less than
140 [a, b] > [c, d] Greater than
141
142 These operators do not make a lot of sense for any practical
143 purpose but sorting. These operators first compare (a) to (c),
144 and if these are equal, compare (b) to (d). That accounts for
145 reasonably good sorting in most cases, which is useful if
146 you want to use ORDER BY with this type
147
148
149 NOTE: The performance of an R-tree index can largely depend on the
150 order of input values. It may be very helpful to sort the input table
151 on the BIOSEG column (see the script sort-segments.pl for an example)
152
153
154 INDEXES
155 =======
156
157 A GiST index can created for bioseg columns that will greatly speed up
158 overlaps and contains queries. For example:
159
160 CREATE TABLE tt (range bioseg, id integer);
161 CREATE INDEX tt_range_idx ON tt USING gist (range);
162
163
164 INTERBASE COORDINATES
165 =====================
166
167 The standard bioseg type uses the common convention of numbering the bases
168 starting at 1. If you wish to use "interbase" coordinates (also known as "0
169 based" or "half-open intervals") run the build with INTERBASE_COORDS defined
170 in make, ie.:
171
172 make INTERBASE_COORDS=t
173 make install INTERBASE_COORDS=t
174
175 This will compile and install the implementation for the "bioseg0" type.
176 The "0" in the name being a mnemonic for "0-based".
177
178 Then restart PostgreSQL and read "bioseg0.sql":
179 psql -d databasename < bioseg0.sql
180 as to install the type in a database.
181
182 Note
183 ----
184 In the interbase system '1..10'::bioseg0 and '10..20'::bioseg0 don't overlap,
185 whereas in the 1-based system '1..10'::bioseg and '10..20'::bioseg have a one
186 base overlap. Also note that the length of '1..10'::bioseg0 is 9, whereas the
187 length of '1..10'::bioseg is 10.
188
189 See:
190 http://www.gmod.org/wiki/index.php/Introduction_to_Chado#Interbase_Coordinates
191 for a longer discussion of the differences between the coordinate systems.
192
193
194 TESTS
195 =====
196
197 The installation of bioseg can be checked by running:
198
199 make installcheck
200
201
202 CREDITS
203 =======
204
205 Note from the author: Most of the code and all of the hard work needed to
206 implement BIOSEG was by Gene Selkov, Jr, author of the SEG type (contrib/seg
207 in the PostgreSQL source). All bugs are due to me (kmr).
208
209
210 AUTHOR
211 ======
212
213 Kim Rutherford <kmr@flymine.org>
214
215 SEG code by Gene Selkov, Jr.