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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 external 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
76 USAGE
77 =====
78
79 Available operators include:
80
81 [a, b] && [c, d] Overlaps
82
83 Returns true if and only if segments [a, b] and [c, d] overlap
84
85 [a, b] << [c, d] Is left of
86
87 The left operand, [a, b], occurs entirely to the left of the
88 right operand, [c, d]. It means, [a, b] << [c, d] is true if b
89 < c and false otherwise
90
91 [a, b] >> [c, d] Is right of
92
93 [a, b] is occurs entirely to the right of [c, d].
94 [a, b] >> [c, d] is true if a > d and false otherwise
95
96 [a, b] &< [c, d] Overlaps or is left of
97
98 This might be better read as "does not extend to right of".
99 It is true when b <= d.
100
101 [a, b] &> [c, d] Overlaps or is right of
102
103 This might be better read as "does not extend to left of".
104 It is true when a >= c.
105
106 [a, b] = [c, d] Same as
107
108 The segments [a, b] and [c, d] are identical, that is, a == b
109 and c == d
110
111 [a, b] @> [c, d] Contains
112
113 The segment [a, b] contains the segment [c, d], that is,
114 a <= c and b >= d
115
116 [a, b] <@ [c, d] Contained in
117
118 The segment [a, b] is contained in [c, d], that is,
119 a >= c and b <= d
120
121 Although the mnemonics of the following operators is questionable, I
122 preserved them to maintain visual consistency with other geometric
123 data types defined in PostgreSQL.
124
125 Other operators:
126
127 [a, b] < [c, d] Less than
128 [a, b] > [c, d] Greater than
129
130 These operators do not make a lot of sense for any practical
131 purpose but sorting. These operators first compare (a) to (c),
132 and if these are equal, compare (b) to (d). That accounts for
133 reasonably good sorting in most cases, which is useful if
134 you want to use ORDER BY with this type
135
136
137 NOTE: The performance of an R-tree index can largely depend on the
138 order of input values. It may be very helpful to sort the input table
139 on the BIOSEG column (see the script sort-segments.pl for an example)
140
141
142 INDEXES
143 =======
144
145 A GiST index can created for bioseg columns that will greatly speed up
146 overlaps and contains queries. For example:
147
148 CREATE TABLE tt (range bioseg, id integer);
149 CREATE INDEX tt_range_idx ON tt USING gist (range);
150
151
152 INTERBASE COORDINATES
153 =====================
154
155 The standard bioseg type uses the common convention of numbering the bases
156 starting at 1. If you wish to use "interbase" coordinates (also known as "0
157 based" or "half-open intervals") run the build with INTERBASE_COORDS defined
158 in make, ie.:
159
160 make INTERBASE_COORDS=t
161 make install INTERBASE_COORDS=t
162
163 This will compile and install the implementation for the "bioseg0" type.
164 The "0" in the name being a mnemonic for "0-based".
165
166 Then restart PostgreSQL and run:
167 psql -d databasename < bioseg.sql
168 as usual to install the type in the database.
169
170 Note
171 ----
172 In the interbase system '1..10'::bioseg0 and '10..20'::bioseg0 don't overlap,
173 whereas in the 1-based system '1..10'::bioseg and '10..20'::bioseg have a one
174 base overlap. Also note that the length of '1..10'::bioseg0 is 9, whereas the
175 length of '1..10'::bioseg is 10.
176
177 See:
178 http://www.gmod.org/wiki/index.php/Introduction_to_Chado#Interbase_Coordinates
179 for a longer discussion of the differences between the coordinate systems.
180
181
182 TESTS
183 =====
184
185 The installation of bioseg can be checked by running:
186
187 make installcheck
188
189
190 CREDITS
191 =======
192
193 Note from the author: Most of the code and all of the hard work needed to
194 implement BIOSEG was by Gene Selkov, Jr, author of the SEG type (contrib/seg
195 in the PostgreSQL source). All bugs are due to me.
196
197
198 AUTHOR
199 ======
200
201 Kim Rutherford <kmr@flymine.org>