This file describes the most commonly used modules,
and the code conventions used throughout the code base in
and under this directory.
SOURCE TREE ORGANIZATION
The major source subdirectories of this source code are:
o - lib - General purpose library routines, some with a biological bent,
many just generally useful for computing.
o - inc - Interfaces to the library modules.
o - utils - Command line utility programs. Like the library a mix of
bioinformatically motivated, and general purpose.
o - hg - Stuff developed for the Human Genome Project and it's successors.
Much of the code in this directory requires MySQL.
o - hg/lib - Human Genome Project specific libraries.
o - hg/inc - Interfaces to the same libraries
o - hg/hgTracks - The part of the UCSC Genome Browser that displays
annotation tracks graphically.
o - hg/hgc - The part of the Genome Browser that responds to a click
on an item in a track.
o - hg/hgTrackUi - The part of the Genome Browser that allows users to configure
a particular track.
o - hg/hgTables - The UCSC Table Browser
o - jkOwnLib - Libraries that support blat, isPcr, gfClient, gfServer.
In general each program, either command line, or web CGI based, has its source in
a different subdirectory. For simple programs, like what is in utils, these often
just have a single C module that is linked with the libraries. For more complex
programs, such as the hgTracks CGI, there may be multiple C source modules in the dir.
COMMONLY USED LIBRARY MODULES
o - common - String handling, singly-linked list handling.
Other basic stuff every other module uses.
o - hash - Simple but effective hash table routines.
o - linefile - Line oriented file input, on some systems
much faster than fgets().
o - dystring - Dynamically sized strings in C.
o - cheapcgi - Parses out cgi variables for scripts called
from web pages.
o - htmshell - Helps generate HTML output for scripts that
are called from web pages or just want to make web
o - htmlPage - Read html pages, programatically submit html forms.
o - memgfx - Creates a 256 color image in memory which
can be drawn on, then saved as a .GIF file which
can be encorperated into a web page.
o - dnautils and dnaseq - Simple utilities on DNA.
o - fa - Read/write fasta format files.
o - basicBed - Functions for working with BED format files.
o - psl - Functions for working with PSL (blat) format files.
o - twoBit - Functions for working with twoBit DNA files.
o - bPlusTree - Create/user B+ Tree indexes, the backbone of
o - udc - URL Data Cache - code to locally cache remote files.
INDENTATION AND SPACING:
The code follows an indentation convention that is a bit
unusual for C. Opening and closing braces are on
a line by themselves and are indented at the same
level as the block they enclose:
Each block of code is indented by 4 from the previous block.
As per Unix standard practice, tab stops are set to 8, not 4
as is the common practice in Windows, so some care must be
taken when using tabs for indenting.
Tabs continue to be a problem for the programmer even in 2012.
Currently our makefiles require tabs, while our python code forbids
them. The C code can go either way so long as tabs are treated
as advancing to the next multiple-of-eight column. Please consult local
users of your favorite editor for help configuring it with these
indentation and tab standards.
Lines should be no more than 100 characters wide. Lines that are
longer than this are broken and indented at least 8 spaces
more than the original line to indicate the line continuation.
Where possible simplifying techniques should be applied to the code
in preference to using line continuations, since line continuations
obscure the logic conveyed in the indentation of the program.
Line continuations may be unavoidable when calling functions with long
parameter lists. In most other situations lines can be shortened
in better ways than line continuations. Complex expressions can be
broken into parts that are assigned to intermediate variables. Long
variable names can be revisited and sometimes shortened. Deep indenting
can be avoided by simplifying logic and by moving blocks into their own
functions. These are just some ways of avoiding long lines.
Symbol names generally begin with a lower-case letter. The second
and subsequent words in a name begin with a capital letter
to help visually separate the words. Abbreviation of words
is strongly discouraged. Words of five letters and less should
generally not be abbreviated. If a word is abbreviated in
general it is abbreviated to the first three letters:
tabSeparatedFile -> tabSepFile
In some cases, for local variables abbreviating
to a single letter for each word is ok:
tabSeparatedFile -> tsf
In complex cases you may treat the abbreviation itself as a word, and
only the first letter is capitalized.
genscanTabSeparatedFile -> genscanTsf
Numbers are considered words. You would
represent "chromosome 22 annotations"
as "chromosome22Annotations" or "chr22Ann."
Note the capitalized 'A" after the 22. Since both numbers and
single letter words (or abbreviations) disrupt the visual flow
of the word separation by capitalization, it is better to avoid
these except at the end of the name.
These naming rules apply to variables, constants, functions, fields,
and structures. They generally are used for file names, database tables,
database columns, and C macros as well, though there is a bit less
consistency there in the existing code base.
ERROR HANDLING AND MEMORY ALLOCATION
Another convention is that errors are reported
at a fairly low level, and the programs simply
print an error message and abort using errAbort. If
you need to catch errors underneath you see the
file errAbort.h and install an "abort handler".
Memory is generally allocated through "needMem"
(which aborts on failure to allocate) and the
macros "AllocVar" and "AllocArray". This
memory is initially set to zero, and the programs
very much depend on this fact.
Every module should have a comment at the start of
a file that explains concisely what the module
does. Explanations of algorithms also belong
at the top of the file in most cases. Comments can
be of the /* */ or the // form. Structures should be
commented following the pattern of this example:
/* Dynamically resizable string that you can do formatted
* output to. */
struct dyString *next; /* Next in list. */
char *string; /* Current buffer. */
int bufSize; /* Size of buffer. */
int stringSize; /* Size of string. */
That is, there is a comment describing the overall purpose
of the object between the struct name, and the opening brace,
and there is a short comment by each field. In many cases
these may not say much more than well-chosen field names,
but that's ok.
Almost any structure with more than three or four
elements includes a "next" pointer as its first
member, so that it can be part of a singly-linked
list. There's a whole set of routines (see
common.c and common.h) which work on singly-linked
lists where the next field comes first. Their
names all start with "sl."
Functions which work on a structure by convention begin with
the name of the structure, simulating an object-oriented
coding style. In general these functions are all grouped
in a file, in this case in dyString.c. Static functions in
this file need not have the prefix, though they may. Functions
have a comment between their prototype and the opening brace
as in this example:
char dyStringAppendC(struct dyString *ds, char c)
// Append char to end of string.
if (ds->stringSize >= ds->bufSize)
s = ds->string + ds->stringSize++;
*s++ = c;
*s = 0;
For short functions like this, the opening comment may be the only
comment. Longer functions should be broken into logical 'paragraphs'
with a comment at the start of each paragraph and blank lines
between paragraphs as in this example:
struct twoBit *twoBitFromDnaSeq(struct dnaSeq *seq, boolean doMask)
/* Convert dnaSeq representation in memory to twoBit representation.
* If doMask is true interpret lower-case letters as masked. */
/* Allocate structure and fill in name and size fields. */
struct twoBit *twoBit;
int ubyteSize = packedSize(seq->size);
UBYTE *pt = AllocArray(twoBit->data, ubyteSize);
twoBit->name = cloneString(seq->name);
twoBit->size = seq->size;
/* Convert to 4-bases per byte representation. */
char *dna = seq->dna;
int i, end;
end = seq->size - 4;
for (i=0; i<end; i += 4)
*pt++ = packDna4(dna+i);
/* Take care of conversion of last few bases, padding arbitrarily with 'T'. */
last4 = last4 = last4 = last4 = 'T';
memcpy(last4, dna+i, seq->size-i);
*pt = packDna4(last4);
/* Deal with blocks of N, saving end points of blocks. */
twoBit->nBlockCount = countBlocksOfN(dna, seq->size);
if (twoBit->nBlockCount > 0)
storeBlocksOfN(dna, seq->size, twoBit->nStarts, twoBit->nSizes);
/* Deal with masking, saving end points of blocks. */
twoBit->maskBlockCount = countBlocksOfLower(dna, seq->size);
if (twoBit->maskBlockCount > 0)
Though code paragraphs help make long functions readable, in general
smaller functions are preferred. It is rare that a function longer than
100 lines couldn't be improved by moving some blocks of code into new
functions or simplifying what the function is trying to do.
STRUCTURE OF A TYPICAL C MODULE
To avoid having to declare function prototypes, C modules are generally
ordered with the lowest level functions written before higher level
functions. In particular, if a module includes a main() routine, then
it is the last function in the module.
If a structure is broadly used in a module, it is declared near the start
of the module, just after the module opening comment and any includes.
This is followed by broadly used module local (static) variables. Less
broadly used structs and variables may be grouped with the functions they
are used with.
If a module is used by other modules, it will be represented in a header
file. In the majority of cases one .h file corresponds to one .c file.
Typically the opening comment is duplicated in .h and .c files, as are
the public structure and function declarations and opening comments.
In general we try, with mixed success, to keep modules less than 2000 lines.
Sadly many of the Genome Browser specific modules are currently quite long.
On the bright side the vast majority of the library modules are reasonably
In order to prevent SQL-Injection (sqli), we use primarily
a special function called sqlSafef() to construct properly
escaped SQL strings.
The main article about preventing sqli is found here on genomewiki:
There are several other related and supporting
functions to defeat sqli. The function reference is found here:
Apache/2.2.15 (CentOS) Server at hgwdev.cse.ucsc.edu Port 80