Memory is memory. It doesn't have to track the contents of the pari block to notice clobbering happening outside it.
Sure -- but that's not the problem (and it won't be the problem). Every time the library uses the stack it ensures that there's room for what it's creating. Also, the stack is very large -- at least 20 MB and sometimes as big as 1 GB, with its pointer avma moving by [only] several bytes per call.
The real problem with memory management is leaving garbage on the stack (another possibility is returning corrupted objects). The usual technique for is
which ensures that you're not leaving garbage on the stack. But this is somewhat more complicated by returning complicated objects like vectors. For example:
Memory diagram:
(vector with pointers to its members A, B, and C)(A)(garbage)(B)(garbage)(C)
I'm trying to compile and install both most recent version of 'make' and the
most recent version of 'openssh' on my Sparc20.
I've run into the following problems... and I don't know what they mean. Can
someone please help me resolve these issues?
I'm using the 'make' version that was... (5 Replies)
I renamed ld.so.1 on a Sun machine running Solaris 2.6. Now I cannot boot the system and I can use only very few commands in Maintenance Mode.
Can someone help me? (3 Replies)
Hello Friends,
I got stuck with fgets () & rewind() function .. Please need help..
Actually I am doing a like,
The function should read lines from a txt file until the function is called..
If the data from the txt file ends then it goes to the top and then again when the function is called... (1 Reply)
Assume client send the message " Hello ", i get output such as
Sent mesg: hello
Bytes Sent to Client: 6
bytes_received = recv(clientSockD, data, MAX_DATA, 0);
if(bytes_received)
{
send(clientSockD, data, bytes_received, 0);
data = '\0';... (2 Replies)
Hi all,
I have this method to read a string from a STDIN:
void readLine(char* inputBuffer){
fgets (inputBuffer, MAX_LINE, stdin);
fflush(stdin);
/* remove '\n' char from string */
if(strlen(inputBuffer) != 0)
inputBuffer = '\0';
}
All work fine but if i... (1 Reply)
Hello,
I am having problems with using less on
Linux version 2.6.18-92.1.17.el5 (brewbuilder@hs20-bc1-7.build.redhat.com) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)). I am using csh but have the same problems on bash.
If I pipe something to less it works perfectly i.e. cat file | less... (9 Replies)
hello,
i'm trying to write a C-program that reads a file line by line.
(and searches each line for a given string)
This file is an special ASCII-database-file, with a lot of entries.
I checked the line with most length, and it was about 4000 characters.
With google i found several... (4 Replies)
Hi,
I have a string like this,
char str ="This, a sample string.\\nThis is the second line, \\n \\n, we will have one blank line";
if I want to use strtok() to seperate the string, which token should I use?
I tried "\n", "\\n", either not working.
peter (1 Reply)
Any ideas how to clear this error as it seems I dont understand if,do,while and els commands
#!/bin/ksh
set -x
print "This script creates test messages"
print "Please enter test case name"
read testcasename
echo $testcasename
skipfield=Y
while
print "Do you want to skip this field... (4 Replies)
Discussion started by: andrew.p.mcderm
4 Replies
LEARN ABOUT DEBIAN
bio::tools::gel
Bio::Tools::Gel(3pm) User Contributed Perl Documentation Bio::Tools::Gel(3pm)NAME
Bio::Tools::Gel - Calculates relative electrophoretic migration distances
SYNOPSIS
use Bio::PrimarySeq;
use Bio::Restriction::Analysis;
use Bio::Tools::Gel;
# get a sequence
my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);
# cut it with an enzyme
my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
@cuts = $ra->fragments('EcoRI'), 3;
# analyse the fragments in a gel
my $gel = Bio::Tools::Gel->new(-seq=>@cuts,-dilate=>10);
my %bands = $gel->bands;
foreach my $band (sort {$b <=> $a} keys %bands){
print $band," ", sprintf("%.1f", $bands{$band}),"
";
}
#prints:
#20 27.0
#25 26.0
#10 30.0
DESCRIPTION
This takes a set of sequences or Bio::Seq objects, and calculates their respective migration distances using:
distance = dilation * (4 - log10(length(dna));
Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis. CSHL Press, 1989.
Bio::Tools::Gel currently calculates migration distances based solely on the length of the nucleotide sequence. Secondary or tertiary
structure, curvature, and other biophysical attributes of a sequence are currently not considered. Polypeptide migration is currently not
supported.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Allen Day
Email allenday@ucla.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $gel = Bio::Tools::Gel->new(-seq => $sequence,-dilate => 3);
Function: Initializes a new Gel
Returns : Bio::Tools::Gel
Args : -seq => Bio::Seq(s), scalar(s) or list of either/both
(default: none)
-dilate => Expand band migration distances (default: 1)
add_band
Title : add_band
Usage : $gel->add_band($seq);
Function: Calls _add_band with a (possibly created) Bio::Seq object.
Returns :
Args : Bio::Seq, scalar sequence, or list of either/both.
_add_band
Title : _add_band
Usage : $gel->_add_band($seq);
Function: Adds a new band to the gel.
Returns :
Args : Bio::Seq object
dilate
Title : dilate
Usage : $gel->dilate(1);
Function: Sets/retrieves the dilation factor.
Returns : dilation factor
Args : Float or none
bands
Title : bands
Usage : $gel->bands;
Function: Calculates migration distances of sequences.
Returns : hash of (seq_id => distance)
Args :
log10
Title : log10
Usage : log10($n);
Function: returns base 10 log of $n.
Returns : float
Args : float
perl v5.14.2 2012-03-02 Bio::Tools::Gel(3pm)