Bio::Root IO
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Summary
Bio::Root::IO - module providing several methods often needed when dealing with file IO
Package variables
Privates (from "my" definitions)
$HAS_WIN32 = 0
$TEMPCOUNTER;
Included modules
Bio::Root::HTTPget
IO::Handle
POSIX qw ( dup )
Symbol
Inherit
Bio::Root::Root
Synopsis
    # utilize stream I/O in your module
$self->{'io'} = Bio::Root::IO->new(-file => "myfile");
$self->{'io'}->_print("some stuff");
$line = $self->{'io'}->_readline();
$self->{'io'}->_pushback($line);
$self->{'io'}->close();
# obtain platform-compatible filenames $path = Bio::Root::IO->catfile($dir, $subdir, $filename); # obtain a temporary file (created in $TEMPDIR) ($handle) = $io->tempfile();
Description
This module provides methods that will usually be needed for any sort
of file- or stream-related input/output, e.g., keeping track of a file
handle, transient printing and reading from the file handle, a close
method, automatically closing the handle on garbage collection, etc.
To use this for your own code you will either want to inherit from
this module, or instantiate an object for every file or stream you are
dealing with. In the first case this module will most likely not be
the first class off which your class inherits; therefore you need to
call _initialize_io() with the named parameters in order to set file
handle, open file, etc automatically.
Most methods start with an underscore, indicating they are private. In
OO speak, they are not private but protected, that is, use them in
your module code, but a client code of your module will usually not
want to call them (except those not starting with an underscore).
In addition this module contains a couple of convenience methods for
cross-platform safe tempfile creation and similar tasks. There are
some CPAN modules related that may not be available on all
platforms. At present, File::Spec and File::Temp are attempted. This
module defines $PATHSEP, $TEMPDIR, and $ROOTDIR, which will always be set,
and $OPENFLAGS, which will be set if either of File::Spec or File::Temp fails.
The -noclose boolean (accessed via the noclose method) prevents a
filehandle from being closed when the IO object is cleaned up. This
is special behavior when a object like a parser might share a
filehandle with an object like an indexer where it is not proper to
close the filehandle as it will continue to be reused until the end of the
stream is reached. In general you won't want to play with this flag.
Methods
BEGIN Code
newDescriptionCode
_initialize_ioDescriptionCode
_fhDescriptionCode
modeDescriptionCode
fileDescriptionCode
formatDescriptionCode
variantDescriptionCode
_printDescriptionCode
_insertDescriptionCode
_readlineDescriptionCode
_pushbackDescriptionCode
closeDescriptionCode
flushDescriptionCode
nocloseDescriptionCode
_io_cleanup
No description
Code
exists_exeDescriptionCode
tempfileDescriptionCode
tempdirDescriptionCode
catfileDescriptionCode
rmtreeDescriptionCode
_flush_on_writeDescriptionCode
save_tempfilesDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage :
Function: Overridden here to automatically call _initialize_io().
Example :
Returns : new instance of this class
Args : named parameters
_initialize_iocodeprevnextTop
 Title   : initialize_io
Usage : $self->_initialize_io(@params);
Function: Initializes filehandle and other properties from the parameters.
Currently recognizes the following named parameters: -file name of file to open -string a string that is to be converted to a filehandle -url name of URL to open -input name of file, or GLOB, or IO::Handle object -fh file handle (mutually exclusive with -file) -flush boolean flag to autoflush after each write -noclose boolean flag, when set to true will not close a filehandle (must explicitly call close($io->_fh) -retries number of times to try a web fetch before failure -ua_parms hashref of key => value parameters to pass to LWP::UserAgent->new() (only meaningful with -url is set) A useful value might be, for example, { timeout => 60 } (ua default is 180 sec) Returns : TRUE Args : named parameters
_fhcodeprevnextTop
 Title   : _fh
Usage : $obj->_fh($newval)
Function: Get/set the file handle for the stream encapsulated.
Example :
Returns : value of _filehandle
Args : newvalue (optional)
modecodeprevnextTop
 Title   : mode
Usage : $obj->mode()
Function:
Example :
Returns : mode of filehandle:
'r' for readable
'w' for writable
'?' if mode could not be determined
Args : -force (optional), see notes.
Notes : once mode() has been called, the filehandle's mode is cached
for further calls to mode(). to override this behavior so
that mode() re-checks the filehandle's mode, call with arg
-force
filecodeprevnextTop
 Title   : file
Usage : $obj->file($newval)
Function: Get/set the filename, if one has been designated.
Example :
Returns : value of file
Args : newvalue (optional)
formatcodeprevnextTop
 Title   : format
Usage : $self->format($newval)
Function: Get the format of a Bio::Root::IO sequence file or filehandle. Every
object inheriting Bio::Root::IO is guaranteed to have a format.
Returns : format of the file or filehandle, e.g. fasta, fastq, genbank, embl.
Args : none
variantcodeprevnextTop
 Title   : format
Usage : $self->format($newval)
Function: Get the variant of a Bio::Root::IO sequence file or filehandle.
The format variant depends on the specific format used. Note that not
all formats have variants
Returns : variant of the file or filehandle, e.g. sanger, solexa or illumina for
the fastq format, or undef for formats that do not have variants.
Args : none
Note : The Bio::Root::IO-implementing modules that require access to variants
need to define a global hash that has the allowed variants as its keys.
_printcodeprevnextTop
 Title   : _print
Usage : $obj->_print(@lines)
Function:
Example :
Returns : 1 on success, undef on failure
_insertcodeprevnextTop
    Title   : _insert
Usage : $obj->_insert($string,1)
Function: Insert some text in a file at the given line number (1-based).
Returns : 1 on success
Args : string to write in file
line number to insert the string at
_readlinecodeprevnextTop
 Title   : _readline
Usage : $obj->_readline(%args)
Function: Reads a line of input.
Note that this method implicitely uses the value of $/ that is in effect when called. Note also that the current implementation does not handle pushed back input correctly unless the pushed back input ends with the value of $/. Example : Args : Accepts a hash of arguments, currently only -raw is recognized passing (-raw => 1) prevents \r\n sequences from being changed to \n. The default value of -raw is undef, allowing \r\n to be converted to \n. Returns :
_pushbackcodeprevnextTop
 Title   : _pushback
Usage : $obj->_pushback($newvalue)
Function: puts a line previously read with _readline back into a buffer.
buffer can hold as many lines as system memory permits.
Example : $obj->_pushback($newvalue)
Returns : none
Args : newvalue
Note : This is only supported for pushing back data ending with the
current, localized value of $/. Using this method to push modified
data back onto the buffer stack is not supported; see bug 843.
closecodeprevnextTop
 Title   : close
Usage : $io->close()
Function: Closes the file handle associated with this IO instance.
Will not close the FH if -noclose is specified
Returns : none
Args : none
flushcodeprevnextTop
 Title   : flush
Usage : $io->flush()
Function: Flushes the filehandle
Returns : none
Args : none
noclosecodeprevnextTop
 Title   : noclose
Usage : $obj->noclose($newval)
Function: Get/Set the NOCLOSE flag - setting this to true will
prevent a filehandle from being closed
when an object is cleaned up or explicitly closed
This is a bit of hack
Returns : value of noclose (a scalar)
Args : on set, new value (a scalar or undef, optional)
exists_execodeprevnextTop
 Title   : exists_exe
Usage : $exists = $obj->exists_exe('clustalw');
$exists = Bio::Root::IO->exists_exe('clustalw')
$exists = Bio::Root::IO::exists_exe('clustalw')
Function: Determines whether the given executable exists either as file
or within the path environment. The latter requires File::Spec
to be installed.
On Win32-based system, .exe is automatically appended to the program
name unless the program name already ends in .exe.
Example :
Returns : 1 if the given program is callable as an executable, and 0 otherwise
Args : the name of the executable
tempfilecodeprevnextTop
 Title   : tempfile
Usage : my ($handle,$tempfile) = $io->tempfile();
Function: Returns a temporary filename and a handle opened for writing and
and reading.
Caveats : If you do not have File::Temp on your system you should avoid specifying TEMPLATE and SUFFIX. (We don't want to recode everything, okay?) Returns : a 2-element array, consisting of temporary handle and temporary file name Args : named parameters compatible with File::Temp: DIR (defaults to $Bio::Root::IO::TEMPDIR), TEMPLATE, SUFFIX.
tempdircodeprevnextTop
 Title   : tempdir
Usage : my ($tempdir) = $io->tempdir(CLEANUP=>1);
Function: Creates and returns the name of a new temporary directory.
Note that you should not use this function for obtaining "the" temp directory. Use $Bio::Root::IO::TEMPDIR for that. Calling this method will in fact create a new directory. Returns : The name of a new temporary directory. Args : args - ( key CLEANUP ) indicates whether or not to cleanup dir on object destruction, other keys as specified by File::Temp
catfilecodeprevnextTop
 Title   : catfile
Usage : $path = Bio::Root::IO->catfile(@dirs,$filename);
Function: Constructs a full pathname in a cross-platform safe way.
If File::Spec exists on your system, this routine will merely delegate to it. Otherwise it tries to make a good guess. You should use this method whenever you construct a path name from directory and filename. Otherwise you risk cross-platform compatibility of your code. You can call this method both as a class and an instance method. Returns : a string Args : components of the pathname (directories and filename, NOT an extension)
rmtreecodeprevnextTop
 Title   : rmtree
Usage : Bio::Root::IO->rmtree($dirname );
Function: Remove a full directory tree
If File::Path exists on your system, this routine will merely delegate to it. Otherwise it runs a local version of that code. You should use this method to remove directories which contain files. You can call this method both as a class and an instance method. Returns : number of files successfully deleted Args : roots - rootdir to delete or reference to list of dirs verbose - a boolean value, which if TRUE will cause rmtree to print a message each time it
examines a file, giving the name of the file, and
indicating whether it's using rmdir or
unlink to remove it, or that it's skipping it.
(defaults to FALSE)
safe - a boolean value, which if TRUE will cause rmtree
to skip any files to which you do not have delete
access (if running under VMS) or write access (if
running under another OS). This will change in the
future when a criterion for 'delete permission'
under OSs other than VMS is settled. (defaults to
FALSE)
_flush_on_writecodeprevnextTop
 Title   : _flush_on_write
Usage : $obj->_flush_on_write($newval)
Function: Boolean flag to indicate whether to flush
the filehandle on writing when the end of
a component is finished (Sequences,Alignments,etc)
Returns : value of _flush_on_write
Args : newvalue (optional)
save_tempfilescodeprevnextTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles(1)
Function: Boolean flag to indicate whether to retain tempfiles/tempdir
Returns : Boolean value : 1 = save tempfiles/tempdirs, 0 = remove (default)
Args : Value evaluating to TRUE or FALSE
Methods code
BEGINTop
BEGIN {
    $TEMPCOUNTER = 0;
    $FILESPECLOADED = 0;
    $FILETEMPLOADED = 0;
    $FILEPATHLOADED = 0;
    $VERBOSE = 0;

    # try to load those modules that may cause trouble on some systems
eval { require File::Path; $FILEPATHLOADED = 1; }; if( $@ ) { print STDERR "Cannot load File::Path: $@" if( $VERBOSE > 0 ); # do nothing
} eval { require LWP::UserAgent; }; if( $@ ) { print STDERR "Cannot load LWP::UserAgent: $@" if( $VERBOSE > 0 ); $HAS_LWP = 0; } else { $HAS_LWP = 1; } # If on Win32, attempt to find Win32 package
if($^O =~ /mswin/i) { eval { require Win32; $HAS_WIN32 = 1; }; } # Try to provide a path separator. Why doesn't File::Spec export this,
# or did I miss it?
if($^O =~ /mswin/i) { $PATHSEP = "\\"; } elsif($^O =~ /macos/i) { $PATHSEP = ":"; } else { # unix
$PATHSEP = "/"; } eval { require File::Spec; $FILESPECLOADED = 1; $TEMPDIR = File::Spec->tmpdir(); $ROOTDIR = File::Spec->rootdir(); require File::Temp; # tempfile creation
$FILETEMPLOADED = 1; }; if( $@ ) { if(! defined($TEMPDIR)) { # File::Spec failed
# determine tempdir
if (defined $ENV{'TEMPDIR'} && -d $ENV{'TEMPDIR'} ) { $TEMPDIR = $ENV{'TEMPDIR'}; } elsif( defined $ENV{'TMPDIR'} && -d $ENV{'TMPDIR'} ) { $TEMPDIR = $ENV{'TMPDIR'}; } if($^O =~ /mswin/i) { $TEMPDIR = 'C:\TEMP' unless $TEMPDIR; $ROOTDIR = 'C:'; } elsif($^O =~ /macos/i) { $TEMPDIR = "" unless $TEMPDIR; # what is a reasonable default on Macs?
$ROOTDIR = ""; # what is reasonable??
} else { # unix
$TEMPDIR = "/tmp" unless $TEMPDIR; $ROOTDIR = "/"; } if (!( -d $TEMPDIR && -w $TEMPDIR )) { $TEMPDIR = '.'; # last resort
} } # File::Temp failed (alone, or File::Spec already failed)
#
# determine open flags for tempfile creation -- we'll have to do this
# ourselves
use Fcntl; use Symbol; $OPENFLAGS = O_CREAT | O_EXCL | O_RDWR; for my $oflag (qw/FOLLOW BINARY LARGEFILE EXLOCK NOINHERIT TEMPORARY/){ my ($bit, $func) = (0, "Fcntl::O_" . $oflag); no strict 'refs'; $OPENFLAGS |= $bit if eval { $bit = &$func(); 1 }; } } $ONMAC = "\015" eq "\n";
}
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    my $self = $caller->SUPER::new(@args);

    $self->_initialize_io(@args);
    return $self;
}
_initialize_iodescriptionprevnextTop
sub _initialize_io {
    my($self, @args) = @_;

    $self->_register_for_cleanup(\&_io_cleanup);

    my ($input, $noclose, $file, $fh, $string, $flush, $url,
    $retries, $ua_parms) =
    $self->_rearrange([qw(INPUT NOCLOSE FILE FH STRING FLUSH URL RETRIES UA_PARMS)],
                      @args);

    if($url){
        $retries ||= 5;

        if($HAS_LWP) { #use LWP::UserAgent
require LWP::UserAgent; my $ua = LWP::UserAgent->new(%$ua_parms); my $http_result; my($handle,$tempfile) = $self->tempfile(); CORE::close($handle); for(my $try = 1 ; $try <= $retries ; $try++){ $http_result = $ua->get($url, ':content_file' => $tempfile); $self->warn("[$try/$retries] tried to fetch $url, but server ". "threw ". $http_result->code . ". retrying...") if !$http_result->is_success; last if $http_result->is_success; } $self->throw("failed to fetch $url, server threw ". $http_result->code) if !$http_result->is_success; $input = $tempfile; $file = $tempfile; } else { #use Bio::Root::HTTPget
#$self->warn("no lwp");
$fh = Bio::Root::HTTPget::getFH($url); } } delete $self->{'_readbuffer'}; delete $self->{'_filehandle'}; $self->noclose( $noclose) if defined $noclose; # determine whether the input is a file(name) or a stream
if($input) { if(ref(\$input) eq "SCALAR") { # we assume that a scalar is a filename
if($file && ($file ne $input)) { $self->throw("input file given twice: $file and $input disagree"); } $file = $input; } elsif(ref($input) && ((ref($input) eq "GLOB") || $input->isa('IO::Handle'))) { # input is a stream
$fh = $input; } else { # let's be strict for now
$self->throw("unable to determine type of input $input: ". "not string and not GLOB"); } } if(defined($file) && defined($fh)) { $self->throw("Providing both a file and a filehandle for reading - ". "only one please!"); } if ($string) { if(defined($file) || defined($fh)) { $self->throw("File or filehandle provided with -string,". " please unset if you are using -string as a file"); } open($fh, "<",\$ string) } if(defined($file) && ($file ne '')) { $fh = Symbol::gensym(); open ($fh,$file) || $self->throw("Could not open $file: $!"); $self->file($file); } if (defined $fh) { # check filehandle to ensure it's one of:
# a GLOB reference, as in: open(my $fh, "myfile");
# an IO::Handle or IO::String object
# the UNIVERSAL::can added to fix Bug2863
unless ( ( ref $fh && ( ref $fh eq 'GLOB' ) ) || ( ref $fh && ( UNIVERSAL::can( $fh, 'can' ) && ( $fh->isa('IO::Handle') || $fh->isa('IO::String') ) ) ) ) { $self->throw("file handle $fh doesn't appear to be a handle"); } } if ($HAS_EOL) { binmode $fh, ':raw:eol(LF-Native)'; } $self->_fh($fh) if $fh; # if not provided, defaults to STDIN and STDOUT
$self->_flush_on_write(defined $flush ? $flush : 1); return 1;
}
_fhdescriptionprevnextTop
sub _fh {
    my ($obj, $value) = @_;
    if ( defined $value) {
    $obj->{'_filehandle'} = $value;
    }
    return $obj->{'_filehandle'};
}
modedescriptionprevnextTop
sub mode {
    my ($obj, @arg) = @_;
    my %param = @arg;
    return $obj->{'_mode'} if defined $obj->{'_mode'} and !$param{-force};

    # Previous system of:
# my $iotest = new IO::Handle;
# $iotest->fdopen( dup(fileno($fh)) , 'r' );
# if ($iotest->error == 0) { ... }
# didn't actually seem to work under any platform, since there would no
# no error if the filehandle had been opened writable only. Couldn't be
# hacked around when dealing with unseekable (piped) filehandles.
#
# Just try and do a simple readline, turning io warnings off, instead:
my $fh = $obj->_fh || return '?'; no warnings "io"; # we expect a warning if this is writable only
my $line = <$fh>; if (defined $line) { $obj->_pushback($line); $obj->{'_mode'} = 'r'; } else { $obj->{'_mode'} = 'w'; } return $obj->{'_mode'};
}
filedescriptionprevnextTop
sub file {
    my ($obj, $value) = @_;
    if ( defined $value) {
    $obj->{'_file'} = $value;
    }
    return $obj->{'_file'};
}
formatdescriptionprevnextTop
sub format {
    my ($self) = @_;
    my $format = (split '::', ref($self))[-1];
    return $format;
}
variantdescriptionprevnextTop
sub variant {
    my ($self, $variant) = @_;
    if (defined $variant) {
        $variant = lc $variant;
        my $var_name = '%'.ref($self).'::variant';
        my %ok_variants = eval $var_name; # e.g. %Bio::Assembly::IO::ace::variant
if (scalar keys %ok_variants == 0) { $self->throw('Cannot check for validity of variant because global '. "variant $var_name is not set or is empty\n"); } if (not exists $ok_variants{$variant}) { $self->throw($variant.' is not a valid variant of the '.$self->format. ' format'); } $self->{variant} = $variant; } return $self->{variant};
}
_printdescriptionprevnextTop
sub _print {
    my $self = shift;
    my $fh = $self->_fh() ||\* STDOUT;
    my $ret = print $fh @_;
    return $ret;
}
_insertdescriptionprevnextTop
sub _insert {
    my ($self, $string, $line_num) = @_;
    # Line number check
if ($line_num < 1) { $self->throw("Cannot insert text at line $line_num because the minimum". " line number possible is 1"); } # File check
my $file = $self->file; if (not defined $file) { $self->throw('Cannot insert a line in a IO object initialized with ".
"anything else than a file.'
); } $file =~ s/^\+?[><]?//; # transform '+>output.ace' into 'output.ace'
# Everything that needs to be written is written before we read it
$self->flush; # Edit the file in place, line by line (no slurping)
{ local @ARGV = ($file); # input file
#local $^I = '~'; # backup file extension, e.g. ~, .bak, .ori
local $^I = ''; # no backup file
while (<>) { if ($. == $line_num) { # right line for new data
print $string.$_; } else { print; } } } # Line number check (again)
if ( $. > 0 && $line_num > $. ) { $self->throw("Cannot insert text at line $line_num because there are ". "only $. lines in file $file"); } # Re-open the file in append mode to be ready to add text at the end of it
# when the next _print() statement comes
open my $new_fh, ">>$file" or $self->throw("Cannot append to file $file: $!"); $self->_fh($new_fh); # If file is empty and we're inserting at line 1, simply append text to file
if ( $. == 0 && $line_num == 1 ) { $self->_print($string); } return 1;
}
_readlinedescriptionprevnextTop
sub _readline {
    my $self = shift;
    my %param =@_;
    my $fh = $self->_fh or return;
    my $line;

    # if the buffer been filled by _pushback then return the buffer
# contents, rather than read from the filehandle
if( @{$self->{'_readbuffer'} || [] } ) { $line = shift @{$self->{'_readbuffer'}}; } else { $line = <$fh>; } #don't strip line endings if -raw is specified
# $line =~ s/\r\n/\n/g if( (!$param{-raw}) && (defined $line) );
# Dave Howorth's fix
if( !$HAS_EOL && !$param{-raw} && (defined $line) ) { $line =~ s/\015\012/\012/g; # Change all CR/LF pairs to LF
$line =~ tr/\015/\n/ unless $ONMAC; # Change all single CRs to NEWLINE
} return $line;
}
_pushbackdescriptionprevnextTop
sub _pushback {
    my ($obj, $value) = @_;
    return unless $value;
    unshift @{$obj->{'_readbuffer'}}, $value;
}
closedescriptionprevnextTop
sub close {
   my ($self) = @_;

   # don't close if we explicitly asked not to
return if $self->noclose; if( defined( my $fh = $self->{'_filehandle'} )) { $self->flush; return if ref $fh eq 'GLOB' && (\* STDOUT == $fh ||\* STDERR == $fh ||\* STDIN == $fh ); # don't close IO::Strings
close $fh unless ref $fh && $fh->isa('IO::String'); } $self->{'_filehandle'} = undef; delete $self->{'_readbuffer'};
}
flushdescriptionprevnextTop
sub flush {
  my ($self) = shift;

  if( !defined $self->{'_filehandle'} ) {
    $self->throw("Attempting to call flush but no filehandle active");
  }

  if( ref($self->{'_filehandle'}) =~ /GLOB/ ) {
    my $oldh = select($self->{'_filehandle'});
    $| = 1;
    select($oldh);
  } else {
    $self->{'_filehandle'}->flush();
  }
}
noclosedescriptionprevnextTop
sub noclose {
    my $self = shift;

    return $self->{'_noclose'} = shift if @_;
    return $self->{'_noclose'};
}
_io_cleanupdescriptionprevnextTop
sub _io_cleanup {
    my ($self) = @_;
    $self->close();
    my $v = $self->verbose;

    # we are planning to cleanup temp files no matter what
if( exists($self->{'_rootio_tempfiles'}) && ref($self->{'_rootio_tempfiles'}) =~ /array/i && !$self->save_tempfiles) { if( $v > 0 ) { warn( "going to remove files ", join(",", @{$self->{'_rootio_tempfiles'}}), "\n"); } unlink (@{$self->{'_rootio_tempfiles'}} ); } # cleanup if we are not using File::Temp
if( $self->{'_cleanuptempdir'} && exists($self->{'_rootio_tempdirs'}) && ref($self->{'_rootio_tempdirs'}) =~ /array/i && !$self->save_tempfiles) { if( $v > 0 ) { warn( "going to remove dirs ", join(",", @{$self->{'_rootio_tempdirs'}}), "\n"); } $self->rmtree( $self->{'_rootio_tempdirs'}); }
}
exists_exedescriptionprevnextTop
sub exists_exe {
    my ($self, $exe) = @_;
    $self->throw("Must pass a defined value to exists_exe") unless defined $exe;
    $exe = $self if (!(ref($self) || $exe));
    $exe .= '.exe' if(($^O =~ /mswin/i) && ($exe !~ /\.(exe|com|bat|cmd)$/i));
    return $exe if ( -f $exe && -x $exe ); # full path and exists
# Ewan's comment. I don't think we need this. People should not be
# asking for a program with a pathseparator starting it
# $exe =~ s/^$PATHSEP//;
# Not a full path, or does not exist. Let's see whether it's in the path.
if($FILESPECLOADED) { foreach my $dir (File::Spec->path()) { my $f = Bio::Root::IO->catfile($dir, $exe); return $f if( -f $f && -x $f ); } } return 0;
}
tempfiledescriptionprevnextTop
sub tempfile {
    my ($self, @args) = @_;
    my ($tfh, $file);
    my %params = @args;

    # map between naming with and without dash
foreach my $key (keys(%params)) { if( $key =~ /^-/ ) { my $v = $params{$key}; delete $params{$key}; $params{uc(substr($key,1))} = $v; } else { # this is to upper case
my $v = $params{$key}; delete $params{$key}; $params{uc($key)} = $v; } } $params{'DIR'} = $TEMPDIR if(! exists($params{'DIR'})); unless (exists $params{'UNLINK'} && defined $params{'UNLINK'} && ! $params{'UNLINK'} ) { $params{'UNLINK'} = 1; } else { $params{'UNLINK'} = 0 } if($FILETEMPLOADED) { if(exists($params{'TEMPLATE'})) { my $template = $params{'TEMPLATE'}; delete $params{'TEMPLATE'}; ($tfh, $file) = File::Temp::tempfile($template, %params); } else { ($tfh, $file) = File::Temp::tempfile(%params); } } else { my $dir = $params{'DIR'}; $file = $self->catfile($dir, (exists($params{'TEMPLATE'}) ? $params{'TEMPLATE'} : sprintf( "%s.%s.%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++))); # sneakiness for getting around long filenames on Win32?
if( $HAS_WIN32 ) { $file = Win32::GetShortPathName($file); } # Try to make sure this will be marked close-on-exec
# XXX: Win32 doesn't respect this, nor the proper fcntl,
# but may have O_NOINHERIT. This may or may not be in Fcntl.
local $^F = 2; # Store callers umask
my $umask = umask(); # Set a known umaskr
umask(066); # Attempt to open the file
if ( sysopen($tfh, $file, $OPENFLAGS, 0600) ) { # Reset umask
umask($umask); } else { $self->throw("Could not open tempfile $file: $!\n"); } } if( $params{'UNLINK'} ) { push @{$self->{'_rootio_tempfiles'}}, $file; } return wantarray ? ($tfh,$file) : $tfh;
}
tempdirdescriptionprevnextTop
sub tempdir {
    my ( $self, @args ) = @_;
    if($FILETEMPLOADED && File::Temp->can('tempdir') ) {
        return File::Temp::tempdir(@args);
    }

    # we have to do this ourselves, not good
#
# we are planning to cleanup temp files no matter what
my %params = @args; $self->{'_cleanuptempdir'} = ( defined $params{CLEANUP} && $params{CLEANUP} == 1); my $tdir = $self->catfile($TEMPDIR, sprintf("dir_%s-%s-%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++)); mkdir($tdir, 0755); push @{$self->{'_rootio_tempdirs'}}, $tdir; return $tdir;
}
catfiledescriptionprevnextTop
sub catfile {
    my ($self, @args) = @_;

    return File::Spec->catfile(@args) if($FILESPECLOADED);
    # this is clumsy and not very appealing, but how do we specify the
# root directory?
if($args[0] eq '/') { $args[0] = $ROOTDIR; } return join($PATHSEP, @args);
}
rmtreedescriptionprevnextTop
sub rmtree {
    my($self,$roots, $verbose, $safe) = @_;
    if( $FILEPATHLOADED ) {
    return File::Path::rmtree ($roots, $verbose, $safe);
    }

    my $force_writable = ($^O eq 'os2' || $^O eq 'dos' || $^O eq 'MSWin32'
               || $^O eq 'amigaos' || $^O eq 'cygwin');
    my $Is_VMS = $^O eq 'VMS';

    my(@files);
    my($count) = 0;
    $verbose ||= 0;
    $safe ||= 0;
    if ( defined($roots) && length($roots) ) {
    $roots = [$roots] unless ref $roots;
    } else {
    $self->warn("No root path(s) specified\n");
    return 0;
    }

    my($root);
    foreach $root (@{$roots}) {
    $root =~ s#/\z##;
    (undef, undef, my $rp) = lstat $root or next;
    $rp &= 07777;   # don't forget setuid, setgid, sticky bits
if ( -d _ ) { # notabene: 0777 is for making readable in the first place,
# it's also intended to change it to writable in case we have
# to recurse in which case we are better than rm -rf for
# subtrees with strange permissions
chmod(0777, ($Is_VMS ? VMS::Filespec::fileify($root) : $root)) or $self->warn("Can't make directory $root read+writable: $!") unless $safe; if (opendir(DIR, $root) ){ @files = readdir DIR; closedir(DIR); } else { $self->warn( "Can't read $root: $!"); @files = (); } # Deleting large numbers of files from VMS Files-11 filesystems
# is faster if done in reverse ASCIIbetical order
@files = reverse @files if $Is_VMS; ($root = VMS::Filespec::unixify($root)) =~ s#\.dir\z## if $Is_VMS; @files = map("$root/$_", grep $_!~/^\.{1,2}\z/s,@files); $count += $self->rmtree([@files],$verbose,$safe); if ($safe && ($Is_VMS ? !&VMS::Filespec::candelete($root) : !-w $root)) { print "skipped $root\n" if $verbose; next; } chmod 0777, $root or $self->warn( "Can't make directory $root writable: $!") if $force_writable; print "rmdir $root\n" if $verbose; if (rmdir $root) { ++$count; } else { $self->warn( "Can't remove directory $root: $!"); chmod($rp, ($Is_VMS ? VMS::Filespec::fileify($root) : $root)) or $self->warn("and can't restore permissions to " . sprintf("0%o",$rp) . "\n"); } } else { if ($safe && ($Is_VMS ? !&VMS::Filespec::candelete($root) : !(-l $root || -w $root))) { print "skipped $root\n" if $verbose; next; } chmod 0666, $root or $self->warn( "Can't make file $root writable: $!") if $force_writable; warn "unlink $root\n" if $verbose; # delete all versions under VMS
for (;;) { unless (unlink $root) { $self->warn( "Can't unlink file $root: $!"); if ($force_writable) { chmod $rp, $root or $self->warn("and can't restore permissions to " . sprintf("0%o",$rp) . "\n"); } last; } ++$count; last unless $Is_VMS && lstat $root; } } } $count;
}
_flush_on_writedescriptionprevnextTop
sub _flush_on_write {
    my ($self,$value) = @_;
    if( defined $value) {
    $self->{'_flush_on_write'} = $value;
    }
    return $self->{'_flush_on_write'};
}
save_tempfilesdescriptionprevnextTop
sub save_tempfiles {
    my $self = shift;
    if (@_) {
        my $value = shift;
        $self->{save_tempfiles} = $value ? 1 : 0;
    }
    return $self->{save_tempfiles} || 0;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportTop
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp@gmx.net
CONTRIBUTORSTop
Mark A. Jensen ( maj -at- fortinbras -dot- us )
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _