adding bzip2 support in ruby

[biopieces.git] / code_perl / Maasha / Common.pm

diff --git a/code_perl/Maasha/Common.pm b/code_perl/Maasha/Common.pm
index 83c963301942ff9e01a27e4f3a624c22f9b142e6..079587ba4eb013f0b3d9f5179edb3efc4c204d24 100644 (file)
--- a/code_perl/Maasha/Common.pm
+++ b/code_perl/Maasha/Common.pm
@@ -29,6 +29,7 @@ package Maasha::Common;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Carp;
 use Data::Dumper;
@@ -117,6 +118,30 @@ int match_m( char *str, char *substr, size_t str_len, size_t substr_len, size_t
 }
 
 
+void str_analyze_C( const char *string )
+{
+    /* Martin A. Hansen, July 2009 */
+
+    /* Scans a string incrementing the char count in an array. */
+
+    int count[ 256 ] = { 0 };   /* Integer array spanning the ASCII alphabet */
+    int i;
+
+    for ( i = 0; i < strlen( string ); i++ ) {
+        count[ ( int ) string[ i ] ]++;
+    }
+
+    Inline_Stack_Vars;
+    Inline_Stack_Reset;
+
+    for ( i = 0; i < 256; i++ ) {
+        Inline_Stack_Push( sv_2mortal( newSViv( count[ i ] ) ) );
+    }
+
+    Inline_Stack_Done;
+}
+
+
 END_C
 
 
@@ -155,7 +180,7 @@ sub error
     $file_max    = length "File";
     $line_max    = length "Line";
 
-    if ( $line =~ /^ at (.+) line (\d+)$/ )
+    if ( $line =~ /^ at (.+) line (\d+)\.?$/ )
     {
         $file    = $1;
         $line_no = $2;
@@ -294,38 +319,6 @@ sub pipe_open
 }
 
 
-sub file_store
-{
-    # Martin A. Hansen, December 2004.
-
-    # writes a data structure to file.
-
-    my ( $path,      # full path to file
-         $data,      # data structure
-       ) = @_;
-    
-    Storable::store( $data, $path ) or Maasha::Common::error( qq(Could not write-open file "$path": $!) );
-}
-
-
-sub file_retrieve
-{
-    # Martin A. Hansen, December 2004.
-
-    # retrieves hash data structure
-    # (this routines needs to test if its a hash, array or else)
-
-    my ( $path,   # full path to data file
-       ) = @_;
-
-    my ( $data );
-
-    $data = Storable::retrieve( $path ) or Maasha::Common::error( qq(Could not read-open file "$path": $!) );
-
-    return wantarray ? %{ $data } : $data;
-}
-
-
 sub read_args
 {
     # Martin A. Hansen, December 2006
@@ -626,6 +619,10 @@ sub time_stamp_diff
     $min0  = $5;
     $sec0  = $6;
 
+    $sec0 += $day0 * 24 * 60 * 60;
+    $sec0 += $hour0 * 60 * 60;;
+    $sec0 += $min0  * 60;
+
     $t1 =~ /(\d+)-(\d+)-(\d+) (\d+):(\d+):(\d+)/;
     $year1 = $1;
     $mon1  = $2;
@@ -634,14 +631,22 @@ sub time_stamp_diff
     $min1  = $5;
     $sec1  = $6;
 
+    $sec1 += $day1 * 24 * 60 * 60;
+    $sec1 += $hour1 * 60 * 60;;
+    $sec1 += $min1  * 60;
+
     $year = $year1 - $year0;
     $mon  = $mon1  - $mon0;
     $day  = $day1  - $day0; 
-    $hour = $hour1 - $hour0;
-    $min  = $min1  - $min0;
-    $sec  = $sec1  - $sec0;
 
-    #return "$year-$mon-$day $hour:$min:$sec";
+    $sec  = $sec1 - $sec0;
+
+    $hour = int( $sec / ( 60 * 60 ) );
+    $sec -= $hour * 60 * 60;
+
+    $min  = int( $sec / 60 );
+    $sec -= $min * 60;
+
     return join( ":", sprintf( "%02d", $hour ), sprintf( "%02d", $min ), sprintf( "%02d", $sec ) );
 }
 
@@ -716,6 +721,29 @@ sub wrap_line
 }
 
 
+sub str_analyze
+{
+    # Martin A. Hansen, July 2009.
+
+    # Analyzes the string composition of a given string.
+
+    my ( $str,   # string to analyze
+       ) = @_;
+
+    # Returns hash
+
+    my ( @composition, %hash, $i );
+
+    @composition = Maasha::Common::str_analyze_C( $str ); 
+
+    for ( $i = 32; $i <= 126; $i++ ) {          # Only include printable chars
+        $hash{ chr $i } = $composition[ $i ]
+    }
+
+    return wantarray ? %hash : \%hash;
+}
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 1;