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revision 1.80, Thu Aug 10 07:34:37 2006 UTC revision 1.92, Mon Oct 16 07:41:50 2006 UTC
# Line 131  Line 131 
131      # Add the option table and XML file name.      # Add the option table and XML file name.
132      $retVal->{_options} = $optionTable;      $retVal->{_options} = $optionTable;
133      $retVal->{_xmlName} = $xmlFileName;      $retVal->{_xmlName} = $xmlFileName;
134        # Set up space for the group file data.
135        $retVal->{groupHash} = undef;
136      # Return it.      # Return it.
137      return $retVal;      return $retVal;
138  }  }
# Line 340  Line 342 
342    
343  =head3 GeneMenu  =head3 GeneMenu
344    
345  C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params); >>  C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params, $selected); >>
346    
347  Return an HTML select menu of genomes. Each genome will be an option in the menu,  Return an HTML select menu of genomes. Each genome will be an option in the menu,
348  and will be displayed by name with the ID and a contig count attached. The selection  and will be displayed by name with the ID and a contig count attached. The selection
# Line 362  Line 364 
364  Reference to a list of values to be substituted in for the parameter marks in  Reference to a list of values to be substituted in for the parameter marks in
365  the filter string.  the filter string.
366    
367    =item selected (optional)
368    
369    ID of the genome to be initially selected.
370    
371    =item fast (optional)
372    
373    If specified and TRUE, the contig counts will be omitted to improve performance.
374    
375  =item RETURN  =item RETURN
376    
377  Returns an HTML select menu with the specified genomes as selectable options.  Returns an HTML select menu with the specified genomes as selectable options.
# Line 372  Line 382 
382    
383  sub GeneMenu {  sub GeneMenu {
384      # Get the parameters.      # Get the parameters.
385      my ($self, $attributes, $filterString, $params) = @_;      my ($self, $attributes, $filterString, $params, $selected, $fast) = @_;
386        my $slowMode = ! $fast;
387        # Default to nothing selected. This prevents an execution warning if "$selected"
388        # is undefined.
389        $selected = "" unless defined $selected;
390        Trace("Gene Menu called with slow mode \"$slowMode\" and selection \"$selected\".") if T(3);
391      # Start the menu.      # Start the menu.
392      my $retVal = "<select " .      my $retVal = "<select " .
393          join(" ", map { "$_=\"$attributes->{$_}\"" } keys %{$attributes}) .          join(" ", map { "$_=\"$attributes->{$_}\"" } keys %{$attributes}) .
# Line 389  Line 404 
404          # Get the data for this genome.          # Get the data for this genome.
405          my ($genomeID, $genus, $species, $strain) = @{$genomeData};          my ($genomeID, $genus, $species, $strain) = @{$genomeData};
406          # Get the contig count.          # Get the contig count.
407            my $contigInfo = "";
408            if ($slowMode) {
409          my $count = $self->ContigCount($genomeID);          my $count = $self->ContigCount($genomeID);
410          my $counting = ($count == 1 ? "contig" : "contigs");          my $counting = ($count == 1 ? "contig" : "contigs");
411                $contigInfo = "[$count $counting]";
412            }
413            # Find out if we're selected.
414            my $selectOption = ($selected eq $genomeID ? " selected" : "");
415          # Build the option tag.          # Build the option tag.
416          $retVal .= "<option value=\"$genomeID\">$genus $species $strain ($genomeID) [$count $counting]</option>\n";          $retVal .= "<option value=\"$genomeID\"$selectOption>$genus $species $strain ($genomeID)$contigInfo</option>\n";
         Trace("Option tag built for $genomeID: $genus $species $strain.") if T(3);  
417      }      }
418      # Close the SELECT tag.      # Close the SELECT tag.
419      $retVal .= "</select>\n";      $retVal .= "</select>\n";
420      # Return the result.      # Return the result.
421      return $retVal;      return $retVal;
422  }  }
423    
424  =head3 Build  =head3 Build
425    
426  C<< $sprout->Build(); >>  C<< $sprout->Build(); >>
# Line 634  Line 655 
655      return ($contigID, $start, $dir, $len);      return ($contigID, $start, $dir, $len);
656  }  }
657    
658    
659    
660  =head3 PointLocation  =head3 PointLocation
661    
662  C<< my $found = Sprout::PointLocation($location, $point); >>  C<< my $found = Sprout::PointLocation($location, $point); >>
# Line 1476  Line 1499 
1499      my %retVal = ();      my %retVal = ();
1500      # Loop through the incoming features.      # Loop through the incoming features.
1501      for my $featureID (@{$featureList}) {      for my $featureID (@{$featureList}) {
1502          # Create a query to get the feature's best hit.          # Ask the server for the feature's best hit.
1503          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my @bbhData = FIGRules::BBHData($featureID);
                                "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",  
                                [$featureID, $genomeID]);  
1504          # Peel off the BBHs found.          # Peel off the BBHs found.
1505          my @found = ();          my @found = ();
1506          while (my $bbh = $query->Fetch) {          for my $bbh (@bbhData) {
1507              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->[0];
1508          }          }
1509          $retVal{$featureID} = \@found;          $retVal{$featureID} = \@found;
1510      }      }
# Line 1497  Line 1518 
1518    
1519  Return a list of the similarities to the specified feature.  Return a list of the similarities to the specified feature.
1520    
1521  Sprout does not support real similarities, so this method just returns the bidirectional  This method just returns the bidirectional best hits for performance reasons.
 best hits.  
1522    
1523  =over 4  =over 4
1524    
# Line 1518  Line 1538 
1538      # Get the parameters.      # Get the parameters.
1539      my ($self, $featureID, $count) = @_;      my ($self, $featureID, $count) = @_;
1540      # Ask for the best hits.      # Ask for the best hits.
1541      my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],      my @lists = FIGRules::BBHData($featureID);
                               "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",  
                               [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],  
                               $count);  
1542      # Create the return value.      # Create the return value.
1543      my %retVal = ();      my %retVal = ();
1544      for my $tuple (@lists) {      for my $tuple (@lists) {
# Line 1531  Line 1548 
1548      return %retVal;      return %retVal;
1549  }  }
1550    
   
   
1551  =head3 IsComplete  =head3 IsComplete
1552    
1553  C<< my $flag = $sprout->IsComplete($genomeID); >>  C<< my $flag = $sprout->IsComplete($genomeID); >>
# Line 2664  Line 2679 
2679      return $retVal;      return $retVal;
2680  }  }
2681    
2682    =head3 PropertyID
2683    
2684    C<< my $id = $sprout->PropertyID($propName, $propValue); >>
2685    
2686    Return the ID of the specified property name and value pair, if the
2687    pair exists.
2688    
2689    =over 4
2690    
2691    =item propName
2692    
2693    Name of the desired property.
2694    
2695    =item propValue
2696    
2697    Value expected for the desired property.
2698    
2699    =item RETURN
2700    
2701    Returns the ID of the name/value pair, or C<undef> if the pair does not exist.
2702    
2703    =back
2704    
2705    =cut
2706    
2707    sub PropertyID {
2708        # Get the parameters.
2709        my ($self, $propName, $propValue) = @_;
2710        # Try to find the ID.
2711        my ($retVal) = $self->GetFlat(['Property'],
2712                                      "Property(property-name) = ? AND Property(property-value) = ?",
2713                                      [$propName, $propValue], 'Property(id)');
2714        # Return the result.
2715        return $retVal;
2716    }
2717    
2718  =head3 MergedAnnotations  =head3 MergedAnnotations
2719    
2720  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>
# Line 2861  Line 2912 
2912      # Get the parameters.      # Get the parameters.
2913      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2914      # Get the list of names.      # Get the list of names.
2915      my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",      my @retVal = $self->GetFlat(['HasRoleInSubsystem'], "HasRoleInSubsystem(from-link) = ?",
2916                                  [$featureID], 'HasSSCell(from-link)');                                  [$featureID], 'HasRoleInSubsystem(to-link)');
2917      # Return the result.      # Return the result, sorted.
2918      return @retVal;      return sort @retVal;
2919  }  }
2920    
2921  =head3 GenomeSubsystemData  =head3 GenomeSubsystemData
# Line 2962  Line 3013 
3013      # Get the parameters.      # Get the parameters.
3014      my ($self, $featureID, $function, $userID) = @_;      my ($self, $featureID, $function, $userID) = @_;
3015      # Get a list of the features that are BBHs of the incoming feature.      # Get a list of the features that are BBHs of the incoming feature.
3016      my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],      my @bbhFeatures = map { $_->[0] } FIGRules::BBHData($featureID);
                                      "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],  
                                      'IsBidirectionalBestHitOf(to-link)');  
3017      # Now we loop through the features, pulling out the ones that have the correct      # Now we loop through the features, pulling out the ones that have the correct
3018      # functional assignment.      # functional assignment.
3019      my @retVal = ();      my @retVal = ();
# Line 3100  Line 3149 
3149      # Loop through the input triples.      # Loop through the input triples.
3150      my $n = length $sequence;      my $n = length $sequence;
3151      for (my $i = 0; $i < $n; $i += 3) {      for (my $i = 0; $i < $n; $i += 3) {
3152          # Get the current triple from the sequence.          # Get the current triple from the sequence. Note we convert to
3153          my $triple = substr($sequence, $i, 3);          # upper case to insure a match.
3154            my $triple = uc substr($sequence, $i, 3);
3155          # Translate it using the table.          # Translate it using the table.
3156          my $protein = "X";          my $protein = "X";
3157          if (exists $table->{$triple}) { $protein = $table->{$triple}; }          if (exists $table->{$triple}) { $protein = $table->{$triple}; }
# Line 3165  Line 3215 
3215      my ($self, $featureID, $cutoff) = @_;      my ($self, $featureID, $cutoff) = @_;
3216      # Create the return hash.      # Create the return hash.
3217      my %retVal = ();      my %retVal = ();
3218      # Create a query to get the desired BBHs.      # Query for the desired BBHs.
3219      my @bbhList = $self->GetAll(['IsBidirectionalBestHitOf'],      my @bbhList = FIGRules::BBHData($featureID, $cutoff);
                                 'IsBidirectionalBestHitOf(sc) <= ? AND IsBidirectionalBestHitOf(from-link) = ?',  
                                 [$cutoff, $featureID],  
                                 ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(sc)']);  
3220      # Form the results into the return hash.      # Form the results into the return hash.
3221      for my $pair (@bbhList) {      for my $pair (@bbhList) {
3222          $retVal{$pair->[0]} = $pair->[1];          $retVal{$pair->[0]} = $pair->[1];
# Line 3243  Line 3290 
3290      return $retVal;      return $retVal;
3291  }  }
3292    
3293    =head3 IsAllGenomes
3294    
3295    C<< my $flag = $sprout->IsAllGenomes(\@list, \@checkList); >>
3296    
3297    Return TRUE if all genomes in the second list are represented in the first list at
3298    least one. Otherwise, return FALSE. If the second list is omitted, the first list is
3299    compared to a list of all the genomes.
3300    
3301    =over 4
3302    
3303    =item list
3304    
3305    Reference to the list to be compared to the second list.
3306    
3307    =item checkList (optional)
3308    
3309    Reference to the comparison target list. Every genome ID in this list must occur at
3310    least once in the first list. If this parameter is omitted, a list of all the genomes
3311    is used.
3312    
3313    =item RETURN
3314    
3315    Returns TRUE if every item in the second list appears at least once in the
3316    first list, else FALSE.
3317    
3318    =back
3319    
3320    =cut
3321    
3322    sub IsAllGenomes {
3323        # Get the parameters.
3324        my ($self, $list, $checkList) = @_;
3325        # Supply the checklist if it was omitted.
3326        $checkList = [$self->Genomes()] if ! defined($checkList);
3327        # Create a hash of the original list.
3328        my %testList = map { $_ => 1 } @{$list};
3329        # Declare the return variable. We assume that the representation
3330        # is complete and stop at the first failure.
3331        my $retVal = 1;
3332        my $n = scalar @{$checkList};
3333        for (my $i = 0; $retVal && $i < $n; $i++) {
3334            if (! $testList{$checkList->[$i]}) {
3335                $retVal = 0;
3336            }
3337        }
3338        # Return the result.
3339        return $retVal;
3340    }
3341    
3342  =head3 GetGroups  =head3 GetGroups
3343    
3344  C<< my %groups = $sprout->GetGroups(\@groupList); >>  C<< my %groups = $sprout->GetGroups(\@groupList); >>
# Line 3264  Line 3360 
3360          # Here we have a group list. Loop through them individually,          # Here we have a group list. Loop through them individually,
3361          # getting a list of the relevant genomes.          # getting a list of the relevant genomes.
3362          for my $group (@{$groupList}) {          for my $group (@{$groupList}) {
3363              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(primary-group) = ?",
3364                  [$group], "Genome(id)");                  [$group], "Genome(id)");
3365              $retVal{$group} = \@genomeIDs;              $retVal{$group} = \@genomeIDs;
3366          }          }
# Line 3272  Line 3368 
3368          # Here we need all of the groups. In this case, we run through all          # Here we need all of the groups. In this case, we run through all
3369          # of the genome records, putting each one found into the appropriate          # of the genome records, putting each one found into the appropriate
3370          # group. Note that we use a filter clause to insure that only genomes          # group. Note that we use a filter clause to insure that only genomes
3371          # in groups are included in the return set.          # in real NMPDR groups are included in the return set.
3372          my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],          my @genomes = $self->GetAll(['Genome'], "Genome(primary-group) <> ?",
3373                                      ['Genome(id)', 'Genome(group-name)']);                                      [$FIG_Config::otherGroup], ['Genome(id)', 'Genome(primary-group)']);
3374          # Loop through the genomes found.          # Loop through the genomes found.
3375          for my $genome (@genomes) {          for my $genome (@genomes) {
3376              # Pop this genome's ID off the current list.              # Pop this genome's ID off the current list.
# Line 3400  Line 3496 
3496      return $retVal;      return $retVal;
3497  }  }
3498    
3499  =head2 Internal Utility Methods  =head3 Fix
3500    
3501  =head3 ParseAssignment  C<< my %fixedHash = Sprout::Fix(%groupHash); >>
3502    
3503  Parse annotation text to determine whether or not it is a functional assignment. If it is,  Prepare a genome group hash (like that returned by L</GetGroups> for processing.
3504  the user, function text, and assigning user will be returned as a 3-element list. If it  Groups with the same primary name will be combined. The primary name is the
3505  isn't, an empty list will be returned.  first capitalized word in the group name.
3506    
3507  A functional assignment is always of the form  =over 4
3508    
3509      C<set >I<YYYY>C< function to\n>I<ZZZZZ>  =item groupHash
3510    
3511  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,  Hash to be fixed up.
 the user and the assigning user (from MadeAnnotation) will be the same, but that is  
 not always the case.  
3512    
3513  In addition, the functional role may contain extra data that is stripped, such as  =item RETURN
 terminating spaces or a comment separated from the rest of the text by a tab.  
3514    
3515  This is a static method.  Returns a fixed-up version of the hash.
3516    
3517  =over 4  =back
3518    
3519  =item user  =cut
3520    
3521  Name of the assigning user.  sub Fix {
3522        # Get the parameters.
3523        my (%groupHash) = @_;
3524        # Create the result hash.
3525        my %retVal = ();
3526        # Copy over the genomes.
3527        for my $groupID (keys %groupHash) {
3528            # Make a safety copy of the group ID.
3529            my $realGroupID = $groupID;
3530            # Yank the primary name.
3531            if ($groupID =~ /([A-Z]\w+)/) {
3532                $realGroupID = $1;
3533            }
3534            # Append this group's genomes into the result hash.
3535            Tracer::AddToListMap(\%retVal, $realGroupID, @{$groupHash{$groupID}});
3536        }
3537        # Return the result hash.
3538        return %retVal;
3539    }
3540    
3541  =item text  =head3 GroupPageName
3542    
3543  Text of the annotation.  C<< my $name = $sprout->GroupPageName($group); >>
3544    
3545    Return the name of the page for the specified NMPDR group.
3546    
3547    =over 4
3548    
3549    =item group
3550    
3551    Name of the relevant group.
3552    
3553  =item RETURN  =item RETURN
3554    
3555  Returns an empty list if the annotation is not a functional assignment; otherwise, returns  Returns the relative page name (e.g. C<../content/campy.php>). If the group file is not in
3556  a two-element list containing the user name and the function text.  memory it will be read in.
3557    
3558  =back  =back
3559    
3560  =cut  =cut
3561    
3562  sub _ParseAssignment {  sub GroupPageName {
3563      # Get the parameters.      # Get the parameters.
3564      my ($user, $text) = @_;      my ($self, $group) = @_;
3565      # Declare the return value.      # Declare the return variable.
3566      my @retVal = ();      my $retVal;
3567      # Check to see if this is a functional assignment.      # Check for the group file data.
3568      my ($type, $function) = split(/\n/, $text);      if (! defined $self->{groupHash}) {
3569      if ($type =~ m/^set function to$/i) {          # Read the group file.
3570          # Here we have an assignment without a user, so we use the incoming user ID.          my %groupData = Sprout::ReadGroupFile($self->{_options}->{dataDir} . "/groups.tbl");
3571          @retVal = ($user, $function);          # Store it in our object.
3572      } elsif ($type =~ m/^set (\S+) function to$/i) {          $self->{groupHash} = \%groupData;
         # Here we have an assignment with a user that is passed back to the caller.  
         @retVal = ($1, $function);  
3573      }      }
3574      # If we have an assignment, we need to clean the function text. There may be      # Compute the real group name.
3575      # extra junk at the end added as a note from the user.      my $realGroup = $group;
3576      if (@retVal > 1) {      if ($group =~ /([A-Z]\w+)/) {
3577          $retVal[1] =~ s/(\t\S)?\s*$//;          $realGroup = $1;
3578      }      }
3579      # Return the result list.      # Return the page name.
3580      return @retVal;      $retVal = "../content/" . $self->{groupHash}->{$realGroup}->[1];
3581        # Return the result.
3582        return $retVal;
3583  }  }
3584    
3585  =head3 FriendlyTimestamp  =head3 ReadGroupFile
3586    
3587  Convert a time number to a user-friendly time stamp for display.  C<< my %groupData = Sprout::ReadGroupFile($groupFileName); >>
3588    
3589  This is a static method.  Read in the data from the specified group file. The group file contains information
3590    about each of the NMPDR groups.
3591    
3592  =over 4  =over 4
3593    
3594  =item timeValue  =item name
3595    
3596  Numeric time value.  Name of the group.
3597    
3598    =item page
3599    
3600    Name of the group's page on the web site (e.g. C<campy.php> for
3601    Campylobacter)
3602    
3603    =item genus
3604    
3605    Genus of the group
3606    
3607    =item species
3608    
3609    Species of the group, or an empty string if the group is for an entire
3610    genus. If the group contains more than one species, the species names
3611    should be separated by commas.
3612    
3613    =back
3614    
3615    The parameters to this method are as follows
3616    
3617    =over 4
3618    
3619    =item groupFile
3620    
3621    Name of the file containing the group data.
3622    
3623  =item RETURN  =item RETURN
3624    
3625  Returns a string containing the same time in user-readable format.  Returns a hash keyed on group name. The value of each hash
3626    
3627  =back  =back
3628    
3629  =cut  =cut
3630    
3631  sub FriendlyTimestamp {  sub ReadGroupFile {
3632      my ($timeValue) = @_;      # Get the parameters.
3633      my $retVal = localtime($timeValue);      my ($groupFileName) = @_;
3634      return $retVal;      # Declare the return variable.
3635        my %retVal;
3636        # Read the group file.
3637        my @groupLines = Tracer::GetFile($groupFileName);
3638        for my $groupLine (@groupLines) {
3639            my ($name, $page, $genus, $species) = split(/\t/, $groupLine);
3640            $retVal{$name} = [$page, $genus, $species];
3641        }
3642        # Return the result.
3643        return %retVal;
3644  }  }
3645    
3646  =head3 AddProperty  =head3 AddProperty
# Line 3546  Line 3700 
3700      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3701  }  }
3702    
3703    =head2 Virtual Methods
3704    
3705    =head3 CleanKeywords
3706    
3707    C<< my $cleanedString = $sprout->CleanKeywords($searchExpression); >>
3708    
3709    Clean up a search expression or keyword list. This involves converting the periods
3710    in EC numbers to underscores, converting non-leading minus signs to underscores,
3711    a vertical bar or colon to an apostrophe, and forcing lower case for all alphabetic
3712    characters. In addition, any extra spaces are removed.
3713    
3714    =over 4
3715    
3716    =item searchExpression
3717    
3718    Search expression or keyword list to clean. Note that a search expression may
3719    contain boolean operators which need to be preserved. This includes leading
3720    minus signs.
3721    
3722    =item RETURN
3723    
3724    Cleaned expression or keyword list.
3725    
3726    =back
3727    
3728    =cut
3729    
3730    sub CleanKeywords {
3731        # Get the parameters.
3732        my ($self, $searchExpression) = @_;
3733        # Perform the standard cleanup.
3734        my $retVal = $self->ERDB::CleanKeywords($searchExpression);
3735        # Fix the periods in EC and TC numbers.
3736        $retVal =~ s/(\d+|\-)\.(\d+|-)\.(\d+|-)\.(\d+|-)/$1_$2_$3_$4/g;
3737        # Fix non-trailing periods.
3738        $retVal =~ s/\.(\w)/_$1/g;
3739        # Fix non-leading minus signs.
3740        $retVal =~ s/(\w)[\-]/$1_/g;
3741        # Fix the vertical bars and colons
3742        $retVal =~ s/(\w)[|:](\w)/$1'$2/g;
3743        # Return the result.
3744        return $retVal;
3745    }
3746    
3747    =head2 Internal Utility Methods
3748    
3749    =head3 ParseAssignment
3750    
3751    Parse annotation text to determine whether or not it is a functional assignment. If it is,
3752    the user, function text, and assigning user will be returned as a 3-element list. If it
3753    isn't, an empty list will be returned.
3754    
3755    A functional assignment is always of the form
3756    
3757        C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3758    
3759    where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3760    the user and the assigning user (from MadeAnnotation) will be the same, but that is
3761    not always the case.
3762    
3763    In addition, the functional role may contain extra data that is stripped, such as
3764    terminating spaces or a comment separated from the rest of the text by a tab.
3765    
3766    This is a static method.
3767    
3768    =over 4
3769    
3770    =item user
3771    
3772    Name of the assigning user.
3773    
3774    =item text
3775    
3776    Text of the annotation.
3777    
3778    =item RETURN
3779    
3780    Returns an empty list if the annotation is not a functional assignment; otherwise, returns
3781    a two-element list containing the user name and the function text.
3782    
3783    =back
3784    
3785    =cut
3786    
3787    sub _ParseAssignment {
3788        # Get the parameters.
3789        my ($user, $text) = @_;
3790        # Declare the return value.
3791        my @retVal = ();
3792        # Check to see if this is a functional assignment.
3793        my ($type, $function) = split(/\n/, $text);
3794        if ($type =~ m/^set function to$/i) {
3795            # Here we have an assignment without a user, so we use the incoming user ID.
3796            @retVal = ($user, $function);
3797        } elsif ($type =~ m/^set (\S+) function to$/i) {
3798            # Here we have an assignment with a user that is passed back to the caller.
3799            @retVal = ($1, $function);
3800        }
3801        # If we have an assignment, we need to clean the function text. There may be
3802        # extra junk at the end added as a note from the user.
3803        if (defined( $retVal[1] )) {
3804            $retVal[1] =~ s/(\t\S)?\s*$//;
3805        }
3806        # Return the result list.
3807        return @retVal;
3808    }
3809    
3810    =head3 FriendlyTimestamp
3811    
3812    Convert a time number to a user-friendly time stamp for display.
3813    
3814    This is a static method.
3815    
3816    =over 4
3817    
3818    =item timeValue
3819    
3820    Numeric time value.
3821    
3822    =item RETURN
3823    
3824    Returns a string containing the same time in user-readable format.
3825    
3826    =back
3827    
3828    =cut
3829    
3830    sub FriendlyTimestamp {
3831        my ($timeValue) = @_;
3832        my $retVal = localtime($timeValue);
3833        return $retVal;
3834    }
3835    
3836    
3837  1;  1;

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