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#!/usr/bin/perl |
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# |
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# @File Interface.pm |
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# @Author andriy |
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# @Created Aug 1, 2016 10:33:50 AM |
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# |
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=head1 NAME |
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SemMed::Interface - A suite of Perl modules that utilize path information |
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present in the Semantic Medline Database in order to calculate the semantic |
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association between two concepts in the UMLS. |
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=head1 INSTALL |
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To install the module, run the following magic commands: |
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perl Makefile.PL |
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make |
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make test |
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make install |
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This will install the module in the standard location. You will, most |
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probably, require root privileges to install in standard system |
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directories. To install in a non-standard directory, specify a prefix |
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during the 'perl Makefile.PL' stage as: |
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perl Makefile.PL PREFIX=/home/sid |
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It is possible to modify other parameters during installation. The |
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details of these can be found in the ExtUtils::MakeMaker |
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documentation. However, it is highly recommended not messing around |
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with other parameters, unless you know what you're doing. |
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=head1 DESCRIPTION |
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This package provides a Perl interface to the Semantic Medline Database |
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=head1 DATABASE SETUP |
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The interface assumes you have installed the Semantic Medline Database onto your |
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MySQL server and in addition, followed the steps present in the INSTALL file to |
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create the appropriate auxilary tables in order to speed up program runtime. |
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The name of the database can be passed through during program runtime but will |
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default to 'SemMedDB' if no parameter is given. |
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The SemMedDB database must contain the following tables: |
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1. CONCEPT |
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2. CONCEPT_SEMTYPE |
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3. PREDICATION_ARGUMENT |
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4. PREDICATION |
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5. SENTENCE_PREDICATION |
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6. SENTENCE |
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7. CITATIONS |
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8. PREDICATION_AGGREGATE |
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9. DISTINCT_PREDICATION_AGGREGATE * |
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*The table 'DISTINCT_PREDICATION_AGGREGATE' does not install alongside the |
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Semantic Medline Database via the .SQL file provided on their website. Steps |
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must be followed in the INSTALL file to set-up this table. Failure to do so |
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will cause fatal errors at runtime. |
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A script inside the INSTALL file details the steps needed to generate |
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the required auxilary tables. These steps are to be done following the Semantic |
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Medline Database install and may take up to several days to complete due to the |
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size of the database. |
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=head1 INITIALIZING THE MODULE |
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To create an instance of the interface module, using default values |
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for all configuration options: |
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use SemMed::Interface; |
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my $SemMedLoginParam = { "driver" => "mysql", |
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"database" => "SemMedDB", |
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"username" => "username", |
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"password" => "password", |
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"socket" => "/home/mysql/mysql.sock", |
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"hostname" => "localhost", |
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"port" => "3306"}; |
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my $AssociationLoginParam = { "driver" => "mysql", |
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"database" => "CUI_BIGRAMS_27JUL15", |
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"username" => "username", |
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"password" => "password", |
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"socket" => "/home/mysql/mysql.sock", |
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"hostname" => "localhost", |
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"port" => "3306"}; |
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my $interface = new SemMed::Interface($SemMedLoginParam, $AssociationLoginParam); |
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=cut |
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package SemMed::Interface; |
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use strict; |
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use warnings; |
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use SemMed::Interface::GraphTraversal; |
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use SemMed::Interface::DataAccess; |
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use vars qw($VERSION); |
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$VERSION = '0.03'; |
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my $connection = ""; |
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my $gt = ""; |
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my @includedPredicates; #only this predicates will be used in the traversal |
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my @excludedPredicates; #these predicates will be excluded in the traversal |
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# method to create a new SemMed::Interface object |
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# input : $SemMedLoginParams <- reference to hash containing SemMed login parameter |
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# $AssociationLoginParams <- reference to hash containing the UMLS::Association login parameters |
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# output: |
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sub new { |
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my $self = {}; |
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my $class = shift; |
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my $SemMedLoginParams = shift; #hash containing the SemMed login parameters |
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my $AssociationLoginParams = shift; #hash containing the UMLS::Association login parameters |
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@includedPredicates = (); |
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@excludedPredicates = (); |
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bless($self, $class); |
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$connection = new DataAccess($SemMedLoginParams, $AssociationLoginParams); |
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$gt = new GraphTraversal($connection); |
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return $self; |
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} |
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####################################### |
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=head3 findPathLength |
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description: |
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Utilizes a breadth first search to find the path length from a source_concept to a destination_concept |
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input: |
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$source_concept <- string containing the concept id of the cui to start seraching from |
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$destination_concept <- string containing the concept id you are searching for |
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output: |
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length of path <- Non-negative Integer | -1 indicating length of path between the two concepts |
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example: |
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#finds path length between Heart and Myocardial Infarction |
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use SemMed::Interface; |
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my $interface = new SemMed::Interface(); |
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my $pathlength = $interface->findPathLength("C0018787", "C0027061"); |
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=cut |
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sub findPathLength{ |
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my $self = shift; |
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my $source_cui = shift; |
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my $destination_cui = shift; |
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# return $gt->findPath($source_cui, $destination_cui, \@includedPredicates, \@excludedPredicates); |
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return $gt->findPath($source_cui, $destination_cui); |
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} |
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####################################### |
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=head3 findPathScore |
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description: |
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Function utilizing a breadth first search along with UMLS::Association to find the aggregate association score |
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along the path between source_concept and destination_concept |
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input: |
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$source_concept <- string containing the concept id of the cui to start seraching from |
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$destination_concept <- string containing the concept id you are searching for |
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$measure <- string containing the UMLS::Association statistic measure to aggregate along paths. |
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output: |
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Aggregate association score <- Non-negative float indicating the aggregate path score |
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example: |
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#finds aggregate association score between Heart and Myocardial Infarction |
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use SemMed::Interface; |
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my $interface = new SemMed::Interface(); |
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my $score = $interface->findPathLength("C0018787", "C0027061", "tscore"); |
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=cut |
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sub findPathScore{ |
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my $self = shift; |
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my $source_cui = shift; |
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my $destination_cui = shift; |
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my $measure = shift; |
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return $gt->findPathScore($source_cui, $destination_cui, $measure, \@includedPredicates, \@excludedPredicates); |
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} |
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=head3 getConceptDegree |
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description: |
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Gets the degree(the number of outgoing relationships) from a particular cui |
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input: |
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$concept <- string containing the concept id of the cui to start seraching from |
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output: |
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Integer >= 0 <- Degree of the concept |
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=cut |
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sub getConceptDegree{ |
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my $self = shift; |
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my $concept = shift; |
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return $connection->getConceptDegree($concept); |
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} |
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=head3 getConnections |
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description: |
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Gets all outgoing predicates and concepts from a given concept |
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input: |
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$concept <- string containing the concept id to get outgoing edges from |
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output: |
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$edges <- array reference of outgoing predicates and concepts |
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example: |
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use SemMed::Interface; |
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my $interface = new SemMed::Interface(); |
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my $edges = $interface->getConnections("C0018787"); |
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foreach @edge (@$edges){ |
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$predicate = $edge[0]; |
238
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$destination_concept = $edge[1]; |
239
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} |
240
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241
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=cut |
242
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243
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sub getConnections { |
244
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my $self = shift; |
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my $concept = shift; |
246
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return $connection->getConnections($concept); |
247
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} |
248
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249
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250
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251
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252
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253
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254
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255
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256
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sub addIncludedPredicates{ |
257
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my $self = shift; |
258
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my $predicates = shift; |
259
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push @includedPredicates, @$predicates; |
260
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} |
261
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262
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263
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264
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sub clearIncludedPredicates{ |
265
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my $self = shift; |
266
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@includedPredicates = (); |
267
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} |
268
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269
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270
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271
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sub addExcludedPredicates{ |
272
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my $self = shift; |
273
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my $predicates = shift; |
274
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push @excludedPredicates, @$predicates; |
275
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} |
276
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277
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278
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279
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sub clearExcludedPredicates{ |
280
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|
my $self = shift; |
281
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|
@excludedPredicates = (); |
282
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} |
283
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284
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285
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286
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287
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1; |