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lib/Algorithm/TrunkClassifier/DataWrapper.pm  view on Meta::CPAN

	my $self = shift(@_);
	return $self->{"class_one"};
}

#Description: Returns the name of class two
#Parameters: (1) TrunkClassifier::DataWrapper object
#Return value: Class name
sub getClassTwoName($){
	my $self = shift(@_);
	return $self->{"class_two"};
}

#Description: Returns a copy of a TrunkClassifier::DataWrapper object
#Parameters: (1) TrunkClassifier::DataWrapper object
#Return value: New TrunkClassifier::DataWrapper object
sub copy($){
	my $self = shift(@_);
	my $newWrapper = Algorithm::TrunkClassifier::DataWrapper->new();
	my @colnames = @{$self->{"colnames"}};
	my @rownames = @{$self->{"rownames"}};
	my @classVector = @{$self->{"class_vector"}};
	my @dataMatrix;
	foreach my $arrayRef (@{$self->{"data_matrix"}}){
		my @arrayCopy = @{$arrayRef};
		push(@dataMatrix, \@arrayCopy);
	}
	$newWrapper->{"colnames"} = \@colnames;
	$newWrapper->{"rownames"} = \@rownames;
	$newWrapper->{"data_matrix"} = \@dataMatrix;
	$newWrapper->{"class_vector"} = \@classVector;
	$newWrapper->{"class_one"} = $self->{"class_one"};
	$newWrapper->{"class_two"} = $self->{"class_two"};
	return $newWrapper;
}

#Description: Removes one sample from a TrunkClassifier::DataWrapper object
#Parameters: (1) TrunkClassifier::DataWrapper object, (2) index of sample to remove
#Return value: TrunkClassifier::DataWrapper object containing the removed sample
sub leaveOneOut($ $){
	my ($self, $index) = @_;
	my @colnames = ($self->{"colnames"}[$index]);
	my @rownames = @{$self->{"rownames"}};
	my @classVector = ($self->{"class_vector"}[$index]);
	my @matrixCol;
	for(my $row = 0; $row < scalar(@rownames); $row++){
		my @colArray = splice(@{$self->{"data_matrix"}[$row]}, $index, 1);
		push(@matrixCol, \@colArray);
	}
	splice(@{$self->{"colnames"}}, $index, 1);
	splice(@{$self->{"class_vector"}}, $index, 1);
	my $newWrapper = Algorithm::TrunkClassifier::DataWrapper->new();
	$newWrapper->{"colnames"} = \@colnames;
	$newWrapper->{"rownames"} = \@rownames;
	$newWrapper->{"data_matrix"} = \@matrixCol;
	$newWrapper->{"class_vector"} = \@classVector;
	$newWrapper->{"class_one"} = $self->{"class_one"};
	$newWrapper->{"class_two"} = $self->{"class_two"};
	return $newWrapper;
}

#Description: Removes a percentage of samples from a TrunkClassifier::DataWrapper object
#Parameters: (1) TrunkClassifier::DataWrapper object, (2) split percent
#Return value: TrunkClassifier::DataWrapper object containing the removed samples
sub splitSamples($ $){
	my ($self, $split) = @_;
	my $totNumSamples = $self->getNumSamples();
	my $testSetSize = floor(($split / 100) * $totNumSamples);
	my @colnames;
	my @rownames = $self->getProbeList();
	my @classVector;
	my @matrix;
	for(my $row = 0; $row < $self->getNumProbes(); $row++){
		my @array;
		push(@matrix, \@array);
	}
	for(my $testIndex = 0; $testIndex < $testSetSize; $testIndex++){
		my $randIndex = int(rand($self->getNumSamples()));
		my $colname = splice(@{$self->{"colnames"}}, $randIndex, 1);
		push(@colnames, $colname);
		my $class = splice(@{$self->{"class_vector"}}, $randIndex, 1);
		push(@classVector, $class);
		for(my $row = 0; $row < $self->getNumProbes(); $row++){
			my $value = splice(@{$self->{"data_matrix"}[$row]}, $randIndex, 1);
			push(@{$matrix[$row]}, $value);
		}
	}
	my $testSet = Algorithm::TrunkClassifier::DataWrapper->new();
	$testSet->{"colnames"} = \@colnames;
	$testSet->{"rownames"} = \@rownames;
	$testSet->{"data_matrix"} = \@matrix;
	$testSet->{"class_vector"} = \@classVector;
	$testSet->{"class_one"} = $self->{"class_one"};
	$testSet->{"class_two"} = $self->{"class_two"};
	return $testSet;
}

#Description: Returns the number of samples in the specified class
#Parameters: (1) TrunkClassifier::DataWrapper object, (2) class
#Return value: Array with column indexes
sub getClassSize($ $){
	my ($self, $class) = @_;
	my $classSize = 0;
	foreach my $sampleClass (@{$self->{"class_vector"}}){
		if($sampleClass eq $class){
			$classSize++;
		}
	}
	return $classSize;
}

#Description: Returns the probe name of the probe row index given as argument
#Parameters: (1) TrunkClassifier::DataWrapper object, (2) probe row index
#Return value: Probe name
sub getProbeName($ $){
	my ($self, $probeIndex) = @_;
	return ${$self->{"rownames"}}[$probeIndex];
}

#Description: Returns the probe row index of the probe name given as argument
#Parameters: (1) TrunkClassifier::DataWrapper object, (2) probe name
#Return value: Probe row index
sub getProbeIndex($ $){