Re^3: Use of uninitialized value $cui1 in print

# UMLS::Similarity::lch.pm
#
# Module implementing the semantic relatedness measure described 
# by Leacock and Chodorow (1998).
#
<code>


sub getRelatedness
{
    my $self = shift;

    return undef if(!defined $self || !ref $self);

    my $concept1 = shift;
    my $concept2 = shift;

        #  get the interfaceg
    my $interface = $self->{'interface'};

    #  find the length of the shortest path
    #  if concept 1 and 2 are the same just return 1
    my $length = 0;
    if($concept1 eq $concept2) { $length = 1; }
    else { $length = $interface->findShortestPathLength($concept1, $co
+ncept2); }

    #  get the depth of the taxonomy
    my $depth = $interface->depth();
    
    #  if the length of hte path is less than zero return -1
    if($length < 0) { return -1; }

    #  calculate lch
    my $score = -1 * log ($length / (2 * $depth));
    
    return $score;

}


=
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this subroutine in code is by default present in umls::similarity package. Where our $t1 is passes as $concept1 and $t2 is passed as $concept 2.So I dont think there is anything wrong in this code.What am I thinking is maybe $t1 is not able to get value as string the way it should be.Well I am beginner so I dont have much knowledge so plz help me

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Re^4: Use of uninitialized value $cui1 in print by AnomalousMonk (Archbishop) on Mar 03, 2017 at 05:12 UTC
I have never used nor even seen the UMLS::Similarity::lch module before and, after a brief perusal, have only the vaguest idea of what it is supposed to do. However, total ignorance should never prevent a righteous monk from offering an opinion! So... `my $cu1 = $umls->getConceptList($t1); #calling function from umls::sim +ilarity #ERRRO 1 as mentioned my $cui1 =pop @{$cu1}; my $cu2 = $umls->getConceptList($t2);*error my $cui2 = pop @{$cu2}; print $cui1; # *ERROR2 unintialized $cui1 my $lvalue = $lch->getRelatedness($cui1, $cui2);` [download] If the value (which should be an array reference) returned to `$cu1` by the call to the `getConceptList()` method in the `my $cu1 = $umls->getConceptList($t1); #calling function from umls::similarity #ERRRO 1 as mentioned` statement is undefined* or is a reference to an empty array, the value assigned to `$cui1` by the pop in `my $cui1 =pop @{$cu1};` will be undefined, as your comment to the `print $cui1; # ***ERROR2 unintialized $cui1` statement suggests. Because an undefined `$cui1` will become an undefined `$concept1` within the call to the `getRelatedness()` method, you will get a warning like `"Use of uninitialized value $concept1 in string eq at UMLS/Similarity/lch.pm ...` at the line number associated with the `if($concept1 eq $concept2) { $length = 1; }` statement in `getRelatedness()`. So your first step is to determine whether `$cu1` is undefined or a reference to an empty array. I would do this with a Data::Dumper print debugging statement after the method call: `my $cu1 = $umls->getConceptList($t1);` `print Dumper $cu1;` Once you know the value of `$cu1`, you can figure out from the documentation (or the source) of `getConceptList()` why* it has this value given that you know the value `$t1`. I hope this helps. It seems you've already gone quite a way through the steps I've outlined, but maybe this will help clarify things a bit. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]

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Re^4: Use of uninitialized value $cui1 in print
by AnomalousMonk (Archbishop) on Mar 03, 2017 at 05:12 UTC

I have never used nor even seen the UMLS::Similarity::lch module before and, after a brief perusal, have only the vaguest idea of what it is supposed to do. However, total ignorance should never prevent a righteous monk from offering an opinion! So...

my $cu1 = $umls->getConceptList($t1); #calling function from umls::sim +ilarity #ERRRO 1 as mentioned my $cui1 =pop @{$cu1}; my $cu2 = $umls->getConceptList($t2);***error my $cui2 = pop @{$cu2}; print $cui1; # ****ERROR2 unintialized $cui1 my $lvalue = $lch->getRelatedness($cui1, $cui2);
[download]

If the value (which should be an array reference) returned to $cu1 by the call to the getConceptList() method in the
my $cu1 = $umls->getConceptList($t1); #calling function from umls::similarity #ERRRO 1 as mentioned
statement is undefined or is a reference to an empty array, the value assigned to $cui1 by the pop in
my $cui1 =pop @{$cu1};
will be undefined, as your comment to the
print $cui1; # ****ERROR2 unintialized $cui1
statement suggests.

Because an undefined $cui1 will become an undefined $concept1 within the call to the getRelatedness() method, you will get a warning like "Use of uninitialized value $concept1 in string eq at UMLS/Similarity/lch.pm ... at the line number associated with the
if($concept1 eq $concept2) { $length = 1; }
statement in getRelatedness().

So your first step is to determine whether $cu1 is undefined or a reference to an empty array. I would do this with a Data::Dumper print debugging statement after the method call:
my $cu1 = $umls->getConceptList($t1);
print Dumper $cu1;
Once you know the value of $cu1, you can figure out from the documentation (or the source) of getConceptList() why it has this value given that you know the value $t1.

I hope this helps. It seems you've already gone quite a way through the steps I've outlined, but maybe this will help clarify things a bit.

Give a man a fish: <%-{-{-{-<

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