Re: supertree construction in perl

[thomas895]

in reply to supertree construction in perl

I always wished I could see into your mind, OP, and figure out your exact problem, and then just searh your $knowledge for the required backstory. But I can't, and you're going to have to use more general terms here so that programmers can understand. Assume we are the normal, entry-level class on your subject in a suburban high school. Assume we're just teenagers(which I in fact am, but I'm speaking metaphorically here), and know next to nothing about the subject. Assume you are the teacher, and someone has written "How do I post a question effectively?" on the blackboard.
Even simple, one-sentence explanations of a concept(as in, what does the data look like in some steps of the process?) can go a long way. I looked at the textbook-thing you linked to, but it's just words-words-words-sciencey-word-words-words-words to me. Maybe it's because I'm just a 15-year-old who is fascinated by his chemistry textbook. Who knows? I'm still a few years away from college.

As for your code, I think you need to choose better variable names. I have great difficulty reading code that just looks like random characters(people often ask me, "thomas, why do you use Perl?"). I hope this isn't supposed to end up as an obfuscation. You will eventually forget the meaning of those names, and then your code becomes a confusing mess. Avoid "a" and "b" aa variable names unless that is in context with sort.
DEBUG() seems to be an empty subroutine. Is that what you intended?

P.S.: Ignore the first part if you want. I'm tired, which causes my writeups to become long and ramble-y. I'll probably remove it tomorrow, after thinking "why would I write that?"

[zing]

Hi Thomas, Yes you are very true. So I have edited the code properly this time and introduces proper variable names and indentation.

#This program read the triplets from file named "data" and returns the
#supertree. 
# ___DATA(triplets)____
#b c a
#a c d
#d e b
#### NOTE ::: SuperTree part hasnt been incorporated yet.
use strict;
use warnings;
use Data::Dumper;
use Graph; 
use Data::Dump qw/ pp /;
####READ IN THE INPUT DATA ########
my @triplets; # Get all the triplets
 while (<>) {
        push @triplets, [ split ];
    }

#Make a deep copy of @triplets 
my @triplet_deep_copy = map { [@$_] } @triplets;


#####AUXILIARY GRAPH   G(L) #######
# In order to generate the G(L)  first of all extract first two column
+s of  @triplets into another matrix
my @auxiliary_edges=@triplets;
splice(@$_, 2, 1)
foreach @auxiliary_edges;
print "----EDGE LIST TO BUILD AUXILIARY GRAPH-----\n";
print Dumper \@auxiliary_edges;


##### CONNECTED COMPONENTS ##########
my $auxiliary_graph = Graph->new( undirected => 1 );

my @from;
my @to;
for (my $p = 0; $p <= 2; $p++) {
        $from[$p]=$triplets[$p][0];
  }

for (my $q = 0; $q <= 2; $q++) {
        $to[$q]=$triplets[$q][1];
  }

for (my $r = 0; $r <= 2; $r++) {
     $auxiliary_graph->add_edge($from[$r], $to[$r]);
 }

my @subgraphs = $auxiliary_graph->connected_components; # Subgraphs
my $V = $auxiliary_graph->vertices; # Number of taxa
my $connected_components=scalar @subgraphs; #Get the number of connect
+ed components

###### FINDING THE TRIPLETS WHICH ARE SUBSET(OR INDUCED BY) OF EACH OF
+ THE CONNECTED COMPONENTS######
Main(@auxiliary_edges);
exit(0);
sub induced {
  my $trip = shift;
  my @matches;
  for my $QT ( @_ ) {
         for my $triplet ( @$trip ) {
                my %seen;        # my %Pie;
                undef @seen{@$QT};
                delete @seen{@$triplet};
                if ( keys( %seen ) <= ( @$QT - @$triplet ) ) {
                     push @matches, $triplet;
      }
    } ## end for my $triplet ( @$trip )
  } ## end for my $QT ( @_ )
  return @matches;
}## end sub induced


sub Main {
  my $tree = Graph->new( undirected => 1 );
  my $dad='u';
  $tree->add_vertex($dad);
  for my $one (@subgraphs) {
      my @matches = induced( \@triplet_deep_copy, $one );
      print "\nTriplet induced by subgraph ", pp( $one => { MATCHES =>
+ \@matches } ), "\n\n";
  }
}