* Start supporting keyword weights

 * Transition from do_it_all_state to function2gene_state
 * Fix invalidate_state function to invalidate state dependencies

git-svn-id: file:///srv/svn/function2gene/trunk@23 a0738b58-4706-0410-8799-fb830574a030

diff --git a/bin/function2gene b/bin/function2gene
index c407047418332d93c80fac96b7712dae31a611e3..f3bd3ddfd7364a89afac2c4d391e43b3787e8b8d 100755 (executable)
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -41,7 +41,9 @@ use Storable;
 
 A file which contains a newline delinated list of keywords to search
 for. Can be specified multiple times. Lines starting with # or ; are
-ignored.
+ignored. An optional weight can be specified after the keyword, which
+is separated from the keyword by a tab. (If not specified, 1 is
+assumed.)
 
 =item B<--results>
 
@@ -158,9 +160,9 @@ $options{keywords} = [map {abs_path($_)} @{$options{keywords}}];
 
 chdir $options{results} or die "Unable to chdir to $options{results}";
 
-if (-e "do_it_all_state") {
+if (-e "function2gene_state") {
      ADVISE("Using existing state information");
-     my $state_fh = IO::File->new("do_it_all_state",'r') or die
+     my $state_fh = IO::File->new("function2gene_state",'r') or die
          "Unable to open state file for reading: $!";
      local $/;
      my $state_file = <$state_fh>;
@@ -190,6 +192,9 @@ if (@{$options{keywords}}) {
               next if /^\s*[#;]/;
               next unless /\w+/;
               chomp;
+              my ($keyword,$weight) = split /\t/, $_;
+              $weight = 1 if not defined $weight;
+              $state{keyword_weight}{$keyword} = $weight;
               if (not $old_keywords{$_}) {
                    DEBUG("Adding new keyword '$_'");
                    push @new_keywords, $_;
@@ -220,17 +225,40 @@ if (exists $options{restart_at} and length $options{restart_at}) {
 if (exists $options{invalidate_state}) {
      for my $invalidate_state (@{$options{invalidate_state}}) {
          my ($method,$database,$keyword) = split /,/, $invalidate_state;
+         if (grep {not defined $_ } ($method,$database,$keyword) ) {
+              print STDERR "The invalidate state option '$invalidate_state' is invalid.\n";
+              next;
+         }
          if (not exists $state{done_keywords}{$method}) {
               print STDERR "Method '$method' does not exist, and cannot be invalidated\n";
+              next;
          }
-         elsif (not exists $state{done_keywords}{$method}{$database}) {
+         if (not exists $state{done_keywords}{$method}{$database}) {
               print STDERR "Database '$database' does not exist for method '$method', and cannot be invalidated\n";
+              next;
+         }
+         if (not length $keyword) {
+              delete $state{done_keywords}{$method}{$database};
+              if ($method eq 'get') {
+                   delete $state{done_keywords}{parse}{$database};
+                   delete $state{done_keywords}{combine}{$database};
+              }
+              if ($method eq 'parse') {
+                   delete $state{done_keywords}{combine}{$database};
+              }
+              next;
          }
-         elsif (not exists $state{done_keywords}{$method}{$database}{$keyword}) {
+         if (not exists $state{done_keywords}{$method}{$database}{$keyword}) {
               print STDERR "Keyword '$keyword' does not exist for database '$database' and method '$method', and cannot be invalidated\n";
+              next;
          }
-         else {
-              delete $state{done_keywords}{$method}{$database}{$keyword};
+         delete $state{done_keywords}{$method}{$database}{$keyword};
+         if ($method eq 'get') {
+              delete $state{done_keywords}{parse}{$database}{$keyword};
+              delete $state{done_keywords}{combine}{$database}{$keyword};
+         }
+         if ($method eq 'parse') {
+              delete $state{done_keywords}{combine}{$database}{$keyword};
          }
      }
 }
@@ -296,7 +324,7 @@ for my $state (qw(get parse)) {
      }
      save_state(\%state);
      if ($ERRORS) {
-         WARN("Stoping, as there are errors");
+         WARN("Stoping, asthere are errors");
          exit 1;
      }
 }
@@ -310,8 +338,12 @@ if ($actions{combine}) {
                                } keys %{$state{done_keywords}{parse}{$db}}
                           } keys %{$state{done_keywords}{parse}};
 
+     # create temporary file to store keyword weights
+
      write_command_to_file('combined_results.txt',
                           "$base_dir/combine_results",
+                          '--keywords',
+                          
                           @parsed_results,
                          );
      for my $result (@parsed_results) {
@@ -383,7 +415,7 @@ sub handle_action{
 
 sub save_state{
      my ($state) = @_;
-     my $state_fh = IO::File->new("do_it_all_state",'w') or die
+     my $state_fh = IO::File->new("function2gene_state",'w') or die
          "Unable to open state file for writing: $!";
      print {$state_fh} freeze($state) or die "Unable to freeze state file";
      close $state_fh or die "Unable to close state file: $!";