Fix for Bug #3251, plus fixed a couple of regular expressions. Also a…

…dded tests.

All Blast tests pass.

Bio/SearchIO/blast.pm

@@ -447,7 +447,7 @@ sub next_result {
     my $data   = '';
     my $flavor = '';
     $self->{'_seentop'} = 0;     # start next report at top
-    $self->{'_seentop'} = 0;
+
     my ( $reporttype, $seenquery, $reportline, $reportversion );
     my ( $seeniteration, $found_again );
     my $incl_threshold = $self->inclusion_threshold;
@@ -462,7 +462,7 @@ sub next_result {
         next if (/^\s+$/);       # skip empty lines
         next if (/CPU time:/);
         next if (/^>\s*$/);
-        next if (/\Q[*]+\s+No hits found\s+[*]+\E/);
+        next if (/[*]+\s+No hits found\s+[*]+/);
         if (
                /^((?:\S+?)?BLAST[NPX]?)\s+(.+)$/i  # NCBI BLAST, PSIBLAST
                                                    # RPSBLAST, MEGABLAST
@@ -630,6 +630,27 @@ sub next_result {
                     'Data' => "$acc$version"
                 }
             ) if $acc;
+
+            # these elements are dropped with some multiquery reports; add
+            # back here
+            $self->element(
+                {
+                    'Name' => 'BlastOutput_db-len',
+                    'Data' => $self->{'_blsdb_length'}
+                }
+            ) if $self->{'_blsdb_length'};
+            $self->element(
+                {
+                    'Name' => 'BlastOutput_db-let',
+                    'Data' => $self->{'_blsdb_letters'}
+                }
+            ) if $self->{'_blsdb_letters'};
+            $self->element(
+                {
+                    'Name' => 'BlastOutput_db',
+                    'Data' => $self->{'_blsdb'}
+                }
+            ) if $self->{'_blsdb_letters'};
         }
 		# added check for WU-BLAST -echofilter option (bug 2388)
 		elsif (/^>Unfiltered[+-]1$/) {
@@ -655,26 +676,6 @@ sub next_result {
             if ( !$self->in_element('iteration') ) {
                 $self->start_element( { 'Name' => 'Iteration' } );
             }
-            # these elements are dropped with some multiquery reports; add
-            # back here
-            $self->element(
-                {
-                    'Name' => 'BlastOutput_db-len',
-                    'Data' => $self->{'_blsdb_length'}
-                }
-            ) if $self->{'_blsdb_length'};
-            $self->element(
-                {
-                    'Name' => 'BlastOutput_db-let',
-                    'Data' => $self->{'_blsdb_letters'}
-                }
-            ) if $self->{'_blsdb_letters'};
-            $self->element(
-                {
-                    'Name' => 'BlastOutput_db',
-                    'Data' => $self->{'_blsdb'}
-                }
-            ) if $self->{'_blsdb_letters'};
 
             # changed 8/28/2008 to exit hit table if blank line is found after an
             # appropriate line
@@ -757,7 +758,7 @@ sub next_result {
             }
 
         }
-        elsif (/^Database:\s*(.+)$/) {
+        elsif (/^Database:\s*(.+?)\s*$/) {
 
             $self->debug("blast.pm: Database: $1\n");
             my $db = $1;

t/SearchIO/blast.t

@@ -8,7 +8,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 1357);
+    test_begin(-tests => 1360);
 
     use_ok('Bio::SearchIO');
 }
@@ -1171,7 +1171,7 @@ is( $r->algorithm,                           'MEGABLAST' );
 is( $r->query_name,                          '503384' );
 is( $r->query_description,                   '11337 bp 2 contigs' );
 is( $r->query_length,                        11337 );
-is( $r->database_name,                       'cneoA.nt ' );
+is( $r->database_name,                       'cneoA.nt' );
 is( $r->database_letters,                    17206226 );
 is( $r->database_entries,                    4935 );
 is( $r->get_statistic('querylength'),        11318 );
@@ -2211,3 +2211,13 @@ $searchio = Bio::SearchIO->new(
 is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298");
 is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298");
 is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298");
+
+# testing for Bug #3251
+$searchio = Bio::SearchIO->new(
+    '-format' => 'blast',
+    '-file'   => test_input_file('rpsblast_no_hits.bls')
+);
+
+is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251");
+is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251");
+is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251");

t/data/rpsblast_no_hits.bls

@@ -0,0 +1,58 @@
+RPS-BLAST 2.2.18 [Mar-02-2008]
+
+Database: CDD.v.2.13 
+           24,083 sequences; 5,982,884 total letters
+
+Searching..................................................done
+
+Query= lcl|YP_134044.1|Plus1 F 4437 4742 NC_006391 hypothetical
+protein {Haloarcula marismortui ATCC 43049}
+         (101 letters)
+
+ ***** No hits found ******
+
+
+Query= lcl|YP_134045.1|Plus1 F 4742 5065 NC_006391 transcription
+regulator {Haloarcula marismortui ATCC 43049}
+         (107 letters)
+
+ ***** No hits found ******
+
+
+Query= lcl|YP_134046.1|Plus1 F 5275 5808 NC_006391 hypothetical
+protein {Haloarcula marismortui ATCC 43049}
+         (177 letters)
+
+ ***** No hits found ******
+
+
+  Database: CDD.v.2.13
+    Posted date:  Nov 8, 2007  6:30 PM
+  Number of letters in database: 5,982,884
+  Number of sequences in database:  24,083
+
+Lambda     K      H
+   0.308    0.126    0.352 
+
+Gapped
+Lambda     K      H
+   0.267   0.0606    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Sequences: 24083
+Number of Hits to DB: 200,397,591
+Number of extensions: 14170162
+Number of successful extensions: 17150
+Number of sequences better than 1.0e-005: 6
+Number of HSP's gapped: 17124
+Number of HSP's successfully gapped: 29
+Length of database: 5,982,884
+Neighboring words threshold: 11
+Window for multiple hits: 40
+X1: 15 ( 6.7 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 40 (20.8 bits)
+S2: 102 (43.3 bits)