move bugzilla tests to relevant test files, data to t/data, and remove

svn path=/bioperl-live/trunk/; revision=16093

t/Align/SimpleAlign.t

@@ -684,7 +684,7 @@ foreach my $seq ( $removed->each_seq ) {
     }
 }
 
-# work out mask_columns()
+# work out mask_columns(), see bug 2842
 SKIP: {
     test_skip(-tests => 6, -requires_module => 'IO::String');
     my $io = Bio::AlignIO->new( -file => test_input_file("testaln.aln") );

t/SearchIO/exonerate.t

@@ -7,7 +7,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin( -tests => 45 );
+    test_begin( -tests => 49 );
 
     use_ok('Bio::SearchIO');
 }
@@ -74,3 +74,34 @@ while ( my $r = $searchio->next_result ) {
         is( $hsp->hit->strand, shift @$d );
     }
 }
+
+# bug 2346
+
+my @cts = (7, 1);
+
+$searchio = Bio::SearchIO->new(
+   -format => 'exonerate',
+   -file   => test_input_file('exonerate.output.works'),
+);
+parse($searchio);
+
+$searchio = Bio::SearchIO->new(
+   -format => 'exonerate',
+   -file   => test_input_file('exonerate.output.dontwork'),
+);
+parse($searchio);
+
+sub parse {
+    my ($searchio) = @_;
+    while( my $r = $searchio->next_result ) {
+        my $hsp_ct = 0;
+        while(my $hit = $r->next_hit){
+            while(my $hsp = $hit->next_hsp){
+                $hsp_ct++;
+            }
+        }
+        ok($r->query_name, "query_name");
+        is($hsp_ct, shift @cts);
+    }
+}
+

t/SearchIO/fasta.t

@@ -7,7 +7,7 @@ BEGIN {
 	use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 287);
+    test_begin(-tests => 289);
 
 	use_ok('Bio::SearchIO');
 }
@@ -384,3 +384,22 @@ while(my $res = $searchio->next_result) {
     is($res->algorithm, 'FASTN');
 }
 
+# bug 2537
+
+$searchio = Bio::SearchIO->new(
+   -format => 'fasta',
+   -file   => test_input_file('in.fasta'),
+);
+
+while ( my $result = $searchio->next_result() ) {
+   while( my $hit = $result->next_hit ) {
+      # process the Bio::Search::Hit::HitI object
+      while( my $hsp = $hit->next_hsp ) {
+         # process the Bio::Search::HSP::HSPI object
+         is($hsp->num_identical, 30, "num_identical()");
+         is($hsp->num_conserved, 30, "num_conserved()");
+      }
+   }
+}
+
+

t/SearchIO/psl.t

@@ -7,7 +7,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 52);
+    test_begin(-tests => 53);
 
     use_ok('Bio::SearchIO');
 }
@@ -96,3 +96,12 @@ TODO: {
     local $TODO = "next_result should really return undef, not empty string";
     is( $pslparser->next_result, undef, 'next_result should be undef');
 }
+
+# bug 2850
+
+my $searchio = Bio::SearchIO->new(
+    -format => 'psl',
+    -file   => test_input_file('headerless.psl'),
+);
+
+lives_ok { my $result = $searchio->next_result };

t/Seq/Quality.t

@@ -7,11 +7,13 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 60);
+    test_begin(-tests => 61);
 
     use_ok('Bio::Seq::Quality');
 }
 
+use Bio::SeqIO;
+
 my $DEBUG = test_debug();
 
 # create some random sequence object with no id
@@ -266,3 +268,14 @@ is scalar @ranges, 3;
 my $min_length = 10;
 @ranges = $seq->get_all_clean_ranges($min_length);
 is scalar @ranges, 2;
+
+my $seqio = Bio::SeqIO->new(
+    -file   => test_input_file('test_clear_range.fastq'),
+    -format => 'fastq'
+);
+
+while ( my $seq = $seqio->next_seq() ) {
+    $seq->threshold(15);
+    lives_ok { my $newqualobj = $seq->get_clear_range };
+}
+