tests for new and rewritten methods

modules/t/archiveStableId.t

@@ -4,7 +4,7 @@ no warnings qw(uninitialized);
 
 BEGIN { $| = 1;  
 	use Test;
-	plan tests => 9;
+	plan tests => 20;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -19,21 +19,40 @@ our $verbose = 0;
 #
 ok(1);
 
+
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
 my $db    = $multi->get_DBAdaptor('core');
 
 my $asia = $db->get_ArchiveStableIdAdaptor();
 
-my $asi = $asia->fetch_by_stable_id( "G1" );
 
-_print_asi( $asi );
+#
+# 2-4 ArchiveStableId retrieval
+#
+my $asi = $asia->fetch_by_stable_id("T1");
+ok( $asi->release == 2);
+
+$asi = $asia->fetch_by_stable_id_version("T2", 3);
+ok( $asi->release == 3);
+
+$asi = $asia->fetch_by_stable_id_dbname("T1", "release_2");
+ok( $asi->release == 2);
+
 
 #
-# 2 retrieval of an archiveStableId
+# 5 retrieval of an archiveStableId
 #
+$asi = $asia->fetch_by_stable_id( "G1" );
+_print_asi( $asi );
+
 ok( $asi );
 
+
+#
+# 6 how many predecessors does it have
+#
 my $pre_asis = $asi->get_all_predecessors();
+ok( scalar( @$pre_asis ) == 2 );
 
 for my $asi ( @$pre_asis ) {
   debug( "\tPre G1" );
@@ -42,41 +61,35 @@ for my $asi ( @$pre_asis ) {
 
 
 #
-# 3 how many predecessors does it have
+# 7 transcripts for a gene
 #
-ok( scalar( @$pre_asis ) == 2 );
-
 my $transcripts = $pre_asis->[0]->get_all_transcript_archive_ids();
 
 for my $asi ( @$transcripts ) {
   debug( "\tTranscripts G1" );
   _print_asi( $asi );
   
-  #get_translation_archive_id was changed to give back listref.
-  #this makes the function poorly named, but it is what the
-  #webteam uses so....
   my $tl = $asi->get_all_translation_archive_ids();
   foreach my $asi2 (@$tl) {
     _print_asi( $asi2 );
   }
 }
 
-#
-# 4 transcripts for a gene
-#
 ok( scalar( @$transcripts ) == 1);
 
 
-
+#
+# 8 no predecessor case
+#
 $pre_asis = $pre_asis->[0]->get_all_predecessors();
 debug( "\tPredecessors: ".scalar( @$pre_asis ) );
 
+ok( scalar( @$pre_asis ) == 0 );
+
 
 #
-# 5 no predecessor case
+# 9 successor case
 #
-ok( scalar( @$pre_asis ) == 0 );
-
 $asi = $asia->fetch_by_stable_id_dbname( "G4", "release_1" );
 my $succ_asis = $asi->get_all_successors();
  
@@ -85,11 +98,11 @@ for my $asi ( @$succ_asis ) {
   _print_asi( $asi );
 }
 
-#
-# 6 successor case
-#
 ok( scalar( @$succ_asis ) == 1 );
 
+#
+# 10 no successor case
+#
 $succ_asis = $succ_asis->[0]->get_all_successors();
 
 for my $asi ( @$succ_asis ) {
@@ -97,17 +110,12 @@ for my $asi ( @$succ_asis ) {
   _print_asi( $asi );
 }
 
-
-#
-# 7 no successor case
-#
-
 ok( scalar( @$succ_asis ) == 0 );
 
+
 #
-# 8 fetch_successor_history
+# 11 fetch_successor_history
 #
-
 $asi = $asia->fetch_by_stable_id_dbname( "G2", "release_1" );
 my $asis = $asia->fetch_successor_history( $asi );
 
@@ -119,15 +127,57 @@ for my $asi ( @$asis ) {
 ok(( $asis->[-1]->db_name eq "release_4" ) &&
    ( scalar @$asis == 5 ));
 
+#
+# 12-16 history tree
+#
+$asi = $asia->fetch_by_stable_id_dbname( "G2", "release_1" );
+my $history = $asi->get_history_tree;
+
+my @asis = @{ $history->get_all_ArchiveStableIds };
+ok( scalar(@asis) == 9);
+
+my @events = @{ $history->get_all_StableIdEvents };
+ok( scalar(@events) == 10);
+
+ok( scalar(@{ $history->get_release_display_names }) == 4);
+ok( scalar(@{ $history->get_unique_stable_ids }) == 3);
+
+my ($x, $y) = @{ $history->coords_by_ArchiveStableId($asi) };
+ok( $x == 0 and $y == 1 );
+
+
+#
+# 17-18 check for current version and fetch latest incarnation
+#
+ok( ! $asi->is_latest );
+
+$asi = $asi->get_latest_incarnation;
+ok( $asi->is_latest and $asi->version == 4 );
+
 
 #
-# 9 reject unknown stable ids
+# 19 associated IDs in archive
 #
+$asi = $asia->fetch_by_stable_id_version( "G2", "2" );
+my @assoc = @{ $asi->get_all_associated_archived };
+ok( scalar(@assoc) == 2 and
+    $assoc[0]->[0]->type eq 'Gene' and
+    $assoc[0]->[1]->type eq 'Transcript' and
+    $assoc[0]->[2]->type eq 'Translation' and
+    $assoc[0]->[3] =~ /^PT/
+);
 
-ok( ! defined $asia->fetch_by_stable_id_dbname( "FooBar", "release_unknown" ));
 
+#
+# 20 archived peptide sequence
+#
+$asi = $asia->fetch_by_stable_id_version("P2", 1);
+ok( $asi->get_peptide eq 'PTWOVERSIONONE*' );
 
 
+#
+# debug helper
+#
 sub _print_asi {
   my $asi = shift;