links.rb in sequenceserver-2.0.0.beta1

- old
+ new

@@ -7,12 +7,14 @@
     include ERB::Util
     alias encode url_encode
 
     NCBI_ID_PATTERN    = /gi\|(\d+)\|/
     UNIPROT_ID_PATTERN = /sp\|(\w+)\|/
+    PFAM_ID_PATTERN = /(PF\d{5}\.?\d*)/
+    RFAM_ID_PATTERN = /(RF\d{5})/
 
-    # Link generators return a Hash like below.
+    # Link generators are methods that return a Hash as defined below.
     #
     # {
     #   # Required. Display title.
     #   :title => "title",
     #
@@ -43,44 +45,74 @@
     #
     #     e.g:
     #         sequence_id = encode sequence_id
     #         url = "http://www.ncbi.nlm.nih.gov/nucleotide/#{sequence_id}"
     #
-    #   querydb:
-    #     Returns an array of databases that were used for BLASTing.
+    #   dbtype:
+    #     Returns the database type (nucleotide or protein) that was used for
+    #     BLAST search.
     #
     #   whichdb:
-    #     Returns the database from which the given hit came from.
+    #     Returns the databases from which the hit could have originated. To
+    #     ensure that one and the correct database is returned, ensure that
+    #     your sequence ids are unique across different FASTA files.
+    #     NOTE: This method is slow.
     #
-    #     e.g:
+    #   coordinates:
+    #     Returns min alignment start and max alignment end coordinates for
+    #     query and hit sequences.
     #
-    #         hit_database = whichdb
-    #
-    # Examples:
-    # ---------
-    # See methods provided by default for an example implementation.
+    #     e.g.,
+    #     query_coords = coordinates[0]
+    #     hit_coords = coordinates[1]
 
     def ncbi
-      return nil unless id.match(NCBI_ID_PATTERN)
+      return nil unless id.match(NCBI_ID_PATTERN) or title.match(NCBI_ID_PATTERN)
       ncbi_id = Regexp.last_match[1]
       ncbi_id = encode ncbi_id
-      url = "http://www.ncbi.nlm.nih.gov/#{querydb.first.type}/#{ncbi_id}"
+      url = "https://www.ncbi.nlm.nih.gov/#{dbtype}/#{ncbi_id}"
       {
         order: 2,
         title: 'NCBI',
         url:   url,
         icon:  'fa-external-link'
       }
     end
 
     def uniprot
-      return nil unless id.match(UNIPROT_ID_PATTERN)
+      return nil unless id.match(UNIPROT_ID_PATTERN) or title.match(UNIPROT_ID_PATTERN)
       uniprot_id = Regexp.last_match[1]
       uniprot_id = encode uniprot_id
-      url = "http://www.uniprot.org/uniprot/#{uniprot_id}"
+      url = "https://www.uniprot.org/uniprot/#{uniprot_id}"
       {
         order: 2,
-        title: 'Uniprot',
+        title: 'UniProt',
+        url:   url,
+        icon:  'fa-external-link'
+      }
+    end
+ 
+    def pfam
+      return nil unless id.match(PFAM_ID_PATTERN) or title.match(PFAM_ID_PATTERN)
+      pfam_id = Regexp.last_match[1]
+      pfam_id = encode pfam_id
+      url = "https://pfam.xfam.org/family/#{pfam_id}"
+      {
+        order: 2,
+        title: 'Pfam',
+        url:   url,
+        icon:  'fa-external-link'
+      }
+    end
+
+    def rfam
+      return nil unless id.match(RFAM_ID_PATTERN) or title.match(RFAM_ID_PATTERN)
+      rfam_id = Regexp.last_match[1]
+      rfam_id = encode rfam_id
+      url = "https://rfam.xfam.org/family/#{rfam_id}"
+      {
+        order: 2,
+        title: 'Rfam',
         url:   url,
         icon:  'fa-external-link'
       }
     end
   end