Add Others database type.

fcyu · Jan 29, 2018 · 924f103 · 924f103
1 parent 8738c4e
commit 924f103
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/src/main/java/proteomics/TheoSeq/DbTool.java b/src/main/java/proteomics/TheoSeq/DbTool.java
@@ -26,7 +26,10 @@ public DbTool(String db_name, String databaseType) {
             header_pattern = Pattern.compile("^>([^\\s]+)[\\s|]+(.+)$");
         } else if (databaseType.contentEquals("UniProt") || databaseType.contentEquals("SwissProt")) {
             header_pattern = Pattern.compile("^>[^|]+\\|(.+)\\|(.+)$");
-        } else {
+        } else if (databaseType.contentEquals("Others")) {
+            header_pattern = Pattern.compile("^>(.+)$");
+        }
+        else {
             header_pattern = null;
             logger.error("Incorrect database type ({}) in the parameter file.", databaseType);
             System.exit(1);
@@ -44,7 +47,11 @@ public DbTool(String db_name, String databaseType) {
                         pro_seq_map.put(id, seq.toString());
                     }
                     id = head_matcher.group(1).trim();
-                    annotate = head_matcher.group(2).trim();
+                    if (databaseType.contentEquals("Others")) {
+                        annotate = id;
+                    } else {
+                        annotate = head_matcher.group(2).trim();
+                    }
                     pro_annotate_map.put(id, annotate);
                     new_pro = true;
                 } else if (!line.isEmpty()) {

diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def
@@ -6,7 +6,7 @@ dev = 0 # Output development information.
 
 # Database
 db = small+random50.fasta # The protein database.
-database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR
+database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR, Others
 missed_cleavage = 2 # Maximum number of allowed missed cleavage.
 min_precursor_mass = 1000
 max_precursor_mass = 12000