diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java index e5d9a07b665e5986ca68490ba947d7625646dfd5..0ee5b1f23b11e03997ea1abfa84eba5823445122 100644 --- a/uk/ac/sanger/artemis/util/DatabaseDocument.java +++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java @@ -81,6 +81,17 @@ public class DatabaseDocument extends Document this.feature_id = feature_id; } + /** + * + * Create a new Document from a database. + * @param location This should be a URL string giving: + * jdbc:postgresql://host:port/datbase_name?user=username + * @param feature_id ID of a feature to be extracted. + * @param splitGFFEntry split into separate entries based on feature + * types. + * @param progress_listener input stream progress listener + * + **/ public DatabaseDocument(String location, String feature_id, boolean splitGFFEntry, InputStreamProgressListener progress_listener) @@ -124,7 +135,7 @@ public class DatabaseDocument extends Document int ind = ((String)getLocation()).indexOf("?"); String name = ((String)getLocation()).substring(0,ind); ind = name.lastIndexOf("/"); - return name.substring(ind); + return name.substring(ind+1); } return name; } @@ -237,6 +248,12 @@ public class DatabaseDocument extends Document return null; } + /** + * + * Called (by DatabaseEntrySource) to retrieve all the documents for each + * entry created. + * + */ public DatabaseDocument[] getGffDocuments(String location, String id) { int nentries = 0; @@ -403,6 +420,11 @@ public class DatabaseDocument extends Document return (String)cvterm.get(new Long(id)); } + /** + * + * Look up cvterms names and id and return in a hashtable. + * + */ private Hashtable getCvterm(Connection conn, String cv_name) { String sql = "SELECT cvterm.cvterm_id, cvterm.name " +