From aea79a954f0a2b9bdec0a5e2d3608a13853f5b51 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 1 Nov 2005 09:40:55 +0000
Subject: [PATCH] tidy and fix entry name
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3796 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 24 ++++++++++++++++++-
1 file changed, 23 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index e5d9a07b6..0ee5b1f23 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 " +
--
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