diff --git a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java index fce01171e666054d342648629827937aacbb8a1b..62167f7725ffa6f43b6bee4ae09ee7551fc02091 100644 --- a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java +++ b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java @@ -233,7 +233,7 @@ public class DatabaseEntrySource implements EntrySource schemas = doc.getSchemaEntries(); DefaultMutableTreeNode top = new DefaultMutableTreeNode("PSU Organism List"); - createNodes(top, organism, entries); + createNodes(top, doc.getSchema(), entries); final JTree tree = new JTree(top); tree.getSelectionModel().setSelectionMode( TreeSelectionModel.SINGLE_TREE_SELECTION); @@ -287,10 +287,13 @@ public class DatabaseEntrySource implements EntrySource (DefaultMutableTreeNode)type_node.getParent(); String org = (String)org_node.getUserObject(); - if(schemas.containsKey(org)) - return (String) schemas.get(org); - else - return null; + + System.out.println(org); + return org; +// if(schemas.containsKey(org)) +// return (String) schemas.get(org); +// else +// return null; } /** @@ -305,10 +308,9 @@ public class DatabaseEntrySource implements EntrySource * sequences collection * */ - private void createNodes(DefaultMutableTreeNode top, Vector org, + private void createNodes(DefaultMutableTreeNode top, List org, Hashtable organism) { - Enumeration enum_org = org.elements(); DefaultMutableTreeNode org_node; DefaultMutableTreeNode seq_node; DefaultMutableTreeNode typ_node; @@ -317,17 +319,17 @@ public class DatabaseEntrySource implements EntrySource final int v_organism_size = v_organism.length; Arrays.sort(v_organism); - while(enum_org.hasMoreElements()) + for(int i=0; i<org.size(); i++) { - String name = (String)enum_org.nextElement(); + String name = (String)org.get(i); org_node = new DefaultMutableTreeNode(name); top.add(org_node); Hashtable seq_type_node = new Hashtable(); - for(int i = 0; i < v_organism_size; i++) + for(int j = 0; j < v_organism_size; j++) { - String seq_name = (String)v_organism[i]; + String seq_name = (String)v_organism[j]; if(seq_name.startsWith(name)) { int ind1 = seq_name.indexOf("- "); diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java index f8f74e8757ba9c6a175976eb775869b5bb3096b5..784c1497567b9d7c23c6c04b17aca3c0d36f7a74 100644 --- a/uk/ac/sanger/artemis/util/DatabaseDocument.java +++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java @@ -567,6 +567,11 @@ public class DatabaseDocument extends Document return org2schema; } + private List schema_list; + public List getSchema() + { + return schema_list; + } /** * @@ -582,7 +587,7 @@ public class DatabaseDocument extends Document try { ChadoDAO dao = getDAO(); - List schema_list = dao.getSchema(); + schema_list = dao.getSchema(); Iterator it = schema_list.iterator(); while(it.hasNext()) @@ -602,7 +607,7 @@ public class DatabaseDocument extends Document String org = feature.getAbbreviation(); String typeName = getCvtermName(feature.getType_id()); - db.put(org + " - " + typeName + " - " + feature.getName(), + db.put(schema + " - " + typeName + " - " + feature.getName(), Integer.toString(feature.getId())); if(!organism.contains(org)) organism.add(org);