diff --git a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
index 03974a70ab4e93e402ba3849beafd0604e3ad025..ce2d44c82abcff806a22ea733ab9b9caa8ec4df5 100644
--- a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
+++ b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
@@ -54,6 +54,7 @@ public class DatabaseEntrySource implements EntrySource
{
private String location;
private Hashtable entries;
+ private boolean splitGFFEntry;
/**
* Create a new DatabaseEntrySource.
@@ -301,6 +302,10 @@ public class DatabaseEntrySource implements EntrySource
}
}
+ protected void setSplitGFF(final boolean splitGFFEntry)
+ {
+ this.splitGFFEntry = splitGFFEntry;
+ }
/**
*
@@ -326,17 +331,13 @@ public class DatabaseEntrySource implements EntrySource
{
DatabaseDocumentEntry db_entry = null;
-// final EntryInformation entry_information =
-// new SimpleEntryInformation(Options.getArtemisEntryInformation());
-
if(read_only)
{
}
else
{
- DatabaseDocument doc = new DatabaseDocument(location, id, progress_listener);
-// DatabaseDocument doc = new DatabaseDocument("jdbc:postgresql://localhost:13001/chadoCVS?user=es2",
-// id, progress_listener);
+ DatabaseDocument doc = new DatabaseDocument(location, id,
+ splitGFFEntry, progress_listener);
db_entry = new DatabaseDocumentEntry(doc);
}
@@ -379,4 +380,29 @@ public class DatabaseEntrySource implements EntrySource
return null;
}
+ protected DatabaseDocumentEntry[]
+ makeFromGff(final DatabaseDocument doc, String id)
+ throws OutOfRangeException, IOException
+ {
+ DatabaseDocumentEntry[] db_entry = null;
+
+ try
+ {
+ DatabaseDocument[] new_docs = doc.getGffDocuments(location, id);
+ db_entry = new DatabaseDocumentEntry[new_docs.length];
+
+ for(int i=1; i<new_docs.length; i++)
+ db_entry[i-1] = new DatabaseDocumentEntry(new_docs[i]);
+ }
+ catch(EntryInformationException e)
+ {
+ JOptionPane.showMessageDialog(null,
+ "Failed to get entry: " + e,
+ "Entry Information Exception",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ return db_entry;
+ }
+
}
diff --git a/uk/ac/sanger/artemis/components/DatabaseJFrame.java b/uk/ac/sanger/artemis/components/DatabaseJFrame.java
index 0fb34b5f8c680fa814126a2fbb10b4b6b535127f..1abe12e4295375fdcdf2647baa1c714f9933f231 100644
--- a/uk/ac/sanger/artemis/components/DatabaseJFrame.java
+++ b/uk/ac/sanger/artemis/components/DatabaseJFrame.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/DatabaseJFrame.java,v 1.4 2005-06-18 07:01:16 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/DatabaseJFrame.java,v 1.5 2005-08-04 15:58:05 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -29,6 +29,8 @@ import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import javax.swing.JFrame;
import javax.swing.JTree;
@@ -37,6 +39,7 @@ import javax.swing.JSeparator;
import javax.swing.JMenuBar;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JPanel;
import javax.swing.JLabel;
import javax.swing.BorderFactory;
@@ -57,6 +60,7 @@ import javax.swing.tree.DefaultMutableTreeNode;
public class DatabaseJFrame extends JFrame
{
private JLabel status_line = new JLabel("");
+ private boolean splitGFFEntry = true;
public DatabaseJFrame(final DatabaseEntrySource entry_source,
final ArtemisMain art_main)
@@ -146,6 +150,7 @@ public class DatabaseJFrame extends JFrame
final InputStreamProgressListener progress_listener =
art_main.getInputStreamProgressListener();
+ entry_source.setSplitGFF(splitGFFEntry);
final Entry entry = entry_source.getEntry(id, progress_listener);
if(entry == null)
{
@@ -155,6 +160,24 @@ public class DatabaseJFrame extends JFrame
}
final EntryEdit new_entry_edit = art_main.makeEntryEdit(entry);
+
+ // add gff entries
+ if(splitGFFEntry)
+ {
+ DatabaseDocumentEntry db_entry = (DatabaseDocumentEntry)entry.getEMBLEntry();
+
+ final DatabaseDocumentEntry[] entries =
+ entry_source.makeFromGff((DatabaseDocument)db_entry.getDocument(), id);
+ for(int i=0; i< entries.length; i++)
+ {
+ if(entries[i] == null)
+ continue;
+
+ final Entry new_entry = new Entry(new_entry_edit.getEntryGroup().getBases(), entries[i]);
+ new_entry_edit.getEntryGroup().add(new_entry);
+ }
+ }
+
new_entry_edit.setVisible(true);
status_line.setText("Sequence loaded.");
}
@@ -209,6 +232,23 @@ public class DatabaseJFrame extends JFrame
});
fileMenu.add(fileMenuClose);
+ JMenu optionMenu = new JMenu("Options");
+ mBar.add(optionMenu);
+
+ final JCheckBoxMenuItem splitGFF = new JCheckBoxMenuItem("Split GFF into entries",
+ splitGFFEntry);
+ splitGFF.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(splitGFF.isSelected())
+ splitGFFEntry = true;
+ else
+ splitGFFEntry = false;
+ }
+ });
+ optionMenu.add(splitGFF);
+
return mBar;
}
}
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 8ade09fbfaeffdc322eb10ddd394597bfa550372..669c7bb9eab357f6a91ec706b8772c3d8f14616c 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -50,6 +50,10 @@ public class DatabaseDocument extends Document
private Vector organism;
private String sqlLog = System.getProperty("user.home")+
System.getProperty("file.separator")+"art_sql_debug.log";
+ private StringBuffer[] gff_buffer;
+ private StringBuffer gff_buff;
+ private String[] types = { "exon", "gene", "CDS", "transcript" };
+ private boolean splitGFFEntry;
/**
*
@@ -78,13 +82,24 @@ public class DatabaseDocument extends Document
}
public DatabaseDocument(String location, String feature_id,
+ boolean splitGFFEntry,
InputStreamProgressListener progress_listener)
{
super(location);
this.feature_id = feature_id;
+ this.splitGFFEntry = splitGFFEntry;
this.progress_listener = progress_listener;
}
+ public DatabaseDocument(String location, String feature_id,
+ StringBuffer gff_buff, String name)
+ {
+ super(location);
+ this.feature_id = feature_id;
+ this.gff_buff = gff_buff;
+ this.name = name;
+ }
+
/**
*
* Append a String to the Document location.
@@ -173,15 +188,34 @@ public class DatabaseDocument extends Document
**/
public InputStream getInputStream() throws IOException
{
+ ByteArrayInputStream instream;
+
+ if(gff_buff != null)
+ {
+ instream = new ByteArrayInputStream(gff_buff.toString().getBytes());
+ return instream;
+ }
+
try
{
Connection conn = getConnection();
System.out.println("Connected");
- String entry = getGFF(conn,feature_id) + getSequence(conn);
-// String entry = getSequence(conn);
+ gff_buffer = getGFF(conn,feature_id);
+ String entry;
+
+ if(splitGFFEntry)
+ entry = gff_buffer[0] + getSequence(conn);
+ else
+ {
+ entry = new String();
+ for(int i=0; i<gff_buffer.length; i++)
+ entry = entry + gff_buffer[i];
+ entry = entry + getSequence(conn);
+ }
+
appendToLogFile(entry,sqlLog);
- ByteArrayInputStream instream = new ByteArrayInputStream(entry.getBytes());
+ instream = new ByteArrayInputStream(entry.getBytes());
conn.close();
return instream;
@@ -195,6 +229,24 @@ public class DatabaseDocument extends Document
return null;
}
+ public DatabaseDocument[] getGffDocuments(String location, String id)
+ {
+ DatabaseDocument[] new_docs = new DatabaseDocument[gff_buffer.length-1];
+ for(int i=1; i<gff_buffer.length; i++)
+ {
+ String name;
+ if(i >= types.length)
+ name = "other";
+ else
+ name = types[i];
+
+ if(gff_buffer[i].length() > 0)
+ new_docs[i-1] = new DatabaseDocument(location, id, gff_buffer[i], name);
+ }
+
+ return new_docs;
+ }
+
/**
*
@@ -202,34 +254,28 @@ public class DatabaseDocument extends Document
* in the form of a GFF stream.
*
*/
- private String getGFF(Connection conn, String parentFeatureID)
+ private StringBuffer[] getGFF(Connection conn, String parentFeatureID)
throws java.sql.SQLException
{
Statement st = conn.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_UPDATABLE);
-// String sql = "SELECT strand, fmin, fmax, uniquename, feature.type_id, featureprop.type_id AS prop_type_id, value"+
-// " FROM feature, featureloc, featureprop WHERE srcfeature_id = "+parentFeatureID+
-// " and featureloc.feature_id=featureprop.feature_id"+
-// " and featureloc.feature_id=feature.feature_id";
-
-// String sql = "SELECT feature.feature_id, object_id, strand, fmin, fmax, uniquename, feature.type_id, "+
-// " featureprop.type_id AS prop_type_id, featureprop.value FROM feature, featureloc, featureprop, feature_relationship "+
-// " WHERE srcfeature_id = "+parentFeatureID+" and featureloc.feature_id=featureprop.feature_id and "+
-// " featureloc.feature_id=feature.feature_id and feature_relationship.subject_id=feature.feature_id";
-
String sql = "SELECT timelastmodified, feature.feature_id, object_id, strand, fmin, fmax, uniquename, feature.type_id, "+
" featureprop.type_id AS prop_type_id, featureprop.value FROM featureloc, featureprop, "+
" feature LEFT JOIN feature_relationship ON feature_relationship.subject_id=feature.feature_id "+
" WHERE srcfeature_id = "+parentFeatureID+" and featureloc.feature_id=featureprop.feature_id and "+
- " featureloc.feature_id=feature.feature_id ORDER BY uniquename";
+ " featureloc.feature_id=feature.feature_id ORDER BY feature.type_id, uniquename";
appendToLogFile(sql,sqlLog);
ResultSet rs = st.executeQuery(sql);
- StringBuffer cdsBuffer = new StringBuffer();
+
+ StringBuffer[] buffers = new StringBuffer[types.length+1];
+ for(int i=0; i<buffers.length; i++)
+ buffers[i] = new StringBuffer();
String parentFeature = getFeatureName(parentFeatureID,conn);
Hashtable hstore = new Hashtable();
+ StringBuffer this_buff;
while(rs.next())
{
@@ -250,29 +296,38 @@ public class DatabaseDocument extends Document
parent_id = (String)hstore.get(parent_id);
// make gff format
- cdsBuffer.append(parentFeature+"\t"); // seqid
- cdsBuffer.append("chado\t"); // source
- cdsBuffer.append(typeName+"\t"); // type
- cdsBuffer.append(fmin+"\t"); // start
- cdsBuffer.append(fmax+"\t"); // end
- cdsBuffer.append(".\t"); // score
+
+ // select buffer
+ this_buff = buffers[types.length];
+ for(int i=0; i<types.length; i++)
+ {
+ if(types[i].equals(typeName))
+ this_buff = buffers[i];
+ }
+
+ this_buff.append(parentFeature+"\t"); // seqid
+ this_buff.append("chado\t"); // source
+ this_buff.append(typeName+"\t"); // type
+ this_buff.append(fmin+"\t"); // start
+ this_buff.append(fmax+"\t"); // end
+ this_buff.append(".\t"); // score
if(strand == -1) // strand
- cdsBuffer.append("-\t");
+ this_buff.append("-\t");
else if(strand == 1)
- cdsBuffer.append("+\t");
+ this_buff.append("+\t");
else
- cdsBuffer.append(".\t");
+ this_buff.append(".\t");
- cdsBuffer.append(".\t"); // phase
- cdsBuffer.append("ID="+name+";");
+ this_buff.append(".\t"); // phase
+ this_buff.append("ID="+name+";");
if(parent_id != null)
- cdsBuffer.append("Parent="+parent_id+";");
+ this_buff.append("Parent="+parent_id+";");
- cdsBuffer.append("timelastmodified="+timelastmodified+";");
+ this_buff.append("timelastmodified="+timelastmodified+";");
String value = GFFStreamFeature.encode(rs.getString("value"));
- cdsBuffer.append(propTypeName+"="+value); // attributes
+ this_buff.append(propTypeName+"="+value); // attributes
int rewind = 0;
while(rs.next() && rs.getString("uniquename").equals(name))
@@ -280,19 +335,19 @@ public class DatabaseDocument extends Document
prop_type_id = rs.getLong("prop_type_id");
propTypeName = getCvtermName(conn,prop_type_id);
value = GFFStreamFeature.encode(rs.getString("value"));
- cdsBuffer.append(";"+propTypeName+"="+value);
+ this_buff.append(";"+propTypeName+"="+value);
rewind++;
}
if(rewind > 0)
rs.previous();
- cdsBuffer.append("\n");
+ this_buff.append("\n");
progress_listener.progressMade("Read from database: "+name);
}
- return cdsBuffer.toString();
+ return buffers;
}
public static Long getCvtermID(String name)