diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
index 9e4ba111b7f968af7f9be26b5ec025a83ef11aff..170d4e0c4836a908378eff203c728efb8d05fba3 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.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/database/DatabaseJPanel.java,v 1.18 2008-10-30 15:37:00 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java,v 1.19 2008-11-17 13:51:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.database;
@@ -45,6 +45,7 @@ import javax.swing.BorderFactory;
import javax.swing.border.Border;
import javax.swing.tree.TreePath;
+import org.gmod.schema.organism.Organism;
import org.gmod.schema.sequence.Feature;
import java.awt.BorderLayout;
@@ -56,15 +57,8 @@ import java.awt.Toolkit;
import java.awt.Cursor;
import java.awt.FontMetrics;
import java.io.*;
-import java.net.ConnectException;
-import java.sql.SQLException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
import java.util.HashMap;
-import java.util.Hashtable;
import java.util.List;
-import java.util.Vector;
public class DatabaseJPanel extends JPanel
{
@@ -140,11 +134,7 @@ public class DatabaseJPanel extends JPanel
DatabaseTreeNode seq_node =
(DatabaseTreeNode)path.getLastPathComponent();
String node_name = (String)seq_node.getUserObject();
- String userName;
- if(!doc.isSingleSchema())
- userName = seq_node.getSchema();
- else
- userName = doc.getUserName();
+ String userName = doc.getUserName();
String id = seq_node.getFeatureId();
if(id != null)
@@ -241,6 +231,8 @@ public class DatabaseJPanel extends JPanel
srcComponent.setCursor(cbusy);
try
{
+ while(DatabaseDocument.isCvThreadAlive())
+ Thread.sleep(5);
openEntry(srcfeatureId, entry_source, srcComponent, status_line, stream_progress_listener,
splitGFFEntry, splash_main, dbDocumentName, userName, null);
}
@@ -260,6 +252,10 @@ public class DatabaseJPanel extends JPanel
openEntry(srcfeatureId, entry_source, srcComponent, status_line, stream_progress_listener,
splitGFFEntry, splash_main, dbDocumentName, userName, null);
}
+ catch(InterruptedException e)
+ {
+ e.printStackTrace();
+ }
srcComponent.setCursor(cdone);
return null;
}
@@ -369,115 +365,31 @@ public class DatabaseJPanel extends JPanel
try
{
doc = entry_source.getDatabaseDocument();
- entries = doc.getDatabaseEntries();
-
final DatabaseTreeNode top = new DatabaseTreeNode("");
- createNodes(top, doc, entries);
+
+ final List organisms = doc.getOrganismsContainingSrcFeatures();
+ for(int i=0; i<organisms.size(); i++)
+ {
+ Organism org = (Organism)organisms.get(i);
+
+ String name = org.getCommonName();
+ if(name == null || name.equals(""))
+ name = org.getGenus() + "." + org.getSpecies();
+ DatabaseTreeNode orgNode =
+ new DatabaseTreeNode(name, false, org, doc.getUserName(), doc);
+ top.add(orgNode);
+ }
return new DatabaseJTree(top);
}
- catch(ConnectException e)
- {
- entry_source.setLocation(true);
- }
- catch(SQLException e)
- {
- entry_source.setLocation(true);
- }
- catch(RuntimeException p)
+ catch(Exception e)
{
- entry_source.setLocation(true);
+ if(!entry_source.setLocation(true))
+ return null;
}
}
return null;
}
-
-
- /**
- * Create the nodes of the organism JTree
- * @param top root node
- * @param schema <code>List</code>
- * @param doc DatabaseDocument
- * @param organism sequences collection
- */
- private void createNodes(DatabaseTreeNode top,
- DatabaseDocument doc,
- HashMap entries)
- {
- final Object v_organism[] = entries.keySet().toArray();
- final int v_organism_size = v_organism.length;
- Arrays.sort(v_organism, new Comparator()
- {
- public int compare(Object o1, Object o2)
- {
- return ((String)o1).compareToIgnoreCase( (String)o2 );
- }
- });
-
- final Hashtable organismNodes = new Hashtable();
- final List organism = new Vector();
-
- String seqFullName;
- DatabaseTreeNode seq_node;
- DatabaseTreeNode typ_node;
-
- for(int i = 0; i < v_organism_size; i++)
- {
- seqFullName = (String) v_organism[i];
- String seqNames[] = seqFullName.split("-");
-
- final String featureId = (String) entries.get(seqFullName);
- final String schema = seqNames[0].trim();
- String type = seqNames[1].trim();
- String thisSeqName = seqNames[2].trim();
-
- if(!organismNodes.containsKey(schema))
- {
- organismNodes.put(schema, new DatabaseTreeNode(schema));
- organism.add(schema);
- }
-
- DatabaseTreeNode organismNode = (DatabaseTreeNode) organismNodes.get(schema);
- typ_node = getChild(organismNode, type);
- if(typ_node == null)
- {
- typ_node = new DatabaseTreeNode(type);
- organismNode.add(typ_node);
- }
-
- seq_node = new DatabaseTreeNode(thisSeqName, featureId, schema,
- doc.getUserName(), doc.isSingleSchema());
- typ_node.add(seq_node);
- }
-
- // add organism nodes that have child nodes
- Collections.sort(organism);
- for(int i=0; i<organism.size(); i++)
- {
- String name = (String) organism.get(i);
- DatabaseTreeNode organismNode = (DatabaseTreeNode) organismNodes.get(name);
- if(organismNode.getChildCount() > 0)
- top.add(organismNode);
- }
- }
-
- /**
- * Get a child of a parent node with a given name.
- * @param parentNode
- * @param childNodeName
- * @return
- */
- private DatabaseTreeNode getChild(final DatabaseTreeNode parentNode,
- final String childNodeName)
- {
- for(int j=0; j<parentNode.getChildCount(); j++)
- {
- DatabaseTreeNode node = (DatabaseTreeNode) parentNode.getChildAt(j);
- if(((String)node.getUserObject()).equals(childNodeName))
- return node;
- }
- return null;
- }
/**
* An InputStreamProgressListener used to update the error label with the
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJTree.java b/uk/ac/sanger/artemis/components/database/DatabaseJTree.java
index 3a3361c1ae48176b013b9704e36119eee5eee66e..0592f1b26a558e1fadb20327814eca3a5f4e823f 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJTree.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJTree.java
@@ -25,6 +25,7 @@
package uk.ac.sanger.artemis.components.database;
+import java.awt.Cursor;
import java.awt.Point;
import java.awt.datatransfer.Transferable;
import java.awt.dnd.DnDConstants;
@@ -39,6 +40,9 @@ import java.awt.event.InputEvent;
import java.awt.event.MouseEvent;
import javax.swing.JTree;
+import javax.swing.event.TreeExpansionEvent;
+import javax.swing.event.TreeExpansionListener;
+import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreePath;
import javax.swing.tree.TreeSelectionModel;
@@ -72,7 +76,31 @@ public class DatabaseJTree extends JTree
dragSource.createDefaultDragGestureRecognizer(
this, // component where drag originates
DnDConstants.ACTION_COPY_OR_MOVE, // actions
- this); // drag gesture recognizer
+ this); // drag gesture recognizer
+
+ addTreeExpansionListener(new TreeExpansionListener()
+ {
+ public void treeExpanded(TreeExpansionEvent e)
+ {
+ TreePath path = e.getPath();
+ if(path != null)
+ {
+ setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ DatabaseTreeNode node = (DatabaseTreeNode)path.getLastPathComponent();
+
+ if(!node.isExplored())
+ {
+ node.explore();
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ model.nodeStructureChanged(node);
+ }
+ setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ }
+ public void treeCollapsed(TreeExpansionEvent e){}
+ });
+
+
}
private boolean isLeafSelection()
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java b/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java
index d18f18423a85a18e2d38203c92810ca8e788dcce..3f042dc355f6e0a1a61a6b4a02ffbf9d052abd82 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java
@@ -29,8 +29,15 @@ import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.UnsupportedFlavorException;
import javax.swing.tree.DefaultMutableTreeNode;
+import org.gmod.schema.organism.Organism;
+import org.gmod.schema.sequence.Feature;
+
+import uk.ac.sanger.artemis.util.DatabaseDocument;
+
import java.io.Serializable;
import java.io.IOException;
+import java.util.Hashtable;
+import java.util.List;
/**
*
@@ -40,7 +47,7 @@ import java.io.IOException;
public class DatabaseTreeNode extends DefaultMutableTreeNode
implements Transferable, Serializable
{
-
+ private static final long serialVersionUID = 1L;
public static final DataFlavor DATABASETREENODE =
new DataFlavor(DatabaseTreeNode.class, "Work Package");
public static final DataFlavor STRING_DATA_FLAVOUR =
@@ -48,29 +55,106 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
private static final DataFlavor flavors[] =
{ DATABASETREENODE, DataFlavor.stringFlavor };
-
private String featureId;
- private String schema;
+ private Organism organism;
+ private boolean isLeaf = false;
private String userName;
- private boolean singleSchema;
-
+ private DatabaseDocument dbDoc;
+ private boolean explored = false;
+
public DatabaseTreeNode(final String name)
{
super(name);
}
+
+ public DatabaseTreeNode(final String name,
+ final boolean isLeaf)
+ {
+ super(name);
+ this.isLeaf = isLeaf;
+ }
+
+ /**
+ * Top node constructor
+ * @param name
+ * @param isLeaf
+ * @param organism
+ * @param userName
+ * @param dbDoc
+ */
+ public DatabaseTreeNode(final String name,
+ final boolean isLeaf,
+ final Organism organism,
+ final String userName,
+ final DatabaseDocument dbDoc)
+ {
+ super(name);
+ this.isLeaf = isLeaf;
+ this.organism = organism;
+ this.userName = userName;
+ this.dbDoc = dbDoc;
+ }
+ /**
+ * Leaf constructor
+ * @param name
+ * @param organism
+ * @param featureId
+ * @param userName
+ */
public DatabaseTreeNode(final String name,
+ final Organism organism,
final String featureId,
- final String schema,
- final String userName,
- final boolean singleSchema)
+ final String userName)
{
super(name);
- this.featureId = featureId;
- this.schema = schema;
- this.userName = userName;
- this.singleSchema = singleSchema;
+ this.organism = organism;
+ this.featureId = featureId;
+ this.userName = userName;
+ }
+
+ /** @return true if node is a directory */
+ public boolean getAllowsChildren() { return !isLeaf; }
+ /** @return true if node is a file */
+ public boolean isLeaf() { return isLeaf; }
+ /** @return true if node is a directory */
+ public boolean isDirectory() { return !isLeaf; }
+ /** @return true if explored */
+ public boolean isExplored() { return explored; }
+
+ /**
+ * Explore the tree node if this is a node with child nodes.
+ */
+ public void explore()
+ {
+ if(isLeaf)
+ return;
+
+ List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId()));
+ Hashtable sequenceNode = new Hashtable();
+
+ for(int i=0;i<sequenceList.size(); i++)
+ {
+ Feature f = (Feature)sequenceList.get(i);
+ DatabaseTreeNode typeNode;
+ if(!sequenceNode.containsKey(f.getCvTerm().getName()))
+ {
+ typeNode = new DatabaseTreeNode(f.getCvTerm().getName(), false);
+ add(typeNode);
+ sequenceNode.put(f.getCvTerm().getName(), typeNode);
+ }
+ else
+ typeNode = (DatabaseTreeNode) sequenceNode.get(f.getCvTerm().getName());
+
+ DatabaseTreeNode seqNode = new DatabaseTreeNode(
+ f.getUniqueName(), getOrganism(), Integer.toString(f.getFeatureId()), getUserName());
+ seqNode.isLeaf = true;
+ typeNode.add(seqNode);
+ typeNode.explored = true;
+ }
+ explored = true;
}
+
// Transferable
public DataFlavor[] getTransferDataFlavors()
@@ -90,10 +174,15 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
{
if(d.equals(DATABASETREENODE))
return new DatabaseTreeNode((String)getUserObject(),
- getFeatureId(), getSchema(),
- getUserName(), isSingleSchema());
+ organism,
+ getFeatureId(), getUserName());
else if(d.equals(DataFlavor.stringFlavor))
- return getSchema()+":featureId="+getFeatureId();
+ {
+ String name = getOrganism().getCommonName();
+ if(name == null || name.equals(""))
+ name = getOrganism().getGenus() + "." + getOrganism().getSpecies();
+ return name+":featureId="+getFeatureId();
+ }
else throw new UnsupportedFlavorException(d);
}
@@ -103,15 +192,6 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
return featureId;
}
- public String getSchema()
- {
- return schema;
- }
-
- public boolean isSingleSchema()
- {
- return singleSchema;
- }
//Serializable
private void writeObject(java.io.ObjectOutputStream out) throws IOException
@@ -125,11 +205,14 @@ public class DatabaseTreeNode extends DefaultMutableTreeNode
in.defaultReadObject();
}
+ public Organism getOrganism()
+ {
+ return organism;
+ }
+
public String getUserName()
{
return userName;
}
-
-
}