diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
index 585621dd5fd6b361111070aef3cfa135defec7de..b100cb2178d8d9ffcd16e382d79feea7f10dc017 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
@@ -20,89 +20,171 @@
* 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/genebuilder/GeneBuilderFrame.java,v 1.1 2006-05-31 09:49:07 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.2 2006-07-04 15:57:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
import javax.swing.*;
+
import java.awt.*;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.EntryChangeEvent;
+import uk.ac.sanger.artemis.EntryChangeListener;
+import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Feature;
-import uk.ac.sanger.artemis.components.QualifierTextArea;
-import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
-import uk.ac.sanger.artemis.io.EntryInformation;
+import uk.ac.sanger.artemis.FeatureChangeEvent;
+import uk.ac.sanger.artemis.FeatureChangeListener;
+import uk.ac.sanger.artemis.GotoEventSource;
+import uk.ac.sanger.artemis.Selection;
+import uk.ac.sanger.artemis.components.FeatureEdit;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
-import uk.ac.sanger.artemis.io.Qualifier;
-import uk.ac.sanger.artemis.io.QualifierInfo;
-import uk.ac.sanger.artemis.io.QualifierVector;
-import uk.ac.sanger.artemis.io.StreamQualifier;
-import uk.ac.sanger.artemis.util.StringVector;
+
public class GeneBuilderFrame extends JFrame
+ implements EntryChangeListener, FeatureChangeListener
{
- public GeneBuilderFrame(final Feature gene_feature)
+ private Feature active_feature;
+ private FeatureEdit feature_editor;
+
+ public GeneBuilderFrame(final Feature feature,
+ final EntryGroup entry_group,
+ final Selection selection,
+ final GotoEventSource goto_event_source)
{
- super("Artemis Gene Builder: " + gene_feature.getIDString() +
- (gene_feature.isReadOnly() ?
+ super("Artemis Gene Builder: " + feature.getIDString() +
+ (feature.isReadOnly() ?
" - (read only)" :
""));
- QualifierTextArea qualifier_text_area = new QualifierTextArea();
- GFFStreamFeature gff_feature = (GFFStreamFeature)gene_feature.getEmblFeature();
+ this.active_feature = feature;
+
+ GFFStreamFeature gff_feature = (GFFStreamFeature)feature.getEmblFeature();
GeneComponentTree tree = new GeneComponentTree(gff_feature.getChadoGene(),
- qualifier_text_area);
- getContentPane().add(new JScrollPane(tree), BorderLayout.WEST);
+ this);
+
+ JScrollPane jsp_tree = new JScrollPane(tree);
+ jsp_tree.setPreferredSize( new Dimension(150, jsp_tree.getPreferredSize().height) );
+ getContentPane().add(jsp_tree, BorderLayout.WEST);
GeneViewerPanel viewer = new GeneViewerPanel(gff_feature.getChadoGene());
getContentPane().add(viewer, BorderLayout.CENTER);
- qualifier_text_area.setWrapStyleWord(true);
- qualifier_text_area.setText(getQualifierString(gene_feature));
+ if(entry_group != null)
+ {
+ JTabbedPane tabpane = new JTabbedPane();
- getContentPane().add(new JScrollPane(qualifier_text_area), BorderLayout.SOUTH);
+ feature_editor = new FeatureEdit(feature, entry_group,
+ selection, goto_event_source, this);
+ tabpane.addTab("Annotation", feature_editor);
+
+ getContentPane().add(tabpane, BorderLayout.SOUTH);
+ }
+
+ addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent event)
+ {
+ stopListening();
+ dispose();
+ }
+ });
pack();
setVisible(true);
}
+
+ protected void setActiveFeature(final Feature active_feature)
+ {
+ if(this.active_feature != null)
+ stopListening();
+
+ this.active_feature = active_feature;
+ feature_editor.setActiveFeature(active_feature);
+ }
/**
- * Return a string containing one qualifier per line. These are the
- * original qualifiers, not the qualifiers from the qualifier_text_area.
+ * Remove this object as a feature and entry change listener.
**/
- protected static String getQualifierString(final Feature feature)
+ private void stopListening()
{
- final StringBuffer buffer = new StringBuffer();
- final QualifierVector qualifiers = feature.getQualifiers();
+ getEntry().removeEntryChangeListener(this);
+ active_feature.removeFeatureChangeListener(this);
+ }
- for(int qualifier_index = 0; qualifier_index < qualifiers.size();
- ++qualifier_index)
+ /**
+ * Implementation of the EntryChangeListener interface. We listen to
+ * EntryChange events so we can notify the user if of this component if the
+ * feature gets deleted.
+ **/
+ public void entryChanged(EntryChangeEvent event)
+ {
+ switch(event.getType())
{
- final Qualifier this_qualifier = (Qualifier)qualifiers.elementAt(qualifier_index);
-
- final QualifierInfo qualifier_info =
- getEntryInformation(feature).getQualifierInfo(this_qualifier.getName());
-
- final StringVector qualifier_strings =
- StreamQualifier.toStringVector(qualifier_info, this_qualifier);
-
- for(int value_index = 0; value_index < qualifier_strings.size();
- ++value_index)
- {
- final String qualifier_string = (String)qualifier_strings.elementAt(value_index);
- buffer.append(qualifier_string + "\n");
- }
+ case EntryChangeEvent.FEATURE_DELETED:
+ if(event.getFeature() == active_feature)
+ {
+ stopListening();
+ dispose();
+ }
+ break;
+ default:
+ // do nothing;
+ break;
}
-
- return buffer.toString();
}
/**
- * Return the EntryInformation object of the entry containing the feature.
+ * Implementation of the FeatureChangeListener interface. We need to
+ * listen to feature change events from the Features in this object so that
+ * we can update the display.
+ * @param event The change event.
**/
- protected static EntryInformation getEntryInformation(final Feature feature)
+ public void featureChanged(FeatureChangeEvent event)
{
- return feature.getEntry().getEntryInformation();
- }
+ active_feature.resetColour();
+ /*
+ // re-read the information from the feature
+ switch(event.getType())
+ {
+ case FeatureChangeEvent.LOCATION_CHANGED:
+ updateLocation();
+ break;
+ case FeatureChangeEvent.KEY_CHANGED:
+ updateKey();
+ break;
+ case FeatureChangeEvent.QUALIFIER_CHANGED:
+ if(qualifier_text_area.getText().equals(orig_qualifier_text))
+ updateFromFeature();
+ else
+ {
+ final String message =
+ "warning: the qualifiers have changed outside the editor - " +
+ "view now?";
+ final YesNoDialog yes_no_dialog =
+ new YesNoDialog(FeatureEdit.this, message);
+
+ if(yes_no_dialog.getResult())
+ new FeatureViewer(gene_feature);
+ }
+ break;
+ default:
+ updateFromFeature();
+ break;
+ }
+ */
+ }
+
+
+ private Entry getEntry()
+ {
+ return active_feature.getEntry();
+ }
+
+
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
index 0395a0edeaf1f8acb155ce2e616a49e0d2f07f40..70ff8b0b72e691bd8feb67390d0bdf606b12f2cc 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
@@ -20,21 +20,21 @@
* 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/genebuilder/GeneComponentTree.java,v 1.2 2006-05-31 15:40:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.3 2006-07-04 15:57:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
-import uk.ac.sanger.artemis.components.QualifierTextArea;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.Feature;
import uk.ac.sanger.artemis.io.InvalidRelationException;
+import uk.ac.sanger.artemis.chado.ChadoFeature;
import javax.swing.*;
import javax.swing.event.*;
import javax.swing.tree.*;
-import java.util.Vector;
+import java.util.List;
/**
* Tree to display a gene hierarchy.
@@ -43,9 +43,9 @@ public class GeneComponentTree extends JTree
{
public GeneComponentTree(final ChadoCanonicalGene chado_gene,
- final QualifierTextArea qualifier_text_area)
+ final GeneBuilderFrame gene_builder)
{
- final Feature gene = chado_gene.getGene();
+ final Feature gene = (Feature)chado_gene.getGene();
final String gene_id;
try
{
@@ -72,9 +72,8 @@ public class GeneComponentTree extends JTree
if(node == null)
return;
- Feature feature = chado_gene.getFeatureFromId((String)node.getUserObject());
- qualifier_text_area.setText( GeneBuilderFrame.getQualifierString(
- (uk.ac.sanger.artemis.Feature)feature.getUserData() ) );
+ Feature feature = (Feature)chado_gene.getFeatureFromId((String)node.getUserObject());
+ gene_builder.setActiveFeature((uk.ac.sanger.artemis.Feature)feature.getUserData());
}
});
@@ -91,8 +90,8 @@ public class GeneComponentTree extends JTree
final ChadoCanonicalGene chado_gene)
throws InvalidRelationException
{
- Vector transcripts = chado_gene.getTranscripts();
- Vector exons;
+ List transcripts = chado_gene.getTranscripts();
+ List exons;
Feature transcript;
Feature exon;
Feature protein;
@@ -116,13 +115,19 @@ public class GeneComponentTree extends JTree
for(int j=0; j<exons.size(); j++)
{
- exon = (Feature)exons.get(j);
- exon_id = (String)exon.getQualifierByName("ID").getValues().get(0);
+ if(exons.get(j) instanceof Feature)
+ {
+ exon = (Feature)exons.get(j);
+ exon_id = (String)exon.getQualifierByName("ID").getValues().get(0);
+ }
+ else // ChadoFeature
+ exon_id = ((ChadoFeature)exons.get(j)).getUniquename();
+
exon_node = new DefaultMutableTreeNode(exon_id);
transcript_node.add(exon_node);
}
- protein = chado_gene.getProteinOfTranscript(transcript_id);
+ protein = (Feature)chado_gene.getProteinOfTranscript(transcript_id);
if(protein == null)
continue;
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneEdit.java b/uk/ac/sanger/artemis/components/genebuilder/GeneEdit.java
new file mode 100644
index 0000000000000000000000000000000000000000..9967cbd9ddaa3971c442b9248def3e5cf04824a1
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneEdit.java
@@ -0,0 +1,434 @@
+/*
+ *
+ * created: 2006
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2006 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.components.genebuilder;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+
+import java.sql.SQLException;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+
+import javax.swing.JPasswordField;
+import javax.swing.JTextField;
+
+import javax.swing.JComboBox;
+import javax.swing.JScrollPane;
+import javax.swing.JPanel;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.Box;
+
+import uk.ac.sanger.artemis.chado.*;
+import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
+import uk.ac.sanger.artemis.io.InvalidRelationException;
+import uk.ac.sanger.artemis.io.GFFStreamFeature;
+import uk.ac.sanger.artemis.io.ReadFormatException;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.ByteBuffer;
+
+
+/**
+ * Chado data access example code. This searches for features by their
+ * uniquename and returns their properties and attributes.
+ *
+ * @author tjc
+ *
+ */
+public class GeneEdit
+{
+ /** JDBC DAO */
+ private JdbcDAO jdbcDAO = null;
+
+ /** iBatis DAO */
+ private IBatisDAO connIB = null;
+
+ /** database URL */
+ private String location;
+
+ /** password fields */
+ private JPasswordField pfield;
+
+ /** <code>List</code> of <code>ChadoFeature</code> objects */
+ private List featureList;
+
+ /**
+ *
+ *
+ */
+ public GeneEdit()
+ {
+ try
+ {
+ setLocation();
+ final ChadoDAO dao = getDAO();
+ showFeatureSearchPanel(dao);
+ }
+ catch(java.net.ConnectException ce)
+ {
+ ce.printStackTrace();
+ }
+ catch(SQLException sqlExp)
+ {
+ JOptionPane.showMessageDialog(null, "SQL Problems...\n"
+ + sqlExp.getMessage(), "SQL Error", JOptionPane.ERROR_MESSAGE);
+ sqlExp.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Display a window for searching for features.
+ *
+ * @throws java.net.ConnectException
+ * @throws SQLException
+ */
+ private void showFeatureSearchPanel(final ChadoDAO dao)
+ throws java.net.ConnectException, SQLException
+ {
+ int index = location.indexOf('=') + 1;
+ String schema = location.substring(index);
+
+ final List schemas = dao.getSchema();
+
+ Vector v_schemas = new Vector(schemas);
+ v_schemas.add(0, "All");
+
+ final JPanel panel = new JPanel(new BorderLayout());
+ final JComboBox schema_list = new JComboBox(v_schemas);
+ schema_list.setSelectedItem(schema);
+
+
+ JScrollPane jsp = new JScrollPane(schema_list);
+ panel.add(jsp, BorderLayout.EAST);
+
+ Box xbox = Box.createHorizontalBox();
+ final JTextField gene_text = new JTextField(20);
+ gene_text.setText("AfA24A6.005"); //"SPAC212.04c");
+ xbox.add(gene_text);
+ gene_text.selectAll();
+
+
+ JButton findButt = new JButton("RETRIEVE");
+ findButt.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent event)
+ {
+ String search_gene = gene_text.getText();
+ String schema = (String)schema_list.getSelectedItem();
+ List schema_search;
+ if(schema.equalsIgnoreCase("All"))
+ schema_search = schemas;
+ else
+ {
+ schema_search = new Vector();
+ schema_search.add(schema);
+ }
+
+ try
+ {
+ search(search_gene, schema_search, dao);
+ }
+ catch(SQLException sqlExp)
+ {
+ JOptionPane.showMessageDialog(null, "SQL Problems...\n"
+ + sqlExp.getMessage(), "SQL Error", JOptionPane.ERROR_MESSAGE);
+ sqlExp.printStackTrace();
+ }
+ catch(ReadFormatException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ });
+ xbox.add(findButt);
+ xbox.add(Box.createHorizontalGlue());
+ panel.add(xbox, BorderLayout.NORTH);
+
+ JFrame frame = new JFrame("Feature Search");
+ frame.getContentPane().add(panel);
+ frame.setJMenuBar(getJMenuBar(dao));
+ frame.pack();
+ frame.setVisible(true);
+ }
+
+ /**
+ * Build a <code>JMenuBar</code>.
+ *
+ * @return a <code>JMenuBar</code>
+ */
+ public JMenuBar getJMenuBar(final ChadoDAO dao)
+ {
+ JMenuBar mbar = new JMenuBar();
+ JMenu file = new JMenu("File");
+ mbar.add(file);
+
+ JMenuItem exit = new JMenuItem("Exit");
+ exit.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ System.exit(0);
+ }
+ });
+ file.add(exit);
+
+ return mbar;
+ }
+
+
+ /**
+ * Search for a feature/gene name from a <code>List</code> of schemas.
+ *
+ * @param search_gene
+ * the feature name
+ * @param schema_search
+ * the <code>List</code> to search
+ * @param dao
+ * the data access object
+ * @return string array of results
+ * @throws SQLException
+ * @throws ReadFormatException
+ */
+ public void search(final String search_gene, final List schema_search,
+ final ChadoDAO dao) throws SQLException, ReadFormatException
+ {
+ Hashtable id_store = new Hashtable();
+
+ ChadoFeature feature = new ChadoFeature();
+ feature.setUniquename(search_gene);
+ featureList = dao.getLazyFeature(feature,
+ schema_search);
+
+ ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();
+
+ if(featureList.size() > 1)
+ System.err.println("More than one feature found!");
+
+ feature = (ChadoFeature)featureList.get(0);
+ id_store.put(Integer.toString(feature.getId()), feature.getUniquename());
+
+ int src = feature.getFeatureloc().getSrcfeature_id();
+
+ ChadoFeature parent = new ChadoFeature();
+ parent.setId(src);
+ List parentList = dao.getLazyFeature(parent, schema_search);
+ parent = (ChadoFeature)parentList.get(0);
+ chado_gene.setSeqlen( parent.getLength() );
+
+
+ ByteBuffer buff = new ByteBuffer();
+ DatabaseDocument.chadoToGFF(feature, null, null, null, null, dao, buff);
+
+ //System.out.println(new String(buff.getBytes()));
+
+ GFFStreamFeature gff_gene_feature = new GFFStreamFeature(new String(buff.getBytes()));
+ chado_gene.setGene(gff_gene_feature);
+
+ // get children of gene
+ List relations = feature.getFeatureRelationshipsForObjectId();
+
+ for(int i=0;i<relations.size(); i++)
+ {
+ ChadoFeature transcript = new ChadoFeature();
+ transcript.setId( ((ChadoFeatureRelationship)relations.get(i)).getSubject_id() );
+ featureList = dao.getLazyFeature(transcript,
+ schema_search);
+
+ transcript = (ChadoFeature)featureList.get(0);
+ id_store.put(Integer.toString(transcript.getId()), transcript.getUniquename());
+ buff = new ByteBuffer();
+ DatabaseDocument.chadoToGFF(transcript, feature.getUniquename(),
+ null, null, id_store, dao, buff);
+ GFFStreamFeature gff_feature = new GFFStreamFeature(new String(buff.getBytes()));
+
+ new uk.ac.sanger.artemis.Feature(gff_feature);
+ chado_gene.addTranscript(gff_feature);
+
+
+ // get children of transcript - exons and pp
+ List transcipt_relations = transcript.getFeatureRelationshipsForObjectId();
+
+ for(int j=0; j<transcipt_relations.size(); j++)
+ {
+ ChadoFeature child = new ChadoFeature();
+ child.setId( ((ChadoFeatureRelationship)transcipt_relations.get(j)).getSubject_id() );
+ featureList = dao.getLazyFeature(child,
+ schema_search);
+
+ child = (ChadoFeature)featureList.get(0);
+ id_store.put(Integer.toString(child.getId()), child.getUniquename());
+ buff = new ByteBuffer();
+ DatabaseDocument.chadoToGFF(child, transcript.getUniquename(),
+ null, null, id_store, dao, buff);
+
+ gff_feature = new GFFStreamFeature(new String(buff.getBytes()));
+ new uk.ac.sanger.artemis.Feature(gff_feature);
+
+ try
+ {
+ if(child.getCvterm().getName().equalsIgnoreCase("polypeptide"))
+ chado_gene.addProtein(transcript.getUniquename(), child);
+ else if(child.getCvterm().getName().equalsIgnoreCase("exon"))
+ chado_gene.addExon(transcript.getUniquename(), child);
+ }
+ catch(InvalidRelationException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+ }
+
+ gff_gene_feature.setChadoGene(chado_gene);
+
+ GeneBuilderFrame frame =
+ new GeneBuilderFrame(new uk.ac.sanger.artemis.Feature(gff_gene_feature),
+ null, null, null);
+
+ }
+
+
+
+ /**
+ * Get the data access object (DAO).
+ *
+ * @return data access object
+ */
+ private ChadoDAO getDAO() throws java.net.ConnectException, SQLException
+ {
+ if(System.getProperty("ibatis") == null)
+ {
+ if(jdbcDAO == null)
+ jdbcDAO = new JdbcDAO(location, pfield);
+ return jdbcDAO;
+ }
+ else
+ {
+ if(connIB == null)
+ connIB = new IBatisDAO(pfield);
+ return connIB;
+ }
+ }
+
+ /**
+ * Set the database location as:
+ * jdbc:postgresql://localhost:13001/chadoCVS?user=es2
+ *
+ * @return true if location chosen
+ */
+ protected boolean setLocation()
+ {
+ Container bacross = new Container();
+ bacross.setLayout(new GridLayout(6, 2, 5, 5));
+
+ JLabel lServer = new JLabel("Server : ");
+ bacross.add(lServer);
+ JTextField inServer = new JTextField("localhost");
+ bacross.add(inServer);
+
+ JLabel lPort = new JLabel("Port : ");
+ bacross.add(lPort);
+ JTextField inPort = new JTextField("5432");
+ bacross.add(inPort);
+
+ JLabel lDB = new JLabel("Database : ");
+ bacross.add(lDB);
+ JTextField inDB = new JTextField("chado");
+ bacross.add(inDB);
+
+ JLabel lUser = new JLabel("User : ");
+ bacross.add(lUser);
+ JTextField inUser = new JTextField("afumigatus");
+ bacross.add(inUser);
+
+ JLabel lpasswd = new JLabel("Password : ");
+ bacross.add(lpasswd);
+ pfield = new JPasswordField(16);
+ bacross.add(pfield);
+
+ // given -Dchado=localhost:port/dbname?username
+ if(System.getProperty("chado") != null)
+ {
+ String db_url = System.getProperty("chado").trim();
+ int index;
+ if((index = db_url.indexOf(":")) > -1)
+ {
+ inServer.setText(db_url.substring(0, index));
+ int index2;
+ if((index2 = db_url.indexOf("/")) > -1)
+ {
+ inPort.setText(db_url.substring(index + 1, index2));
+ int index3;
+ if((index3 = db_url.indexOf("?")) > -1)
+ {
+ inDB.setText(db_url.substring(index2 + 1, index3));
+ inUser.setText(db_url.substring(index3 + 1));
+
+ /*
+ * if(!prompt_user) { location = "jdbc:postgresql://"
+ * +inServer.getText().trim()+ ":" +inPort.getText().trim()+ "/"
+ * +inDB.getText().trim()+ "?user=" +inUser.getText().trim(); return
+ * true; }
+ */
+ }
+ }
+ }
+ }
+
+ int n = JOptionPane.showConfirmDialog(null, bacross,
+ "Enter Database Address", JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+ if(n == JOptionPane.CANCEL_OPTION)
+ return false;
+
+ location = "jdbc:postgresql://" + inServer.getText().trim() + ":"
+ + inPort.getText().trim() + "/" + inDB.getText().trim() + "?user="
+ + inUser.getText().trim();
+
+ return true;
+ }
+
+
+ public static void main(String args[])
+ {
+ new GeneEdit();
+ }
+}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
index 46506c0ce98c8136e38e6acd91359a0c6c905076..504d73869f2672130dac556ba0b2a3d28d926757 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
@@ -20,28 +20,36 @@
* 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/genebuilder/GeneViewerPanel.java,v 1.2 2006-05-31 15:40:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.3 2006-07-04 15:57:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
import javax.swing.*;
import java.awt.*;
-import java.util.Vector;
+import java.util.List;
+import java.util.Collections;
import java.awt.geom.RoundRectangle2D;
+import uk.ac.sanger.artemis.FeatureSegment;
+import uk.ac.sanger.artemis.FeatureSegmentVector;
+import uk.ac.sanger.artemis.chado.ChadoFeature;
+import uk.ac.sanger.artemis.chado.ChadoFeatureLoc;
import uk.ac.sanger.artemis.io.Feature;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.InvalidRelationException;
+import uk.ac.sanger.artemis.io.Range;
public class GeneViewerPanel extends JPanel
{
+
private ChadoCanonicalGene chado_gene;
private int border = 15;
public GeneViewerPanel(final ChadoCanonicalGene chado_gene)
{
this.chado_gene = chado_gene;
+
Dimension dim = new Dimension(300,300);
setPreferredSize(dim);
setBackground(Color.white);
@@ -49,9 +57,11 @@ public class GeneViewerPanel extends JPanel
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
Graphics2D g2d = (Graphics2D)g;
- Feature embl_gene = chado_gene.getGene();
- uk.ac.sanger.artemis.Feature gene = (uk.ac.sanger.artemis.Feature)embl_gene.getUserData();
+ Feature embl_gene = (Feature)chado_gene.getGene();
+ uk.ac.sanger.artemis.Feature gene =
+ (uk.ac.sanger.artemis.Feature)embl_gene.getUserData();
setFont(uk.ac.sanger.artemis.Options.getOptions().getFont());
final FontMetrics fm = this.getFontMetrics(getFont());
@@ -61,6 +71,7 @@ public class GeneViewerPanel extends JPanel
boolean complement = embl_gene.getLocation().isComplement();
BasicStroke stroke = new BasicStroke(2.f);
+ Stroke original_stroke = g2d.getStroke();
g2d.setStroke(stroke);
g2d.setColor( gene.getColour() );
@@ -72,11 +83,12 @@ public class GeneViewerPanel extends JPanel
g2d.drawLine(border, ypos, getSize().width - border, ypos);
- Vector transcripts = chado_gene.getTranscripts();
+ List transcripts = chado_gene.getTranscripts();
Feature embl_transcript;
uk.ac.sanger.artemis.Feature transcript;
- float fraction = (float)(getSize().width - (2*border))/(float)(end-start);
+ float fraction = (float)(getSize().width - (2*border))/
+ (float)(end-start);
for(int i=0; i<transcripts.size(); i++)
{
ypos += border;
@@ -95,7 +107,7 @@ public class GeneViewerPanel extends JPanel
try
{
- Vector exons = chado_gene.getExonsOfTranscript(
+ List exons = chado_gene.getExonsOfTranscript(
(String)embl_transcript.getQualifierByName("ID").getValues().get(0));
ypos += border;
@@ -103,26 +115,87 @@ public class GeneViewerPanel extends JPanel
if(exons == null)
continue;
+ int offset = 0;
+
+ if(exons.get(0) instanceof ChadoFeature)
+ {
+ int last_ex_start = 0;
+ int last_ex_end = 0;
+ int last_ypos = 0;
+
+ ChadoFeature start_exon = (ChadoFeature)exons.get(0);
+ if(start_exon.getFeatureloc().getStrand() == -1)
+ {
+ if( start_exon.getFeatureloc().getFmin() <
+ ((ChadoFeature)exons.get(exons.size()-1)).getFeatureloc().getFmin())
+ Collections.reverse(exons);
+ }
+
+ for(int j=0; j<exons.size(); j++)
+ {
+ ChadoFeature exon = (ChadoFeature)exons.get(j);
+
+ int ex_start = border+(int)((exon.getFeatureloc().getFmin()+1-start)*fraction);
+ int ex_end = border+(int)((exon.getFeatureloc().getFmax()-start)*fraction);
+
+ Color exon_col = Color.CYAN;
+
+ offset = getFrameID(chado_gene, exon, j, exons) * getFontHeight() * 2;
+
+ boolean isForward = false;
+ if(exon.getFeatureloc().getStrand() == 1)
+ isForward = true;
+
+ drawExons(g2d, ex_start, ex_end,
+ last_ex_start, last_ex_end, last_ypos,
+ offset, ypos, exon_col,
+ original_stroke, stroke, isForward);
+
+ last_ex_end = ex_end;
+ last_ex_start = ex_start;
+ last_ypos = ypos+offset;
+ }
+ continue;
+ }
+
+
for(int j=0; j<exons.size(); j++)
{
+ int last_ex_start = 0;
+ int last_ex_end = 0;
+ int last_ypos = 0;
+
Feature embl_exon = (Feature)exons.get(j);
+
uk.ac.sanger.artemis.Feature exon =
(uk.ac.sanger.artemis.Feature)embl_exon.getUserData();
-
- int ex_start = border+(int)((embl_exon.getFirstBase()-start)*fraction);
- int ex_end = border+(int)((embl_exon.getLastBase()-start)*fraction);
-
- if(exon.getColour() != null)
- g2d.setColor( exon.getColour() );
- RoundRectangle2D e = new RoundRectangle2D.Float(ex_start, ypos, ex_end-ex_start,
- border, 0, ypos);
- GradientPaint gp = new GradientPaint(ex_start, ypos, exon.getColour(),
- ex_start, ypos+(border/2), Color.white, true);
- g2d.setPaint(gp);
- g2d.fill(e);
-
- //g2d.drawLine(ex_start, ypos, ex_end, ypos);
+
+ FeatureSegmentVector segments = exon.getSegments();
+
+ for(int k=0; k<segments.size(); k++)
+ {
+ FeatureSegment segment = segments.elementAt(k);
+
+ Range range = segment.getRawRange();
+ offset = segment.getFrameID() * getFontHeight() * 2;
+
+ int ex_start = border+(int)((range.getStart()-start)*fraction);
+ int ex_end = border+(int)((range.getEnd()-start)*fraction);
+
+ if(exon.getColour() != null)
+ g2d.setColor( exon.getColour() );
+
+ drawExons(g2d, ex_start, ex_end,
+ last_ex_start, last_ex_end, last_ypos,
+ offset, ypos, exon.getColour(),
+ original_stroke, stroke, segment.isForwardSegment());
+
+ last_ex_end = ex_end;
+ last_ex_start = ex_start;
+ last_ypos = ypos+offset;
+ }
}
+
}
catch(InvalidRelationException e)
{
@@ -130,4 +203,157 @@ public class GeneViewerPanel extends JPanel
}
}
}
+
+
+ private void drawExons(Graphics2D g2d, int ex_start, int ex_end,
+ int last_ex_start, int last_ex_end, int last_ypos,
+ int offset, int ypos, Color exon_colour,
+ Stroke original_stroke, Stroke stroke, boolean isForward)
+ {
+ RoundRectangle2D e = new RoundRectangle2D.Float(ex_start, ypos+offset,
+ ex_end-ex_start,
+ getFontHeight(), 0, ypos+offset);
+
+ GradientPaint gp = new GradientPaint(ex_start, ypos+offset,
+ exon_colour,
+ ex_start, ypos+offset+(getFontHeight()/2),
+ Color.white, true);
+ g2d.setPaint(gp);
+ g2d.fill(e);
+
+ // draw connections
+ if(last_ex_end != 0 ||
+ last_ex_start != 0)
+ {
+ g2d.setStroke(original_stroke);
+ int ymid;
+ if(last_ypos < ypos+offset)
+ ymid = last_ypos;
+ else
+ ymid = ypos+offset;
+
+ if(isForward)
+ {
+ g2d.drawLine(last_ex_end, last_ypos,
+ last_ex_end+((ex_start-last_ex_end)/2), ymid-getFontHeight()/2);
+ g2d.drawLine(last_ex_end+((ex_start-last_ex_end)/2), ymid-getFontHeight()/2,
+ ex_start, ypos+offset);
+ }
+ else
+ {
+ g2d.drawLine(last_ex_start, last_ypos,
+ last_ex_start+((ex_end-last_ex_start)/2), ymid-getFontHeight()/2);
+ g2d.drawLine(last_ex_start+((ex_end-last_ex_start)/2), ymid-getFontHeight()/2,
+ ex_end, ypos+offset);
+ }
+ g2d.setStroke(stroke);
+ }
+
+ }
+
+ private int getFrameID(ChadoCanonicalGene chado_gene, ChadoFeature feature,
+ int nexon, List exons)
+ {
+ final int position_on_strand;
+
+ if(feature.getFeatureloc().getStrand() == -1)
+ position_on_strand = chado_gene.getSeqlen()-feature.getFeatureloc().getFmax();
+ else
+ position_on_strand = feature.getFeatureloc().getFmin();
+
+ // this will be 0, 1 or 2 depending on which frame the segment is in
+ final int start_base_modulo =
+ (position_on_strand + getFrameShift(nexon, exons)) % 3;
+
+ if(feature.getFeatureloc().getStrand() == 1)
+ {
+ switch (start_base_modulo)
+ {
+ case 0:
+ return FeatureSegment.FORWARD_FRAME_1;
+ case 1:
+ return FeatureSegment.FORWARD_FRAME_2;
+ case 2:
+ return FeatureSegment.FORWARD_FRAME_3;
+ }
+ }
+ else
+ {
+ switch (start_base_modulo)
+ {
+ case 0:
+ return FeatureSegment.REVERSE_FRAME_1;
+ case 1:
+ return FeatureSegment.REVERSE_FRAME_2;
+ case 2:
+ return FeatureSegment.REVERSE_FRAME_3;
+ }
+ }
+
+ return FeatureSegment.NO_FRAME;
+ }
+
+
+ /**
+ * Returns 0, 1 or 2 depending on which translation frame this segment is
+ * in. A frame shift of zero means that the bases should be translated
+ * starting at the start position of this segment, 1 means start
+ * translating one base ahead of the start position and 2 means start
+ * translating two bases ahead of the start position.
+ **/
+ private int getFrameShift(int nexon, List exons)
+ {
+ // find the number of bases in the segments before this one
+ int base_count = 0;
+ int direction = 0;
+
+ for(int i = 0; i < exons.size(); ++i)
+ {
+ ChadoFeature this_feature = (ChadoFeature)exons.get(i);
+ ChadoFeatureLoc featureLoc = this_feature.getFeatureloc();
+
+ int this_direction;
+ if(featureLoc.getStrand() == 1)
+ this_direction = 1;
+ else
+ this_direction = -1;
+
+ if(i == nexon)
+ {
+ if(i != 0 && this_direction != direction)
+ base_count = 0;
+
+ break;
+ }
+ else
+ {
+ if(i == 0)
+ direction = this_direction;
+ else if(this_direction != direction)
+ base_count = 0;
+
+ base_count += featureLoc.getFmax()-featureLoc.getFmin();
+ }
+ }
+
+ int codon_start = ((ChadoFeature)exons.get(nexon)).getFeatureloc().getPhase();
+ int mod_value = (base_count + 3 - codon_start) % 3;
+
+ //System.out.println("GVP mod_value="+mod_value+" base_count="+base_count + " codon_start="+codon_start);
+ if(mod_value == 1)
+ return 2;
+ else if(mod_value == 2)
+ return 1;
+ else
+ return 0;
+ }
+
+
+
+ private int getFontHeight()
+ {
+ final FontMetrics fm = this.getFontMetrics(getFont());
+ return fm.getHeight();
+ }
+
}
\ No newline at end of file