diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
new file mode 100644
index 0000000000000000000000000000000000000000..585621dd5fd6b361111070aef3cfa135defec7de
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
@@ -0,0 +1,108 @@
+/* GeneBuilderFrame.java
+ *
+ * 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.
+ *
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.1 2006-05-31 09:49:07 tjc Exp $
+ */
+
+package uk.ac.sanger.artemis.components.genebuilder;
+
+import javax.swing.*;
+import java.awt.*;
+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.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
+{
+
+ public GeneBuilderFrame(final Feature gene_feature)
+ {
+ super("Artemis Gene Builder: " + gene_feature.getIDString() +
+ (gene_feature.isReadOnly() ?
+ " - (read only)" :
+ ""));
+
+ QualifierTextArea qualifier_text_area = new QualifierTextArea();
+ GFFStreamFeature gff_feature = (GFFStreamFeature)gene_feature.getEmblFeature();
+ GeneComponentTree tree = new GeneComponentTree(gff_feature.getChadoGene(),
+ qualifier_text_area);
+ getContentPane().add(new JScrollPane(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));
+
+ getContentPane().add(new JScrollPane(qualifier_text_area), BorderLayout.SOUTH);
+
+ pack();
+ setVisible(true);
+ }
+
+ /**
+ * Return a string containing one qualifier per line. These are the
+ * original qualifiers, not the qualifiers from the qualifier_text_area.
+ **/
+ protected static String getQualifierString(final Feature feature)
+ {
+ final StringBuffer buffer = new StringBuffer();
+ final QualifierVector qualifiers = feature.getQualifiers();
+
+ for(int qualifier_index = 0; qualifier_index < qualifiers.size();
+ ++qualifier_index)
+ {
+ 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");
+ }
+ }
+
+ return buffer.toString();
+ }
+
+ /**
+ * Return the EntryInformation object of the entry containing the feature.
+ **/
+ protected static EntryInformation getEntryInformation(final Feature feature)
+ {
+ return feature.getEntry().getEntryInformation();
+ }
+
+}
\ 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
new file mode 100644
index 0000000000000000000000000000000000000000..b156fd91db9e57ffccb29d999ed62b967685bfe7
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
@@ -0,0 +1,136 @@
+/* GeneComponentTree.java
+ *
+ * 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.
+ *
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.1 2006-05-31 09:49:07 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 javax.swing.*;
+import javax.swing.event.*;
+
+import javax.swing.tree.*;
+import java.util.Vector;
+
+/**
+ * Tree to display a gene hierarchy.
+ */
+public class GeneComponentTree extends JTree
+{
+
+ public GeneComponentTree(final ChadoCanonicalGene chado_gene,
+ final QualifierTextArea qualifier_text_area)
+ {
+ final Feature gene = chado_gene.getGene();
+ final String gene_id;
+ try
+ {
+ gene_id = (String)gene.getQualifierByName("ID").getValues().get(0);
+ DefaultMutableTreeNode top =
+ new DefaultMutableTreeNode(gene_id);
+
+ createNodes(top, chado_gene);
+ DefaultTreeModel model = new DefaultTreeModel(top);
+ setModel(model);
+ }
+ catch(InvalidRelationException e)
+ {
+ e.printStackTrace();
+ }
+
+ //Listen for when a file is selected
+ addTreeSelectionListener(new TreeSelectionListener()
+ {
+ public void valueChanged(TreeSelectionEvent e)
+ {
+ DefaultMutableTreeNode node =
+ (DefaultMutableTreeNode)GeneComponentTree.this.getLastSelectedPathComponent();
+ 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() ) );
+ }
+ });
+
+ }
+
+ /**
+ * Build the node hierarchy for this gene, i.e. transcript, exons,
+ * CDS, polypeptide.
+ * @param gene_node
+ * @param chado_gene
+ * @throws InvalidRelationException
+ */
+ private void createNodes(final DefaultMutableTreeNode gene_node,
+ final ChadoCanonicalGene chado_gene)
+ throws InvalidRelationException
+ {
+ Vector transcripts = chado_gene.getTranscripts();
+ Vector exons;
+ Feature transcript;
+ Feature exon;
+ Feature protein;
+ String transcript_id;
+ String exon_id;
+ String protein_id;
+ DefaultMutableTreeNode transcript_node;
+ DefaultMutableTreeNode exon_node;
+ DefaultMutableTreeNode protein_node;
+
+ for(int i=0; i<transcripts.size(); i++)
+ {
+ transcript = (Feature)transcripts.get(i);
+ transcript_id = (String)transcript.getQualifierByName("ID").getValues().get(0);
+ transcript_node = new DefaultMutableTreeNode(transcript_id);
+ gene_node.add(transcript_node);
+
+ exons = chado_gene.getExonsOfTranscript(transcript_id);
+ if(exons == null)
+ continue;
+
+ for(int j=0; j<exons.size(); j++)
+ {
+ exon = (Feature)exons.get(i);
+ exon_id = (String)exon.getQualifierByName("ID").getValues().get(0);
+ exon_node = new DefaultMutableTreeNode(exon_id);
+ transcript_node.add(exon_node);
+ }
+
+ protein = chado_gene.getProteinOfTranscript(transcript_id);
+ if(protein == null)
+ continue;
+
+ protein_id = (String)protein.getQualifierByName("ID").getValues().get(0);
+ protein_node = new DefaultMutableTreeNode(protein_id);
+
+ transcript_node.add(protein_node);
+ }
+ }
+
+}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..8a24dd22200c5e1bd7efbbba8935cf54c74e2677
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
@@ -0,0 +1,128 @@
+/* GeneViewerPanel
+ *
+ * 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.
+ *
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.1 2006-05-31 09:49:07 tjc Exp $
+ */
+
+package uk.ac.sanger.artemis.components.genebuilder;
+
+import javax.swing.*;
+import java.awt.*;
+import java.util.Vector;
+import java.awt.geom.RoundRectangle2D;
+
+import uk.ac.sanger.artemis.io.Feature;
+import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
+import uk.ac.sanger.artemis.io.InvalidRelationException;
+
+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);
+ }
+
+ public void paintComponent(Graphics 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();
+
+ setFont(uk.ac.sanger.artemis.Options.getOptions().getFont());
+ final FontMetrics fm = this.getFontMetrics(getFont());
+
+ int start = embl_gene.getFirstBase();
+ int end = embl_gene.getLastBase();
+ boolean complement = embl_gene.getLocation().isComplement();
+
+ BasicStroke stroke = new BasicStroke(2.f);
+ g2d.setStroke(stroke);
+ g2d.setColor( gene.getColour() );
+
+ int ypos = border;
+
+ ypos += fm.getHeight();
+ g2d.drawString(gene.getIDString(), border, ypos);
+ ypos += fm.getHeight();
+
+ g2d.drawLine(border, ypos, getSize().width - border, ypos);
+
+ Vector transcripts = chado_gene.getTranscripts();
+ Feature embl_transcript;
+ uk.ac.sanger.artemis.Feature transcript;
+
+ float fraction = (float)(getSize().width - (2*border))/(float)(end-start);
+ for(int i=0; i<transcripts.size(); i++)
+ {
+ ypos += border;
+ embl_transcript = (Feature)transcripts.get(i);
+ transcript = (uk.ac.sanger.artemis.Feature)embl_transcript.getUserData();
+
+ int t_start = border+(int)((embl_transcript.getFirstBase()-start)*fraction);
+ int t_end = border+(int)((embl_transcript.getLastBase()-start)*fraction);
+
+ ypos += fm.getHeight();
+ g2d.drawString(transcript.getIDString(), border, ypos);
+ ypos += fm.getHeight();
+
+ g2d.setColor( transcript.getColour() );
+ g2d.drawLine(t_start, ypos, t_end, ypos);
+
+ try
+ {
+ Vector exons = chado_gene.getExonsOfTranscript(
+ (String)embl_transcript.getQualifierByName("ID").getValues().get(0));
+
+ ypos += border;
+ for(int j=0; j<exons.size(); j++)
+ {
+ 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);
+
+ 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);
+ }
+ }
+ catch(InvalidRelationException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+}
\ No newline at end of file