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Commit c5bae4f3 authored by tjc's avatar tjc
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fixes for multiple transcripts 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4525 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 105c710d
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uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
+ 4
− 2
View file @ c5bae4f3
......@@ -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/genebuilder/GeneBuilderFrame.java,v 1.2 2006-07-04 15:57:57 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.3 2006-07-06 15:10:14 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
......@@ -72,7 +72,9 @@ public class GeneBuilderFrame extends JFrame
getContentPane().add(jsp_tree, BorderLayout.WEST);
GeneViewerPanel viewer = new GeneViewerPanel(gff_feature.getChadoGene());
getContentPane().add(viewer, BorderLayout.CENTER);
JScrollPane jsp_viewer = new JScrollPane(viewer);
jsp_viewer.setPreferredSize( viewer.getPreferredSize() );
getContentPane().add(jsp_viewer, BorderLayout.CENTER);
if(entry_group != null)
{
......
uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
+ 11
− 5
View file @ c5bae4f3
......@@ -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/genebuilder/GeneComponentTree.java,v 1.3 2006-07-04 15:57:57 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.4 2006-07-06 15:10:14 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
......@@ -94,7 +94,7 @@ public class GeneComponentTree extends JTree
List exons;
Feature transcript;
Feature exon;
Feature protein;
Object protein;
String transcript_id;
String exon_id;
String protein_id;
......@@ -105,7 +105,8 @@ public class GeneComponentTree extends JTree
for(int i=0; i<transcripts.size(); i++)
{
transcript = (Feature)transcripts.get(i);
transcript_id = (String)transcript.getQualifierByName("ID").getValues().get(0);
transcript_id =
(String)transcript.getQualifierByName("ID").getValues().get(0);
transcript_node = new DefaultMutableTreeNode(transcript_id);
gene_node.add(transcript_node);
......@@ -127,11 +128,16 @@ public class GeneComponentTree extends JTree
transcript_node.add(exon_node);
}
protein = (Feature)chado_gene.getProteinOfTranscript(transcript_id);
protein = chado_gene.getProteinOfTranscript(transcript_id);
if(protein == null)
continue;
protein_id = (String)protein.getQualifierByName("ID").getValues().get(0);
if(protein instanceof Feature)
protein_id =
(String)((Feature)protein).getQualifierByName("ID").getValues().get(0);
else
protein_id = ((ChadoFeature)protein).getUniquename();
protein_node = new DefaultMutableTreeNode(protein_id);
transcript_node.add(protein_node);
......
uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
+ 152
− 23
View file @ c5bae4f3
......@@ -20,13 +20,14 @@
* 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 1.4 2006-07-05 12:30:53 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.5 2006-07-06 15:10:14 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import java.util.List;
import java.util.Collections;
import java.awt.geom.RoundRectangle2D;
......@@ -35,24 +36,49 @@ 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.chado.ChadoFeatureProp;
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;
import uk.ac.sanger.artemis.Options;
public class GeneViewerPanel extends JPanel
{
private ChadoCanonicalGene chado_gene;
private int border = 15;
/** Used to colour the frames. */
private Color light_grey = new Color(240, 240, 240);
/** pop up menu */
private JPopupMenu popup;
/** overlay transcript features */
private boolean overlay_transcripts = false;
public GeneViewerPanel(final ChadoCanonicalGene chado_gene)
{
this.chado_gene = chado_gene;
Dimension dim = new Dimension(300,300);
Dimension dim = new Dimension(400,400);
setPreferredSize(dim);
setBackground(Color.white);
// Popup menu
addMouseListener(new PopupListener());
popup = new JPopupMenu();
JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem("Overlay transcripts");
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
overlay_transcripts = !overlay_transcripts;
repaint();
revalidate();
}
});
popup.add(menuItem);
}
public void paintComponent(Graphics g)
......@@ -64,24 +90,21 @@ public class GeneViewerPanel extends JPanel
(uk.ac.sanger.artemis.Feature)embl_gene.getUserData();
setFont(uk.ac.sanger.artemis.Options.getOptions().getFont());
final FontMetrics fm = this.getFontMetrics(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);
BasicStroke stroke = new BasicStroke(4.f);
Stroke original_stroke = g2d.getStroke();
g2d.setStroke(stroke);
g2d.setColor( gene.getColour() );
int ypos = border;
ypos += fm.getHeight();
// draw gene
g2d.drawString(gene.getIDString(), border, ypos);
ypos += fm.getHeight();
g2d.drawLine(border, ypos, getSize().width - border, ypos);
drawFeature(g2d, border, getSize().width - border, ypos, gene.getColour());
List transcripts = chado_gene.getTranscripts();
Feature embl_transcript;
......@@ -89,29 +112,37 @@ public class GeneViewerPanel extends JPanel
float fraction = (float)(getSize().width - (2*border))/
(float)(end-start);
ypos += border*2;
for(int i=0; i<transcripts.size(); i++)
{
ypos += border;
// draw frame lines
if(!overlay_transcripts || i == 0)
drawFrameLines(g2d, ypos, stroke,
start, end, fraction);
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);
int nframe;
if(!embl_transcript.getLocation().isComplement())
nframe = (3 * getFontHeight() * 2) ;
else
nframe = (4 * getFontHeight() * 2) ;
g2d.drawString(transcript.getIDString(), border, ypos+nframe);
drawFeature(g2d, t_start, t_end, ypos+nframe, transcript.getColour());
try
{
List exons = chado_gene.getExonsOfTranscript(
(String)embl_transcript.getQualifierByName("ID").getValues().get(0));
ypos += border;
if(exons == null)
continue;
......@@ -133,7 +164,7 @@ public class GeneViewerPanel extends JPanel
((ChadoFeature)exons.get(exons.size()-1)).getFeaturelocsForFeatureId(),
chado_gene.getSrcfeature_id());
if( loc.getFmin() < loc_last.getFmin())
if(loc.getFmin() < loc_last.getFmin())
Collections.reverse(exons);
}
......@@ -145,9 +176,9 @@ public class GeneViewerPanel extends JPanel
int ex_start = border+(int)((loc.getFmin()+1-start)*fraction);
int ex_end = border+(int)((loc.getFmax()-start)*fraction);
Color exon_col = Color.CYAN;
Color exon_col = getColorFromAttributes(exon);
offset = getFrameID(chado_gene, loc, j, exons) * getFontHeight() * 2;
boolean isForward = false;
......@@ -163,6 +194,9 @@ public class GeneViewerPanel extends JPanel
last_ex_start = ex_start;
last_ypos = ypos+offset;
}
if(!overlay_transcripts)
ypos += 9 * getFontHeight() * 2;
continue;
}
......@@ -202,6 +236,8 @@ public class GeneViewerPanel extends JPanel
last_ex_start = ex_start;
last_ypos = ypos+offset;
}
ypos += (8 * getFontHeight() * 2) + (getFontHeight()/2) + border;
}
}
......@@ -210,14 +246,44 @@ public class GeneViewerPanel extends JPanel
e.printStackTrace();
}
}
setPreferredSize(new Dimension(getSize().width, ypos+border));
}
/**
* Draw frame lines
* @param g2d
* @param ypos
* @param stroke
* @param start
* @param end
* @param fraction
*/
private void drawFrameLines(Graphics2D g2d, int ypos,
Stroke stroke,
int start, int end, float fraction)
{
int offset;
g2d.setStroke(new BasicStroke(getFontHeight()));
for(int k=0; k<8; k++)
{
offset = (k * getFontHeight() * 2) + (getFontHeight()/2);
if(k == 3 || k == 4)
g2d.setColor( Color.LIGHT_GRAY );
else
g2d.setColor(light_grey);
g2d.drawLine(border, ypos+offset,
(int)((end-start)*fraction)+border, ypos+offset);
}
g2d.setStroke(stroke);
}
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);
......@@ -228,7 +294,10 @@ public class GeneViewerPanel extends JPanel
Color.white, true);
g2d.setPaint(gp);
g2d.fill(e);
*/
drawFeature(g2d, ex_start, ex_end, ypos+offset, exon_colour);
// draw connections
if(last_ex_end != 0 ||
last_ex_start != 0)
......@@ -259,6 +328,43 @@ public class GeneViewerPanel extends JPanel
}
private void drawFeature(Graphics2D g2d, int start, int end,
int ypos, Color colour)
{
RoundRectangle2D e = new RoundRectangle2D.Float(start, ypos,
end-start,
getFontHeight(), 0, ypos);
if(colour == null)
colour = Color.BLACK;
GradientPaint gp = new GradientPaint(start, ypos,
colour,
start, ypos+(getFontHeight()/2),
Color.white, true);
g2d.setPaint(gp);
g2d.fill(e);
}
/**
* Get the <code>Color</code> for a feature from its colour attribute.
* @param feature
* @return
*/
private Color getColorFromAttributes(ChadoFeature feature)
{
List properties = feature.getFeaturepropList();
for(int i=0; i<properties.size(); i++)
{
ChadoFeatureProp property = (ChadoFeatureProp)properties.get(i);
if(property.getCvterm().getName().equals("colour") ||
property.getCvterm().getName().equals("color") )
return Options.getOptions().getColorFromColourNumber(Integer.parseInt(property.getValue()));
}
return Color.CYAN;
}
/**
* Get the frame id for a feature segment
* @param chado_gene the chado representation of the gene model
......@@ -375,4 +481,27 @@ public class GeneViewerPanel extends JPanel
return fm.getHeight();
}
/**
* Popup listener
*/
class PopupListener extends MouseAdapter
{
public void mousePressed(MouseEvent e)
{
maybeShowPopup(e);
}
public void mouseReleased(MouseEvent e)
{
maybeShowPopup(e);
}
private void maybeShowPopup(MouseEvent e)
{
if(e.isPopupTrigger())
popup.show(e.getComponent(),
e.getX(), e.getY());
}
}
}
\ No newline at end of file
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