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Commit 22b8e060 authored by tjc's avatar tjc
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create / delete feature segs from selection 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4599 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent fcc6cd91
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uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
+ 139
− 39
View file @ 22b8e060
......@@ -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/GeneViewerPanel.java,v 1.13 2006-07-28 08:34:59 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.14 2006-07-28 15:27:00 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
......@@ -83,6 +83,8 @@ public class GeneViewerPanel extends JPanel
private Point last_cursor_position;
private EntryGroup entry_group;
/**
* The shortcut for Delete Selected Features.
**/
......@@ -104,6 +106,7 @@ public class GeneViewerPanel extends JPanel
{
this.chado_gene = chado_gene;
this.selection = selection;
this.entry_group = entry_group;
Dimension dim = new Dimension(400,400);
setPreferredSize(dim);
......@@ -119,6 +122,9 @@ public class GeneViewerPanel extends JPanel
{
public void mouseDragged(MouseEvent event)
{
if(event.isPopupTrigger())
return;
final MarkerRange selected_range = selection.getMarkerRange();
int select_start = (int)((event.getX() - border)/fraction)+start;
......@@ -139,9 +145,6 @@ public class GeneViewerPanel extends JPanel
else
click_range = selected_range.combineRanges(drag_range, true);
System.out.println(click_range.getRawStart().getRawPosition()+".."+
click_range.getRawEnd().getRawPosition());
last_cursor_position = event.getPoint();
selection.setMarkerRange(click_range);
repaint();
......@@ -157,7 +160,7 @@ public class GeneViewerPanel extends JPanel
protected void createMenus(JComponent menu,
final EntryGroup entry_group)
{
JMenuItem deleteMenu = new JMenuItem("Delete selected features");
JMenuItem deleteMenu = new JMenuItem("Delete Selected Features");
deleteMenu.setAccelerator(DELETE_FEATURES_KEY);
deleteMenu.addActionListener(new ActionListener()
{
......@@ -188,8 +191,45 @@ public class GeneViewerPanel extends JPanel
}
}
});
menu.add(deleteMenu);
JMenuItem deleteSegmentMenu = new JMenuItem("Delete Selected Exon");
deleteSegmentMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
FeatureSegmentVector features = selection.getAllSegments();
int option = JOptionPane.showConfirmDialog(null,
"Delete Selected Exon",
"Delete Selected Exon",
JOptionPane.OK_CANCEL_OPTION);
if(option == JOptionPane.CANCEL_OPTION)
return;
try
{
for(int i = 0; i < features.size(); i++)
{
uk.ac.sanger.artemis.FeatureSegment segment =
features.elementAt(i);
segment.removeFromFeature();
}
repaint();
}
catch(ReadOnlyException e)
{
e.printStackTrace();
}
catch(LastSegmentException e)
{
e.printStackTrace();
}
}
});
menu.add(deleteSegmentMenu);
menu.add(new JSeparator());
JMenuItem createTranscript = new JMenuItem("Create transcript");
createTranscript.setAccelerator(CREATE_FEATURES_KEY);
......@@ -197,34 +237,22 @@ public class GeneViewerPanel extends JPanel
{
public void actionPerformed(ActionEvent event)
{
final Entry default_entry = entry_group.getDefaultEntry();
final Location new_location = chado_gene.getGene().getLocation();
uk.ac.sanger.artemis.Feature new_feature;
try
{
String gene_name =
(String)chado_gene.getGene().getQualifierByName("ID").getValues().get(0);
QualifierVector qualifiers = new QualifierVector();
qualifiers.add(new Qualifier("Parent", gene_name));
uk.ac.sanger.artemis.Feature feature = createFeature(
chado_gene.getGene().getLocation(),
entry_group, new Key("mRNA"),
qualifiers);
new_feature = default_entry.createFeature(new Key("mRNA"),
new_location, qualifiers);
selection.set(new_feature);
chado_gene.addTranscript(new_feature.getEmblFeature());
chado_gene.addTranscript(feature.getEmblFeature());
}
catch (EntryInformationException e)
{
}
catch(ReadOnlyException e)
{
e.printStackTrace();
}
catch(OutOfRangeException e)
catch(InvalidRelationException e)
{
// TODO Auto-generated catch block
e.printStackTrace();
}
......@@ -294,7 +322,6 @@ public class GeneViewerPanel extends JPanel
if(selection.getMarkerRange() != null)
{
Range range = selection.getSelectionRange();
System.out.println("Draw selection range "+range.getStart()+".."+range.getEnd());
int ntranscript = (last_cursor_position.y - (border*3))/getTranscriptSize();
if(ntranscript < transcripts.size())
......@@ -310,6 +337,37 @@ public class GeneViewerPanel extends JPanel
setPreferredSize(new Dimension(getSize().width, ypos+border));
}
private uk.ac.sanger.artemis.Feature createFeature(
final Location new_location,
final EntryGroup entry_group,
final Key key,
final QualifierVector qualifiers)
{
final Entry default_entry = entry_group.getDefaultEntry();
uk.ac.sanger.artemis.Feature new_feature = null;
try
{
new_feature = default_entry.createFeature(key,
new_location, qualifiers);
selection.set(new_feature);
return new_feature;
}
catch (EntryInformationException e)
{
}
catch(ReadOnlyException e)
{
e.printStackTrace();
}
catch(OutOfRangeException e)
{
e.printStackTrace();
}
return new_feature;
}
/**
* Macro for getting the size of the transcipt and
* exon image.
......@@ -943,9 +1001,13 @@ public class GeneViewerPanel extends JPanel
{
public void actionPerformed(ActionEvent event)
{
Feature embl_exon = (Feature)exons.get(0);
Feature embl_exon = null;
if(exons != null)
embl_exon = (Feature)exons.get(0);
Range range_selected = selection.getSelectionRange();
addExonFeature(embl_exon, range_selected);
addExonFeature(embl_exon, range_selected, uniquename);
}
});
......@@ -996,9 +1058,46 @@ public class GeneViewerPanel extends JPanel
}
private void addExonFeature(Feature feature, Range range)
/**
* Create an exons feature
* @param feature
* @param range
* @param transcript_name
*/
private void addExonFeature(Feature feature, Range range,
final String transcript_name)
{
try
{
if(feature == null)
{
QualifierVector qualifiers = new QualifierVector();
qualifiers.add(new Qualifier("Parent", transcript_name));
uk.ac.sanger.artemis.Feature exon = createFeature(
new Location(range),
entry_group, new Key("exon"),
qualifiers);
chado_gene.addExon(transcript_name, exon.getEmblFeature());
}
else
{
((uk.ac.sanger.artemis.Feature)feature.getUserData()).addSegment(range);
}
}
catch(OutOfRangeException e)
{
e.printStackTrace();
}
catch(InvalidRelationException e)
{
e.printStackTrace();
}
catch(ReadOnlyException e)
{
e.printStackTrace();
}
}
private void deleteExonFeatures(uk.ac.sanger.artemis.Feature feature,
......@@ -1125,7 +1224,8 @@ public class GeneViewerPanel extends JPanel
popup.show(e.getComponent(),
e.getX(), e.getY());
}
else if(e.getClickCount() == 1)
else if(e.getButton() != e.BUTTON3 &&
e.getClickCount() == 1)
{
if(selection.getMarkerRange() != null &&
e.isShiftDown())
......
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