diff --git a/uk/ac/sanger/artemis/components/genebuilder/ButtonPanel.java b/uk/ac/sanger/artemis/components/genebuilder/ButtonPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..a8c6d97d1b2f8990dd5a60bbd1e63cf6387c3849
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+++ b/uk/ac/sanger/artemis/components/genebuilder/ButtonPanel.java
@@ -0,0 +1,449 @@
+package uk.ac.sanger.artemis.components.genebuilder;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Set;
+
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
+import javax.swing.JToolBar;
+
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.components.MessageDialog;
+import uk.ac.sanger.artemis.components.TransferAnnotationTool;
+import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
+import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
+import uk.ac.sanger.artemis.io.DocumentEntry;
+import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.io.GFFStreamFeature;
+import uk.ac.sanger.artemis.io.Location;
+import uk.ac.sanger.artemis.io.LocationParseException;
+import uk.ac.sanger.artemis.io.Qualifier;
+import uk.ac.sanger.artemis.io.QualifierVector;
+import uk.ac.sanger.artemis.io.Range;
+import uk.ac.sanger.artemis.io.RangeVector;
+import uk.ac.sanger.artemis.sequence.MarkerRange;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+
+
+public class ButtonPanel extends JToolBar
+{
+ private static final long serialVersionUID = 1L;
+ private BasicGeneBuilderFrame gbFrame;
+
+ public ButtonPanel(final BasicGeneBuilderFrame gbFrame,
+ final EntryGroup entry_group)
+ {
+ super();
+
+ this.gbFrame = gbFrame;
+
+ final JButton complement_button = new JButton("Complement");
+ add(complement_button);
+ complement_button.addActionListener(new ActionListener ()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ complementLocation();
+ }
+ });
+
+ if(GeneUtils.isDatabaseEntry(getFeature().getEmblFeature()))
+ {
+ final JButton refresh_button = new JButton("Refresh");
+ add(refresh_button);
+ refresh_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ refresh();
+ }
+ });
+ }
+
+ final JButton grab_button = new JButton("Grab Range");
+ add(grab_button);
+ grab_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ grabSelectedRange();
+ }
+ });
+
+ final JButton remove_button = new JButton("Remove Range");
+ add(remove_button);
+ remove_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ removeSelectedRange();
+ }
+ });
+
+ final JButton select_button = new JButton("Select Feature");
+ add(select_button);
+ select_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ gbFrame.getSelection().set(getFeature());
+ }
+ });
+
+ final JButton transferAnnotationBbutton = new JButton("TAT");
+ add(transferAnnotationBbutton);
+ transferAnnotationBbutton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ java.util.List geneNames = null;
+ if(gbFrame.getMatchForm() != null)
+ geneNames = gbFrame.getMatchForm().getGeneNameList();
+
+ new TransferAnnotationTool(getFeature(), entry_group, geneNames);
+ }
+ });
+
+ }
+
+ private Feature getFeature()
+ {
+ return gbFrame.getFeature();
+ }
+
+ /**
+ * Complement the current location_text.
+ **/
+ private void complementLocation()
+ {
+ if(GeneUtils.isDatabaseEntry(getFeature().getEmblFeature()))
+ {
+ final ChadoCanonicalGene chadoGene =
+ ((GFFStreamFeature)getFeature().getEmblFeature()).getChadoGene();
+ GeneUtils.complementGeneModel(chadoGene);
+ gbFrame.dispose(true);
+ return;
+ }
+
+ if(rationalizeLocation())
+ {
+ if(gbFrame.getLocationText().getText().startsWith("complement("))
+ {
+ final String new_text = gbFrame.getLocationText().getText().substring(11);
+ if (new_text.endsWith(")"))
+ {
+ final String new_text2 =
+ new_text.substring(0, new_text.length () - 1);
+ gbFrame.getLocationText().setText(new_text2);
+ }
+ else
+ gbFrame.getLocationText().setText(new_text);
+ }
+ else
+ {
+ final String new_text = gbFrame.getLocationText().getText ();
+ gbFrame.getLocationText().setText("complement(" + new_text + ")");
+ }
+ }
+ else
+ new MessageDialog(null, "complement failed - " +
+ "current location cannot be parsed");
+ }
+
+ /**
+ * Attempt to parse the current location_text as a Location. If it can be
+ * parsed it will be canonicalized (ie. the complement, if any, will be
+ * outermost). Returns true if and only if the location_text could be
+ * parsed.
+ **/
+ private boolean rationalizeLocation()
+ {
+ try
+ {
+ final Location location = new Location(gbFrame.getLocationText().getText());
+ gbFrame.getLocationText().setText(location.toStringShort());
+ return true;
+ }
+ catch(LocationParseException e)
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Refresh the annotation for the active feature
+ */
+ private void refresh()
+ {
+ Feature edit_feature = gbFrame.getFeature();
+ // refresh from the database
+ final DatabaseDocument originalDocument =
+ (DatabaseDocument)((DocumentEntry)edit_feature.getEmblFeature().getEntry()).getDocument();
+
+ final Set uniquenames =
+ ((GFFStreamFeature)edit_feature.getEmblFeature()).getSegmentRangeStore().keySet();
+ final Iterator it = uniquenames.iterator();
+ final String uniquename = (String)it.next();
+ final DatabaseDocument newDocument = new DatabaseDocument(originalDocument,
+ uniquename, null, true, null);
+ newDocument.setLazyFeatureLoad(false);
+ newDocument.setReadChildren(false);
+
+ try
+ {
+ DatabaseDocumentEntry dbentry = new DatabaseDocumentEntry(newDocument, null);
+ uk.ac.sanger.artemis.io.Feature databaseFeature = dbentry.getAllFeatures().featureAt(0);
+
+ // compare timelastmodified
+ Qualifier qualifier = edit_feature.getQualifierByName("timelastmodified");
+ String active_timelastmodified = (String)qualifier.getValues().get(0);
+ qualifier = databaseFeature.getQualifierByName("timelastmodified");
+ String database_timelastmodified = (String)qualifier.getValues().get(0);
+
+ if(active_timelastmodified.equals(database_timelastmodified))
+ {
+ JOptionPane.showMessageDialog(this,
+ "No new changes found for the feature\n"+
+ uniquename+"\n"+
+ "in the database since:\n"+database_timelastmodified,
+ "No Updates", JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ "Changes found for the feature\n"+
+ uniquename+"\n"+
+ "in the database at:\n"+database_timelastmodified,
+ "Changes Found", JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ final QualifierVector db_qv = databaseFeature.getQualifiers();
+ final QualifierVector qv = edit_feature.getQualifiers();
+ final QualifierVector new_qv = new QualifierVector();
+
+ for(int i=0; i<qv.size(); i++)
+ {
+ Qualifier q = (Qualifier)qv.get(i);
+ if(q.getName().equals("Parent") ||
+ q.getName().equals("Derives_from") ||
+ q.getName().equals("ID") )
+ new_qv.addQualifierValues(q);
+ }
+
+
+ for(int i=0; i<db_qv.size(); i++)
+ {
+ Qualifier q = (Qualifier)db_qv.get(i);
+ if(q.getName().equals("Parent") ||
+ q.getName().equals("Derives_from") ||
+ q.getName().equals("ID") )
+ continue;
+ new_qv.add(q);
+ }
+
+ edit_feature.getQualifiers().removeAllElements();
+ edit_feature.getQualifiers().addAll(new_qv);
+ gbFrame.setQualifiers();
+ }
+ catch(EntryInformationException e) {}
+ catch(IOException e) {}
+ }
+
+
+ /**
+ * Add the currently selected range to location_text.
+ **/
+ private void grabSelectedRange()
+ {
+ if(!rationalizeLocation ())
+ {
+ new MessageDialog(null,
+ "grab failed - current location cannot be parsed");
+ return;
+ }
+
+ final Range selected_range = gbFrame.getSelection().getSelectionRange();
+
+ if(selected_range == null)
+ {
+ new MessageDialog(null, "grab failed - nothing is selected");
+ return;
+ }
+
+ // save it in case it gets mangled
+ final String old_location_text = gbFrame.getLocationText().getText();
+
+ if (old_location_text.endsWith ("))"))
+ {
+ final String new_text =
+ old_location_text.substring(0, old_location_text.length () - 2);
+
+ gbFrame.getLocationText().setText(new_text + "," + selected_range.getStart () +
+ ".." + selected_range.getEnd () + "))");
+ }
+ else
+ {
+ if(old_location_text.endsWith (")"))
+ {
+ final String new_text =
+ old_location_text.substring(0, old_location_text.length () - 1);
+
+ gbFrame.getLocationText().setText(new_text + "," + selected_range.getStart () +
+ ".." + selected_range.getEnd () + ")");
+ }
+ else
+ gbFrame.getLocationText().setText(old_location_text + "," +
+ selected_range.getStart () +
+ ".." + selected_range.getEnd ());
+ }
+
+ if(!rationalizeLocation())
+ {
+ gbFrame.getLocationText().setText (old_location_text);
+ new MessageDialog(null, "grab failed - location cannot be parsed after " +
+ "grabbing");
+ }
+ }
+
+ /**
+ * Remove the currently selected range of bases from location_text.
+ **/
+ private void removeSelectedRange()
+ {
+ if(!rationalizeLocation())
+ {
+ new MessageDialog(null,
+ "grab failed - current location cannot be parsed");
+ return;
+ }
+
+ final MarkerRange selected_marker_range =
+ gbFrame.getSelection().getMarkerRange();
+
+ if(selected_marker_range == null)
+ {
+ new MessageDialog(null, "remove range failed - no bases are selected");
+ return;
+ }
+
+ final Range selected_range = selected_marker_range.getRawRange();
+
+ if (selected_marker_range.getStrand() != getFeature().getStrand())
+ {
+ new MessageDialog(null, "remove range failed - you need to select " +
+ "some bases on the other strand");
+ return;
+ }
+
+ final Location location;
+
+ try
+ {
+ location = new Location(gbFrame.getLocationText().getText ());
+ }
+ catch (LocationParseException e)
+ {
+ // this shouldn't happen because we called rationalizeLocation ()
+ throw new Error("internal error - unexpected exception: " + e);
+ }
+
+ final Range location_total_range = location.getTotalRange();
+
+ if(!selected_range.overlaps(location_total_range))
+ {
+ new MessageDialog(null, "remove range failed - the range you " +
+ "selected does not overlap the feature");
+ return;
+ }
+
+ if(selected_range.contains(location_total_range))
+ {
+ new MessageDialog(null, "remove range failed - the range you " +
+ "selected overlaps the whole feature");
+ return;
+ }
+
+ final RangeVector location_ranges = location.getRanges();
+ final boolean location_is_complemented = location.isComplement();
+
+ final RangeVector new_ranges = new RangeVector();
+
+ // if the selected_range completely covers a range remove the
+ // range. otherwise if the selected_range is completely within one of the
+ // ranges two new ranges are created. if the selected_range is not
+ // completely contained then the appropriate end of the range is truncated
+ for(int i = 0; i < location_ranges.size(); ++i)
+ {
+ final Range this_range = (Range)location_ranges.elementAt(i);
+
+ if(selected_range.overlaps(this_range))
+ {
+ try
+ {
+ if(this_range.contains(selected_range) &&
+ this_range.getStart() != selected_range.getStart() &&
+ this_range.getEnd() != selected_range.getEnd())
+ {
+ // chop a piece out of the middle and make two new ranges
+ final Range new_start_range =
+ this_range.change(selected_range.getEnd() + 1,
+ this_range.getEnd());
+ new_ranges.add(new_start_range);
+ final Range new_end_range =
+ this_range.change(this_range.getStart(),
+ selected_range.getStart() - 1);
+ new_ranges.add(new_end_range);
+ }
+ else
+ {
+ if(selected_range.contains(this_range)) {
+ // delete (ie. don't copy) the range
+ }
+ else
+ {
+ if(this_range.getStart() < selected_range.getStart())
+ {
+ // truncate the end of the range
+ final Range new_start_range =
+ this_range.change(this_range.getStart(),
+ selected_range.getStart() - 1);
+ new_ranges.add(new_start_range);
+ }
+ else
+ {
+ if(this_range.getEnd() > selected_range.getEnd())
+ {
+ // truncate the start of the range
+ final Range new_end_range =
+ this_range.change(selected_range.getEnd() + 1,
+ this_range.getEnd());
+ new_ranges.add(new_end_range);
+ }
+ else
+ throw new Error ("internal error - can't remove range");
+ }
+ }
+ }
+ }
+ catch(OutOfRangeException e)
+ {
+ throw new Error ("internal error - unexpected exception: " + e);
+ }
+ }
+ else
+ new_ranges.add(this_range); // copy it unchanged
+ }
+
+ final Location new_location =
+ new Location(new_ranges, location_is_complemented);
+
+ gbFrame.getLocationText().setText(new_location.toStringShort());
+ }
+
+}
\ No newline at end of file