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Commit 8b39674e authored by tjc's avatar tjc
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use fasta boundaries in creating ORFs 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6143 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 26482fb1
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uk/ac/sanger/artemis/components/AddMenu.java
+ 114
− 49
View file @ 8b39674e
......@@ -20,15 +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/AddMenu.java,v 1.22 2007-02-22 19:35:24 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AddMenu.java,v 1.23 2007-06-26 08:24:38 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.plot.CodonUsageAlgorithm;
import uk.ac.sanger.artemis.sequence.BasePattern;
import uk.ac.sanger.artemis.sequence.BasePatternFormatException;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.sequence.MarkerRangeVector;
import uk.ac.sanger.artemis.sequence.Strand;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
......@@ -41,18 +47,32 @@ import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.LocationParseException;
import uk.ac.sanger.artemis.io.EntryInformationException;
import java.awt.*;
import java.awt.event.*;
import java.awt.Cursor;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.Vector;
import java.util.Enumeration;
import javax.swing.*;
import javax.swing.Box;
import javax.swing.JCheckBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JTextField;
import javax.swing.KeyStroke;
/**
* A Menu with commands that add new features/entries to an EntryGroup. This
* should have been called CreateMenu.
*
* @author Kim Rutherford
* @version $Id: AddMenu.java,v 1.22 2007-02-22 19:35:24 tjc Exp $
* @version $Id: AddMenu.java,v 1.23 2007-06-26 08:24:38 tjc Exp $
**/
public class AddMenu extends SelectionMenu
{
......@@ -958,36 +978,40 @@ public class AddMenu extends SelectionMenu
final int default_minimum_orf_size =
Options.getOptions ().getMinimumORFSize ();
final TextRequester text_requester =
new TextRequester ("minimum open reading frame size?",
18, String.valueOf (default_minimum_orf_size));
Box inputBox = Box.createVerticalBox();
inputBox.add(new JLabel("Minimum open reading frame size:"));
JTextField minSize = new JTextField(String.valueOf (default_minimum_orf_size));
inputBox.add(minSize);
JCheckBox useFastaBoundary = new JCheckBox("If multiple fasta use boundaries", false);
inputBox.add(useFastaBoundary);
text_requester.addTextRequesterListener (new TextRequesterListener () {
public void actionPerformed (final TextRequesterEvent event) {
if (event.getType () == TextRequesterEvent.CANCEL) {
int select = JOptionPane.showConfirmDialog(getParentFrame(),
inputBox, "ORF options",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE);
if(select == JOptionPane.CANCEL_OPTION)
return;
}
final String requester_text = event.getRequesterText ().trim ();
final String requester_text = minSize.getText().trim();
if (requester_text.length () == 0) {
if (requester_text.length () == 0)
return;
}
try {
try
{
final int minimum_orf_size =
Integer.valueOf (requester_text).intValue ();
markOpenReadingFrames (minimum_orf_size, empty_only);
} catch (NumberFormatException e) {
markOpenReadingFrames(minimum_orf_size, empty_only,
useFastaBoundary.isSelected());
}
catch (NumberFormatException e)
{
new MessageDialog(getParentFrame(),
"this is not a number: " + requester_text);
}
}
});
text_requester.setVisible (true);
}
/**
* Create a new Feature for each open reading frame.
......@@ -997,30 +1021,68 @@ public class AddMenu extends SelectionMenu
* segment will be marked.
**/
private void markOpenReadingFrames (final int minimum_orf_size,
final boolean empty_only) {
final boolean empty_only,
final boolean isMultiFasta) {
try {
final Entry new_entry =
entry_group.createEntry ("ORFS_" + minimum_orf_size + '+');
final int sequence_length = entry_group.getSequenceLength ();
if(isMultiFasta) // ensure ORF's do not cross fasta boundaries
{
final FeatureKeyPredicate predicate =
new FeatureKeyPredicate(new Key("fasta_record"));
final FeatureVector fasta_features = new FeatureVector ();
final FeatureEnumeration feature_enum = entry_group.features ();
while (feature_enum.hasMoreFeatures ())
{
final Feature current_feature = feature_enum.nextFeature ();
if (predicate.testPredicate (current_feature))
fasta_features.add (current_feature);
}
final Strand forward_strand =
entry_group.getBases ().getForwardStrand ();
for(int i=0;i<fasta_features.size();i++)
{
final int start = fasta_features.elementAt(i).getFirstBase();
final int last = fasta_features.elementAt(i).getLastBase();
final MarkerRange forward_range =
forward_strand.makeMarkerRangeFromPositions (1, sequence_length);
entry_group.getBases().getForwardStrand().
makeMarkerRangeFromPositions(start, last);
markOpenReadingFrames(new_entry, forward_range, minimum_orf_size,
empty_only);
final Strand backward_strand =
entry_group.getBases ().getReverseStrand ();
empty_only, last, start);
final MarkerRange backward_range =
backward_strand.makeMarkerRangeFromPositions (1, sequence_length);
entry_group.getBases().getReverseStrand().
makeMarkerRangeFromPositions(start, last);
markOpenReadingFrames(new_entry, backward_range, minimum_orf_size,
empty_only);
empty_only, last, start);
}
}
else
{
final int sequence_length = entry_group.getSequenceLength();
final Strand forward_strand = entry_group.getBases().getForwardStrand();
final MarkerRange forward_range = forward_strand
.makeMarkerRangeFromPositions(1, sequence_length);
markOpenReadingFrames(new_entry, forward_range, minimum_orf_size,
empty_only, sequence_length, 1);
final Strand backward_strand = entry_group.getBases()
.getReverseStrand();
final MarkerRange backward_range = backward_strand
.makeMarkerRangeFromPositions(1, sequence_length);
markOpenReadingFrames(new_entry, backward_range, minimum_orf_size,
empty_only, sequence_length, 1);
}
} catch (OutOfRangeException e) {
throw new Error ("internal error - unexpected OutOfRangeException");
}
......@@ -1065,7 +1127,7 @@ public class AddMenu extends SelectionMenu
getSelection ().getMarkerRange ();
markOpenReadingFrames (new_entry, selection_range, minimum_orf_size,
false);
false, entry_group.getSequenceLength(), 1);
} catch (NumberFormatException e) {
......@@ -1093,9 +1155,12 @@ public class AddMenu extends SelectionMenu
private void markOpenReadingFrames (final Entry entry,
final MarkerRange search_range,
final int minimum_orf_size,
final boolean empty_only) {
final boolean empty_only,
final int sequence_end,
final int sequence_start) {
final MarkerRange [] forward_orf_ranges =
Strand.getOpenReadingFrameRanges (search_range, minimum_orf_size);
Strand.getOpenReadingFrameRanges (search_range, minimum_orf_size, sequence_end,
sequence_start);
String uniquename = promptForUniquename(entry_group, search_range.isForwardMarker());
......
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