Selector.java 33.47 KiB
/* Selector.java
*
* created: Tue Apr 11 2000
*
* This file is part of Artemis
*
* Copyright(C) 2000,2001,2002 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/Selector.java,v 1.11 2008-01-17 16:00:31 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.AminoAcidSequence;
import uk.ac.sanger.artemis.sequence.Strand;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.GFFDocumentEntry;
import uk.ac.sanger.artemis.io.Location;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
import uk.ac.sanger.artemis.util.StringVector;
import java.awt.*;
import java.awt.event.*;
import java.util.Collections;
import java.util.Comparator;
import java.util.StringTokenizer;
import javax.swing.*;
/**
* This component allows the user to set the selection by filtering the
* features in an EntryGroup on key and contents.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
* @version $Id: Selector.java,v 1.11 2008-01-17 16:00:31 tjc Exp $
**/
public class Selector extends JFrame
implements EntryGroupChangeListener {
private static final long serialVersionUID = 1L;
private JCheckBox by_key_button;
private JCheckBox by_qualifier_button;
private JCheckBox by_motif_button;
private JCheckBox less_than_bases_button;
private JCheckBox greater_than_bases_button;
private JCheckBox less_than_exons_button;
private JCheckBox greater_than_exons_button;
private JCheckBox ignore_case_checkbox;
private JCheckBox match_any_word_checkbox;
private JCheckBox forward_strand_checkbox;
private JCheckBox reverse_strand_checkbox; private JCheckBox intron_pattern_button;
private KeyChoice key_selector;
private QualifierChoice qualifier_selector;
private JTextField qualifier_text;
private JTextField motif_text;
private JTextField less_than_bases_text;
private JTextField greater_than_bases_text;
private JTextField less_than_exons_text;
private JTextField greater_than_exons_text;
/**
* If checked the search text is allowed to match a substring of a
* qualifier value.
**/
final private JCheckBox partial_match_checkbox;
/**
* The EntryGroup object that was passed to the constructor.
**/
final private EntryGroup entry_group;
/**
* This is the Selection that was passed to the constructor.
**/
final private Selection selection;
public static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(Selector.class);
/**
* Create a new Selector that van set the given Selection.
* @param selection The Selection that the commands in the menu will
* operate on.
* @param entry_group The component will choose features from this
* EntryGroup.
* @param goto_event_source The object the we will call gotoBase() on.
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
public Selector(final Selection selection,
final GotoEventSource goto_event_source,
final EntryGroup entry_group,
final BasePlotGroup base_plot_group)
{
super("Artemis Feature Selector");
this.selection = selection;
this.entry_group = entry_group;
final Font default_font = Options.getOptions().getFont();
setFont(default_font);
GridBagLayout gridbag = new GridBagLayout();
getContentPane().setLayout(gridbag);
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
c.weighty = 0;
c.gridwidth = GridBagConstraints.REMAINDER;
final JLabel top_label = new JLabel("Select by:");
gridbag.setConstraints(top_label, c);
getContentPane().add(top_label);
by_key_button = new JCheckBox("Key: ", false);
final JPanel by_key_panel = new JPanel(); by_key_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
by_key_panel.add(by_key_button);
c.gridwidth = 2;
gridbag.setConstraints(by_key_panel, c);
getContentPane().add(by_key_panel);
// final EntryInformation default_entry_information =
// Options.getArtemisEntryInformation();
Entry default_entry = getEntryGroup().getDefaultEntry();
if(default_entry == null)
default_entry = getEntryGroup().elementAt(0);
final EntryInformation default_entry_information =
default_entry.getEntryInformation();
key_selector = new KeyChoice(default_entry_information);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(key_selector, c);
getContentPane().add(key_selector);
key_selector.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent _)
{
by_key_button.setSelected(true);
}
});
by_key_button.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
if(!by_key_button.isSelected())
by_qualifier_button.setSelected(false);
}
});
by_qualifier_button = new JCheckBox("Qualifier: ", false);
final JPanel by_qualifier_panel = new JPanel();
by_qualifier_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
by_qualifier_panel.add(by_qualifier_button);
c.gridwidth = 2;
gridbag.setConstraints(by_qualifier_panel, c);
getContentPane().add(by_qualifier_panel);
boolean isGFF = false;
if(getEntryGroup().getDefaultEntry() != null &&
getEntryGroup().getDefaultEntry().getEMBLEntry() instanceof GFFDocumentEntry)
isGFF = true;
qualifier_selector = new QualifierChoice(default_entry_information,
key_selector.getSelectedItem(),
null, isGFF);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(qualifier_selector, c);
getContentPane().add(qualifier_selector);
qualifier_selector.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent _)
{
by_qualifier_button.setSelected(true);
by_key_button.setSelected(true);
}
});
key_selector.addItemListener(new ItemListener() {
public void itemStateChanged(ItemEvent _)
{
qualifier_selector.setKey(key_selector.getSelectedItem());
}
});
by_qualifier_button.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
if(by_qualifier_button.isSelected())
{
if(!by_key_button.isSelected())
by_key_button.setSelected(true);
}
}
});
final JLabel qualifier_text_label =
new JLabel(" Containing this text: ");
c.gridwidth = 2;
gridbag.setConstraints(qualifier_text_label, c);
getContentPane().add(qualifier_text_label);
qualifier_text = new JTextField("", 18);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(qualifier_text, c);
getContentPane().add(qualifier_text);
ignore_case_checkbox = new JCheckBox("Ignore Case", true);
final JPanel ignore_case_panel = new JPanel();
ignore_case_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
ignore_case_panel.add(ignore_case_checkbox);
c.gridwidth = 2;
gridbag.setConstraints(ignore_case_panel, c);
getContentPane().add(ignore_case_panel);
partial_match_checkbox = new JCheckBox("Allow Partial Match", true);
final JPanel partial_match_panel = new JPanel();
partial_match_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
partial_match_panel.add(partial_match_checkbox);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(partial_match_panel, c);
getContentPane().add(partial_match_panel);
match_any_word_checkbox = new JCheckBox("Match Any Word", false);
final JPanel match_any_word_panel = new JPanel();
match_any_word_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
match_any_word_panel.add(match_any_word_checkbox);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(match_any_word_panel, c);
getContentPane().add(match_any_word_panel);
andSeparator(gridbag, c);
less_than_bases_button = new JCheckBox("Up to: ", false);
final JPanel less_than_bases_panel = new JPanel();
less_than_bases_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
less_than_bases_panel.add(less_than_bases_button);
c.gridwidth = 3;
gridbag.setConstraints(less_than_bases_panel, c);
getContentPane().add(less_than_bases_panel);
less_than_bases_text = new JTextField("", 18);
gridbag.setConstraints(less_than_bases_text, c);
getContentPane().add(less_than_bases_text);
final JLabel less_than_bases_label = new JLabel(" bases long");
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(less_than_bases_label, c);
getContentPane().add(less_than_bases_label);
andSeparator(gridbag, c);
greater_than_bases_button = new JCheckBox("At least: ", false);
final JPanel greater_than_bases_panel = new JPanel();
greater_than_bases_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
greater_than_bases_panel.add(greater_than_bases_button);
c.gridwidth = 2;
gridbag.setConstraints(greater_than_bases_panel, c);
getContentPane().add(greater_than_bases_panel);
greater_than_bases_text = new JTextField("", 18);
gridbag.setConstraints(greater_than_bases_text, c);
getContentPane().add(greater_than_bases_text);
final JLabel greater_than_bases_label = new JLabel(" bases long");
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(greater_than_bases_label, c);
getContentPane().add(greater_than_bases_label);
andSeparator(gridbag, c);
less_than_exons_button = new JCheckBox("Up to: ", false);
final JPanel less_than_exons_panel = new JPanel();
less_than_exons_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
less_than_exons_panel.add(less_than_exons_button);
c.gridwidth = 3;
gridbag.setConstraints(less_than_exons_panel, c);
getContentPane().add(less_than_exons_panel);
less_than_exons_text = new JTextField("", 18);
gridbag.setConstraints(less_than_exons_text, c);
getContentPane().add(less_than_exons_text);
final JLabel less_than_exons_label = new JLabel(" exons long");
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(less_than_exons_label, c);
getContentPane().add(less_than_exons_label);
andSeparator(gridbag, c);
greater_than_exons_button = new JCheckBox("At least: ", false);
final JPanel greater_than_exons_panel = new JPanel();
greater_than_exons_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
greater_than_exons_panel.add(greater_than_exons_button);
c.gridwidth = 2; gridbag.setConstraints(greater_than_exons_panel, c);
getContentPane().add(greater_than_exons_panel);
greater_than_exons_text = new JTextField("", 18);
gridbag.setConstraints(greater_than_exons_text, c);
getContentPane().add(greater_than_exons_text);
final JLabel greater_than_exons_label = new JLabel(" exons long");
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(greater_than_exons_label, c);
getContentPane().add(greater_than_exons_label);
andSeparator(gridbag, c);
intron_pattern_button = new JCheckBox("Contains introns without GT/GC start and AG end", false);
final JPanel intron_pattern_panel = new JPanel();
intron_pattern_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
intron_pattern_panel.add(intron_pattern_button);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(intron_pattern_panel, c);
getContentPane().add(intron_pattern_panel);
{
// leave a blank line to give the user a visual clue
final JLabel blank_label = new JLabel("");
gridbag.setConstraints(blank_label, c);
getContentPane().add(blank_label);
final JLabel and_label = new JLabel("And by:");
gridbag.setConstraints(and_label, c);
getContentPane().add(and_label);
}
by_motif_button = new JCheckBox("Amino acid motif: ", false);
final JPanel by_motif_panel = new JPanel();
by_motif_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
by_motif_panel.add(by_motif_button);
c.gridwidth = 2;
gridbag.setConstraints(by_motif_panel, c);
getContentPane().add(by_motif_panel);
motif_text = new JTextField("", 18);
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(motif_text, c);
getContentPane().add(motif_text);
{
// leave a blank line to give the user a visual clue
final JLabel blank_label = new JLabel("");
gridbag.setConstraints(blank_label, c);
getContentPane().add(blank_label);
}
final JPanel strand_panel = new JPanel();
strand_panel.setLayout(new FlowLayout(FlowLayout.LEFT));
forward_strand_checkbox = new JCheckBox("Forward Strand Features", true);
strand_panel.add(forward_strand_checkbox);
forward_strand_checkbox.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent _) {
if(!forward_strand_checkbox.isSelected() &&
!reverse_strand_checkbox.isSelected())
// make sure one of the strand is always selected
reverse_strand_checkbox.setSelected(true);
}
});
reverse_strand_checkbox = new JCheckBox("Reverse Strand Features", true);
strand_panel.add(reverse_strand_checkbox);
reverse_strand_checkbox.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent _)
{
if(!reverse_strand_checkbox.isSelected() &&
!forward_strand_checkbox.isSelected())
// make sure one of the strand is always selected
forward_strand_checkbox.setSelected(true);
}
});
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(strand_panel, c);
getContentPane().add(strand_panel);
final JButton select_button = new JButton("Select");
select_button.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
selection.set(getSelected());
}
});
final JButton view_button = new JButton("View");
view_button.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
final FeaturePredicate predicate =
new FeatureFromVectorPredicate(getSelected());
String title = "All features";
if(by_key_button.isSelected())
title += " with key \"" + key_selector.getSelectedItem() + "\"";
if(by_qualifier_button.isSelected())
{
if(qualifier_text.getText().trim().length() > 0)
title += " with qualifier \"" + qualifier_selector.getSelectedItem() +
"\" containing text \"" + qualifier_text.getText() + "\"";
else
title += " with qualifier \"" +
qualifier_selector.getSelectedItem() + "\"";
}
if(forward_strand_checkbox.isSelected() &&
!reverse_strand_checkbox.isSelected())
title += " on the forward strand";
if(!forward_strand_checkbox.isSelected() && reverse_strand_checkbox.isSelected())
title += " on the reverse strand";
if(by_motif_button.isSelected())
title += " with motif: " + motif_text.getText().trim().toUpperCase();
if(less_than_bases_button.isSelected())
title += " at most " + less_than_bases_text.getText().trim() +
" bases long";
if(greater_than_bases_button.isSelected())
title += " at least " + greater_than_bases_text.getText().trim() +
" bases long";
if(less_than_exons_button.isSelected())
title += " at most " + less_than_exons_text.getText().trim() +
" exons long";
if(greater_than_exons_button.isSelected())
title += " at least " + greater_than_exons_text.getText().trim() +
" exons long";
if(intron_pattern_button.isSelected())
title += " containing introns without GT/GC start and AG end";
final FilteredEntryGroup filtered_entry_group =
new FilteredEntryGroup(entry_group, predicate, title);
final FeatureListFrame feature_list_frame =
new FeatureListFrame(title,
getSelection(),
goto_event_source, filtered_entry_group,
base_plot_group);
feature_list_frame.setVisible(true);
}
});
final JButton close_button = new JButton("Close");
close_button.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
Selector.this.dispose();
}
});
final FlowLayout flow_layout =
new FlowLayout(FlowLayout.CENTER, 15, 5);
final JPanel bottom_button_panel = new JPanel(flow_layout);
bottom_button_panel.add(select_button);
bottom_button_panel.add(view_button);
bottom_button_panel.add(close_button);
gridbag.setConstraints(bottom_button_panel, c);
getContentPane().add(bottom_button_panel);
addWindowListener(new WindowAdapter()
{
public void windowClosing(WindowEvent event)
{
getEntryGroup().removeEntryGroupChangeListener(Selector.this);
Selector.this.dispose();
} });
getEntryGroup().addEntryGroupChangeListener(this);
pack();
final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
setLocation(new Point((screen.width - getSize().width) / 2,
(screen.height - getSize().height) / 2));
setVisible(true);
}
private void andSeparator(GridBagLayout gridbag,
GridBagConstraints c)
{
// leave a blank line to give the user a visual clue
final JLabel blank_label = new JLabel("");
gridbag.setConstraints(blank_label, c);
getContentPane().add(blank_label);
final JLabel and_label = new JLabel("And:");
gridbag.setConstraints(and_label, c);
getContentPane().add(and_label);
}
/**
* Implementation of the EntryGroupChangeListener interface. We listen to
* EntryGroupChange events so that we can get rid of the Navigator when the
* EntryGroup is no longer in use(for example when the EntryEdit is
* closed).
**/
public void entryGroupChanged(final EntryGroupChangeEvent event)
{
switch(event.getType())
{
case EntryGroupChangeEvent.DONE_GONE:
getEntryGroup().removeEntryGroupChangeListener(this);
dispose();
break;
}
}
/**
* Return those features that match the current setting of the Selector.
**/
private FeatureVector getSelected()
{
final FeaturePredicate key_and_qualifier_predicate;
final FeaturePredicate motif_predicate;
if(by_key_button.isSelected())
{
if(by_qualifier_button.isSelected())
{
final String search_text = qualifier_text.getText().trim();
final String qualifier_name =
(String) qualifier_selector.getSelectedItem();
if(search_text.length() == 0)
{
key_and_qualifier_predicate =
new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
qualifier_name,
true);
}
else
{
if(match_any_word_checkbox.isSelected()) {
final FeaturePredicateVector temp_predicates =
new FeaturePredicateVector();
//final StringVector words =
// StringVector.getStrings(search_text, " ");
final StringTokenizer tok = new StringTokenizer(search_text, " \n");
while(tok.hasMoreTokens())
{
final String this_word = tok.nextToken().trim();
final FeaturePredicate new_predicate =
new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
qualifier_name,
this_word,
partial_match_checkbox.isSelected(),
ignore_case_checkbox.isSelected());
temp_predicates.add(new_predicate);
}
key_and_qualifier_predicate =
new FeaturePredicateConjunction(temp_predicates,
FeaturePredicateConjunction.OR);
}
else
{
key_and_qualifier_predicate =
new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
qualifier_name,
search_text,
partial_match_checkbox.isSelected(),
ignore_case_checkbox.isSelected());
}
}
}
else
{
final String search_text = qualifier_text.getText().trim();
if(search_text.length() == 0)
{
key_and_qualifier_predicate =
new FeatureKeyPredicate(key_selector.getSelectedItem());
}
else
{
if(match_any_word_checkbox.isSelected())
{
final FeaturePredicateVector temp_predicates =
new FeaturePredicateVector();
final StringVector words =
StringVector.getStrings(search_text, " ");
for(int i = 0 ; i < words.size() ; ++i)
{
final String this_word =(String)words.elementAt(i);
final FeaturePredicate new_predicate =
new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
null, // match any qialifier
this_word,
partial_match_checkbox.isSelected(),
ignore_case_checkbox.isSelected());
temp_predicates.add(new_predicate);
}
key_and_qualifier_predicate = new FeaturePredicateConjunction(temp_predicates,
FeaturePredicateConjunction.OR);
}
else
{
key_and_qualifier_predicate =
new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
null, // match any qialifier
search_text,
partial_match_checkbox.isSelected(),
ignore_case_checkbox.isSelected());
}
}
}
}
else
key_and_qualifier_predicate = null;
if(by_motif_button.isSelected())
{
final AminoAcidSequence amino_acid_sequence =
new AminoAcidSequence(motif_text.getText().trim());
motif_predicate =
new FeaturePatternPredicate(amino_acid_sequence);
}
else
motif_predicate = null;
FeaturePredicate less_than_bases_predicate = null;
if(less_than_bases_button.isSelected() &&
less_than_bases_text.getText().trim().length() > 0)
{
try
{
final int less_than_bases_int =
Integer.valueOf(less_than_bases_text.getText().trim()).intValue();
less_than_bases_predicate = new FeaturePredicate()
{
public boolean testPredicate(final Feature feature)
{
if(feature.getBaseCount() <= less_than_bases_int)
return true;
else
return false;
}
};
}
catch(NumberFormatException e)
{
new MessageDialog(this,
"warning this is not a number: " +
less_than_bases_text.getText());
less_than_bases_predicate = null;
}
}
FeaturePredicate greater_than_bases_predicate = null;
if(greater_than_bases_button.isSelected() &&
greater_than_bases_text.getText().trim().length() > 0)
{
try
{
final int greater_than_bases_int =
Integer.valueOf(greater_than_bases_text.getText().trim()).intValue();
greater_than_bases_predicate = new FeaturePredicate() {
public boolean testPredicate(final Feature feature)
{
if(feature.getBaseCount() >= greater_than_bases_int)
return true;
else
return false;
}
};
}
catch(NumberFormatException e)
{
new MessageDialog(this,
"warning this is not a number: " +
greater_than_bases_text.getText());
greater_than_bases_predicate = null;
}
}
FeaturePredicate less_than_exons_predicate = null;
if(less_than_exons_button.isSelected() &&
less_than_exons_text.getText().trim().length() > 0)
{
try
{
final int less_than_exons_int =
Integer.valueOf(less_than_exons_text.getText().trim()).intValue();
less_than_exons_predicate = new FeaturePredicate()
{
public boolean testPredicate(final Feature feature)
{
if(feature.getSegments().size() <= less_than_exons_int)
return true;
else
return false;
}
};
}
catch(NumberFormatException e)
{
new MessageDialog(this,
"warning this is not a number: " +
less_than_exons_text.getText());
less_than_exons_predicate = null;
}
}
FeaturePredicate greater_than_exons_predicate = null;
if(greater_than_exons_button.isSelected() &&
greater_than_exons_text.getText().trim().length() > 0)
{
try
{
final int greater_than_exons_int =
Integer.valueOf(greater_than_exons_text.getText().trim()).intValue();
greater_than_exons_predicate = new FeaturePredicate()
{
public boolean testPredicate(final Feature feature)
{
if(feature.getSegments().size() >= greater_than_exons_int)
return true;
else
return false;
}
}; }
catch(NumberFormatException e)
{
new MessageDialog(this,
"warning this is not a number: " +
greater_than_exons_text.getText());
greater_than_exons_predicate = null;
}
}
FeaturePredicate intron_pattern_predicate = null;
if(intron_pattern_button.isSelected())
intron_pattern_predicate = getIntronPredicate();
FeaturePredicate predicate = null;
if(!by_key_button.isSelected() && !by_motif_button.isSelected())
{
// default to selecting all features
predicate = new FeaturePredicate()
{
public boolean testPredicate(final Feature feature)
{
return true;
}
};
}
else
{
if(motif_predicate != null && key_and_qualifier_predicate != null)
{
predicate =
new FeaturePredicateConjunction(key_and_qualifier_predicate,
motif_predicate,
FeaturePredicateConjunction.AND);
}
else
{
if(motif_predicate != null)
predicate = motif_predicate;
else
predicate = key_and_qualifier_predicate;
}
}
if(less_than_bases_predicate != null)
{
predicate =
new FeaturePredicateConjunction(predicate,
less_than_bases_predicate,
FeaturePredicateConjunction.AND);
}
if(greater_than_bases_predicate != null)
{
predicate =
new FeaturePredicateConjunction(predicate,
greater_than_bases_predicate,
FeaturePredicateConjunction.AND);
}
if(less_than_exons_predicate != null)
{
predicate =
new FeaturePredicateConjunction(predicate,
less_than_exons_predicate,
FeaturePredicateConjunction.AND);
}
if(greater_than_exons_predicate != null) {
predicate =
new FeaturePredicateConjunction(predicate,
greater_than_exons_predicate,
FeaturePredicateConjunction.AND);
}
if(intron_pattern_predicate !=null)
{
predicate =
new FeaturePredicateConjunction(predicate,
intron_pattern_predicate,
FeaturePredicateConjunction.AND);
}
final FeatureEnumeration test_enumerator = entry_group.features();
final FeatureVector return_features = new FeatureVector();
while(test_enumerator.hasMoreFeatures())
{
final Feature this_feature = test_enumerator.nextFeature();
if(predicate.testPredicate(this_feature))
{
if(this_feature.isForwardFeature())
{
if(forward_strand_checkbox.isSelected())
return_features.add(this_feature);
}
else
{
if(reverse_strand_checkbox.isSelected())
return_features.add(this_feature);
}
}
}
return return_features;
}
protected static FeaturePredicate getIntronPredicate()
{
return new FeaturePredicate()
{
public boolean testPredicate(final Feature feature)
{
if(feature.getSegments().size() < 2)
return false;
final Location location = feature.getLocation().copy();
final RangeVector ranges = location.getRanges();
Collections.sort(ranges, new Comparator<Range>(){
public int compare(final Range r1, final Range r2)
{
return r1.getStart()-r2.getStart();
}
});
final Strand strand = feature.getStrand();
for(int i = 0; i < ranges.size () -1; ++i)
{
final int end_of_range_1 =
((Range)ranges.elementAt(i)).getEnd ();
final int start_of_range_2 =
((Range)ranges.elementAt(i+1)).getStart ();
// ignore - the exons overlap so there is no room for an intron
if(end_of_range_1 > start_of_range_2)
continue;
try
{
Range feature_range = new Range(end_of_range_1 + 1,
start_of_range_2 - 1);
final char bases[];
if(location.isComplement())
{
final char tmp_bases[] = strand.getRawSubSequenceC(feature_range);
final char tmp2_bases[] = new char[feature_range.getCount()];
for(int j=0; j<tmp2_bases.length; j++)
tmp2_bases[j] = tmp_bases[j];
bases = Bases.reverseComplement( tmp2_bases );
}
else
bases = strand.getRawSubSequenceC(feature_range);
if(bases.length < 3)
return true;
int length = feature_range.getCount();
if( bases[0] != 'g' ||
(bases[1] != 't' && bases[1] != 'c') ||
bases[length-1] != 'g' ||
bases[length-2] != 'a' )
{
if(bases[length-1] != 'g' || bases[length-2] != 'a')
if(location.isComplement())
logger4j.info("INTRON SPLICE SITE MISSING AG: "+end_of_range_1);
else
logger4j.info("INTRON SPLICE SITE MISSING AG: "+start_of_range_2);
else
if(location.isComplement())
logger4j.info("INTRON SPLICE SITE MISSING GT/GC: "+start_of_range_2);
else
logger4j.info("INTRON SPLICE SITE MISSING GT/GC: "+end_of_range_1);
return true;
}
}
catch(uk.ac.sanger.artemis.util.OutOfRangeException oore)
{
}
}
return false;
}
};
}
/**
* Return the Selection object that was passed to the constructor.
**/
private Selection getSelection()
{
return selection;
}
/**
* Return the EntryGroup object that was passed to the constructor.
**/
private EntryGroup getEntryGroup()
{
return entry_group;
}
}