diff --git a/uk/ac/sanger/artemis/components/Selector.java b/uk/ac/sanger/artemis/components/Selector.java
index e3f3f25668b6b23eb204900d34392eaa659c5623..75d373d55d9b3942f2b431a539faa4aeaa87c87a 100644
--- a/uk/ac/sanger/artemis/components/Selector.java
+++ b/uk/ac/sanger/artemis/components/Selector.java
@@ -4,12 +4,12 @@
*
* This file is part of Artemis
*
- * Copyright (C) 2000,2001,2002 Genome Research Limited
+ * 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.
+ * 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
@@ -20,15 +20,20 @@
* 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 1.6 2005-10-11 14:20:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/Selector.java,v 1.7 2006-04-25 15:12:57 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.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.*;
@@ -41,36 +46,75 @@ import javax.swing.*;
* features in an EntryGroup on key and contents.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: Selector.java,v 1.6 2005-10-11 14:20:31 tjc Exp $
+ * @version $Id: Selector.java,v 1.7 2006-04-25 15:12:57 tjc Exp $
**/
public class Selector extends JFrame
implements EntryGroupChangeListener {
+
+ 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 JCheckBox partial_match_checkbox;
+
+ /**
+ * The EntryGroup object that was passed to the constructor.
+ **/
+ final EntryGroup entry_group;
+
+ /**
+ * This is the Selection that was passed to the constructor.
+ **/
+ final private Selection selection;
+
/**
* 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 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,
+ public Selector(final Selection selection,
final GotoEventSource goto_event_source,
final EntryGroup entry_group,
- final BasePlotGroup base_plot_group) {
- super ("Artemis Feature Selector");
+ final BasePlotGroup base_plot_group)
+ {
+ super("Artemis Feature Selector");
this.selection = selection;
this.entry_group = entry_group;
- final Font default_font = Options.getOptions ().getFont ();
+ final Font default_font = Options.getOptions().getFont();
- setFont (default_font);
+ setFont(default_font);
GridBagLayout gridbag = new GridBagLayout();
- getContentPane ().setLayout (gridbag);
+ getContentPane().setLayout(gridbag);
GridBagConstraints c = new GridBagConstraints();
@@ -79,21 +123,21 @@ public class Selector extends JFrame
c.weighty = 0;
c.gridwidth = GridBagConstraints.REMAINDER;
- final JLabel top_label = new JLabel ("Select by:");
- gridbag.setConstraints (top_label, c);
- getContentPane ().add (top_label);
+ 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);
+ 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);
+ gridbag.setConstraints(by_key_panel, c);
+ getContentPane().add(by_key_panel);
// final EntryInformation default_entry_information =
-// Options.getArtemisEntryInformation ();
+// Options.getArtemisEntryInformation();
Entry default_entry = getEntryGroup().getDefaultEntry();
if(default_entry == null)
@@ -102,738 +146,852 @@ public class Selector extends JFrame
final EntryInformation default_entry_information =
default_entry.getEntryInformation();
- key_selector = new KeyChoice (default_entry_information);
+ key_selector = new KeyChoice(default_entry_information);
c.gridwidth = GridBagConstraints.REMAINDER;
- gridbag.setConstraints (key_selector, c);
- getContentPane ().add (key_selector);
+ gridbag.setConstraints(key_selector, c);
+ getContentPane().add(key_selector);
- key_selector.addItemListener (new ItemListener () {
- public void itemStateChanged (ItemEvent _) {
- by_key_button.setSelected (true);
+ 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_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);
+ 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);
+ gridbag.setConstraints(by_qualifier_panel, c);
+ getContentPane().add(by_qualifier_panel);
- qualifier_selector = new QualifierChoice (default_entry_information,
- key_selector.getSelectedItem (),
+ qualifier_selector = new QualifierChoice(default_entry_information,
+ key_selector.getSelectedItem(),
null);
c.gridwidth = GridBagConstraints.REMAINDER;
- gridbag.setConstraints (qualifier_selector, c);
- getContentPane ().add (qualifier_selector);
+ 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);
+ 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 ());
+ 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);
- }
+ 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: ");
+ new JLabel(" Containing this text: ");
c.gridwidth = 2;
- gridbag.setConstraints (qualifier_text_label, c);
- getContentPane ().add (qualifier_text_label);
+ gridbag.setConstraints(qualifier_text_label, c);
+ getContentPane().add(qualifier_text_label);
- qualifier_text = new JTextField ("", 18);
+ qualifier_text = new JTextField("", 18);
c.gridwidth = GridBagConstraints.REMAINDER;
- gridbag.setConstraints (qualifier_text, c);
- getContentPane ().add (qualifier_text);
+ gridbag.setConstraints(qualifier_text, c);
+ getContentPane().add(qualifier_text);
- ignore_case_checkbox = new JCheckBox ("Ignore Case", true);
+ ignore_case_checkbox = new JCheckBox("Ignore Case", true);
- final JPanel ignore_case_panel = new JPanel ();
+ final JPanel ignore_case_panel = new JPanel();
- ignore_case_panel.setLayout (new FlowLayout (FlowLayout.LEFT));
- ignore_case_panel.add (ignore_case_checkbox);
+ 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);
+ gridbag.setConstraints(ignore_case_panel, c);
+ getContentPane().add(ignore_case_panel);
- partial_match_checkbox = new JCheckBox ("Allow Partial Match", true);
+ partial_match_checkbox = new JCheckBox("Allow Partial Match", true);
- final JPanel partial_match_panel = new JPanel ();
+ final JPanel partial_match_panel = new JPanel();
- partial_match_panel.setLayout (new FlowLayout (FlowLayout.LEFT));
- partial_match_panel.add (partial_match_checkbox);
+ 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);
+ gridbag.setConstraints(partial_match_panel, c);
+ getContentPane().add(partial_match_panel);
- match_any_word_checkbox = new JCheckBox ("Match Any Word", false);
+ match_any_word_checkbox = new JCheckBox("Match Any Word", false);
- final JPanel match_any_word_panel = new JPanel ();
+ 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);
+ 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);
-
-
- {
- // leave a blank line to give the user a visual clue
- final JLabel blank_label = new JLabel ("");
+ gridbag.setConstraints(match_any_word_panel, c);
+ getContentPane().add(match_any_word_panel);
- gridbag.setConstraints (blank_label, c);
- getContentPane ().add (blank_label);
+ andSeparator(gridbag, c);
- final JLabel and_label = new JLabel ("And:");
-
- gridbag.setConstraints (and_label, c);
- getContentPane ().add (and_label);
- }
-
-
- 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);
+ 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);
+ gridbag.setConstraints(less_than_bases_panel, c);
+ getContentPane().add(less_than_bases_panel);
- less_than_bases_text = new JTextField ("", 18);
+ less_than_bases_text = new JTextField("", 18);
- gridbag.setConstraints (less_than_bases_text, c);
- getContentPane ().add (less_than_bases_text);
+ gridbag.setConstraints(less_than_bases_text, c);
+ getContentPane().add(less_than_bases_text);
- final JLabel less_than_bases_label = new JLabel (" bases long");
+ 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);
-
- {
- // leave a blank line to give the user a visual clue
- final JLabel blank_label = new JLabel ("");
+ gridbag.setConstraints(less_than_bases_label, c);
+ getContentPane().add(less_than_bases_label);
- gridbag.setConstraints (blank_label, c);
- getContentPane ().add (blank_label);
+ andSeparator(gridbag, c);
- final JLabel and_label = new JLabel ("And:");
-
- gridbag.setConstraints (and_label, c);
- getContentPane ().add (and_label);
- }
-
-
- 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);
+ 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);
+ gridbag.setConstraints(greater_than_bases_panel, c);
+ getContentPane().add(greater_than_bases_panel);
- greater_than_bases_text = new JTextField ("", 18);
+ greater_than_bases_text = new JTextField("", 18);
- gridbag.setConstraints (greater_than_bases_text, c);
- getContentPane ().add (greater_than_bases_text);
+ gridbag.setConstraints(greater_than_bases_text, c);
+ getContentPane().add(greater_than_bases_text);
- final JLabel greater_than_bases_label = new JLabel (" bases long");
+ 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);
-
- {
- // 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);
- }
-
- 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);
+ 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);
+ gridbag.setConstraints(less_than_exons_panel, c);
+ getContentPane().add(less_than_exons_panel);
- less_than_exons_text = new JTextField ("", 18);
+ less_than_exons_text = new JTextField("", 18);
- gridbag.setConstraints (less_than_exons_text, c);
- getContentPane ().add (less_than_exons_text);
+ gridbag.setConstraints(less_than_exons_text, c);
+ getContentPane().add(less_than_exons_text);
- final JLabel less_than_exons_label = new JLabel (" exons long");
+ 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);
-
- {
- // 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);
- }
+ 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);
+ 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);
+ gridbag.setConstraints(greater_than_exons_panel, c);
+ getContentPane().add(greater_than_exons_panel);
- greater_than_exons_text = new JTextField ("", 18);
+ 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");
+ 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);
-
+ 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 ("");
+ final JLabel blank_label = new JLabel("");
- gridbag.setConstraints (blank_label, c);
- getContentPane ().add (blank_label);
+ gridbag.setConstraints(blank_label, c);
+ getContentPane().add(blank_label);
- final JLabel and_label = new JLabel ("And by:");
+ final JLabel and_label = new JLabel("And by:");
- gridbag.setConstraints (and_label, c);
- getContentPane ().add (and_label);
+ 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);
+ 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);
+ gridbag.setConstraints(by_motif_panel, c);
+ getContentPane().add(by_motif_panel);
- motif_text = new JTextField ("", 18);
+ motif_text = new JTextField("", 18);
c.gridwidth = GridBagConstraints.REMAINDER;
- gridbag.setConstraints (motif_text, c);
- getContentPane ().add (motif_text);
+ 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 ("");
+ final JLabel blank_label = new JLabel("");
- gridbag.setConstraints (blank_label, c);
- getContentPane ().add (blank_label);
+ gridbag.setConstraints(blank_label, c);
+ getContentPane().add(blank_label);
}
- final JPanel strand_panel = new JPanel ();
+ final JPanel strand_panel = new JPanel();
- strand_panel.setLayout (new FlowLayout (FlowLayout.LEFT));
+ 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 ()) {
+ 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.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 ()) {
+ 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);
- }
+ forward_strand_checkbox.setSelected(true);
}
});
c.gridwidth = GridBagConstraints.REMAINDER;
- gridbag.setConstraints (strand_panel, c);
- getContentPane ().add (strand_panel);
+ gridbag.setConstraints(strand_panel, c);
+ getContentPane().add(strand_panel);
- final JButton select_button = new JButton ("Select");
+ final JButton select_button = new JButton("Select");
- select_button.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent e) {
- selection.set (getSelected ());
+ select_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ selection.set(getSelected());
}
});
- final JButton view_button = new JButton ("View");
+ final JButton view_button = new JButton("View");
- view_button.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent e) {
+ view_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
final FeaturePredicate predicate =
- new FeatureFromVectorPredicate (getSelected ());
+ 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(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 ()) {
+ if(forward_strand_checkbox.isSelected() &&
+ !reverse_strand_checkbox.isSelected())
title += " on the forward strand";
- }
- if (!forward_strand_checkbox.isSelected () &&
- reverse_strand_checkbox.isSelected ()) {
+ 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(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_bases_button.isSelected())
+ title += " at most " + less_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_bases_button.isSelected())
+ title += " at least " + greater_than_bases_text.getText().trim() +
+ " bases long";
- if (greater_than_exons_button.isSelected ()) {
- title +=
- " at least " + greater_than_exons_text.getText ().trim () +
- " exons 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);
+ new FilteredEntryGroup(entry_group, predicate, title);
final FeatureListFrame feature_list_frame =
- new FeatureListFrame (title,
- getSelection (),
- goto_event_source, filtered_entry_group,
- base_plot_group);
+ new FeatureListFrame(title,
+ getSelection(),
+ goto_event_source, filtered_entry_group,
+ base_plot_group);
- feature_list_frame.setVisible (true);
+ feature_list_frame.setVisible(true);
}
});
- final JButton close_button = new JButton ("Close");
+ final JButton close_button = new JButton("Close");
- close_button.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent e) {
- Selector.this.dispose ();
+ close_button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ Selector.this.dispose();
}
});
final FlowLayout flow_layout =
- new FlowLayout (FlowLayout.CENTER, 15, 5);
+ new FlowLayout(FlowLayout.CENTER, 15, 5);
- final JPanel bottom_button_panel = new JPanel (flow_layout);
+ 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);
+ 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);
+ 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 ();
+ addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent event)
+ {
+ getEntryGroup().removeEntryGroupChangeListener(Selector.this);
+ Selector.this.dispose();
}
});
- getEntryGroup ().addEntryGroupChangeListener (this);
-
- pack ();
+ getEntryGroup().addEntryGroupChangeListener(this);
+ pack();
final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- setLocation (new Point ((screen.width - getSize ().width) / 2,
- (screen.height - getSize ().height) / 2));
+ setLocation(new Point((screen.width - getSize().width) / 2,
+ (screen.height - getSize().height) / 2));
- setVisible (true);
+ 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
+ * 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;
+ 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 () {
+ 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 ();
+ 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 ();
+ (String) qualifier_selector.getSelectedItem();
- if (search_text.length () == 0) {
+ if(search_text.length() == 0)
+ {
key_and_qualifier_predicate =
- new FeatureKeyQualifierPredicate (key_selector.getSelectedItem (),
- qualifier_name,
- true);
- } else {
- if (match_any_word_checkbox.isSelected ()) {
+ new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
+ qualifier_name,
+ true);
+ }
+ else
+ {
+ if(match_any_word_checkbox.isSelected())
+ {
final FeaturePredicateVector temp_predicates =
- new FeaturePredicateVector ();
+ new FeaturePredicateVector();
final StringVector words =
- StringVector.getStrings (search_text, " ");
+ StringVector.getStrings(search_text, " ");
- for (int i = 0 ; i < words.size () ; ++i) {
- final String this_word = (String)words.elementAt (i);
+ 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 (),
- qualifier_name,
- this_word,
- partial_match_checkbox.isSelected (),
- ignore_case_checkbox.isSelected ());
+ new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
+ qualifier_name,
+ this_word,
+ partial_match_checkbox.isSelected(),
+ ignore_case_checkbox.isSelected());
- temp_predicates.add (new_predicate);
+ temp_predicates.add(new_predicate);
}
key_and_qualifier_predicate =
- new FeaturePredicateConjunction (temp_predicates,
- FeaturePredicateConjunction.OR);
- } else {
+ 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 ());
+ 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) {
+ }
+ 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 ()) {
+ new FeatureKeyPredicate(key_selector.getSelectedItem());
+ }
+ else
+ {
+ if(match_any_word_checkbox.isSelected())
+ {
final FeaturePredicateVector temp_predicates =
- new FeaturePredicateVector ();
+ new FeaturePredicateVector();
final StringVector words =
- StringVector.getStrings (search_text, " ");
+ StringVector.getStrings(search_text, " ");
- for (int i = 0 ; i < words.size () ; ++i) {
- final String this_word = (String)words.elementAt (i);
+ 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);
+ 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 {
+ 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 ());
+ new FeatureKeyQualifierPredicate(key_selector.getSelectedItem(),
+ null, // match any qialifier
+ search_text,
+ partial_match_checkbox.isSelected(),
+ ignore_case_checkbox.isSelected());
}
}
}
- } else {
+ }
+ else
key_and_qualifier_predicate = null;
- }
- if (by_motif_button.isSelected ()) {
+ if(by_motif_button.isSelected())
+ {
final AminoAcidSequence amino_acid_sequence =
- new AminoAcidSequence (motif_text.getText ().trim ());
+ new AminoAcidSequence(motif_text.getText().trim());
motif_predicate =
- new FeaturePatternPredicate (amino_acid_sequence);
- } else {
+ 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 {
+ 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 ();
+ 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) {
+ less_than_bases_predicate = new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature feature)
+ {
+ if(feature.getBaseCount() <= less_than_bases_int)
return true;
- } else {
+ else
return false;
- }
}
};
- } catch (NumberFormatException e) {
- new MessageDialog (this,
+ }
+ catch(NumberFormatException e)
+ {
+ new MessageDialog(this,
"warning this is not a number: " +
- less_than_bases_text.getText ());
+ less_than_bases_text.getText());
less_than_bases_predicate = null;
}
- } else {
- 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 {
+ 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 ();
+ 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) {
+ greater_than_bases_predicate = new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature feature)
+ {
+ if(feature.getBaseCount() >= greater_than_bases_int)
return true;
- } else {
+ else
return false;
- }
}
};
- } catch (NumberFormatException e) {
- new MessageDialog (this,
- "warning this is not a number: " +
- greater_than_bases_text.getText ());
+ }
+ catch(NumberFormatException e)
+ {
+ new MessageDialog(this,
+ "warning this is not a number: " +
+ greater_than_bases_text.getText());
greater_than_bases_predicate = null;
}
- } else {
- 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 {
+ 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 ();
+ 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) {
+ less_than_exons_predicate = new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature feature)
+ {
+ if(feature.getSegments().size() <= less_than_exons_int)
return true;
- } else {
+ else
return false;
- }
}
};
- } catch (NumberFormatException e) {
- new MessageDialog (this,
- "warning this is not a number: " +
- less_than_exons_text.getText ());
+ }
+ catch(NumberFormatException e)
+ {
+ new MessageDialog(this,
+ "warning this is not a number: " +
+ less_than_exons_text.getText());
less_than_exons_predicate = null;
}
- } else {
- 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 {
+ 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 ();
+ 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) {
+ greater_than_exons_predicate = new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature feature)
+ {
+ if(feature.getSegments().size() >= greater_than_exons_int)
return true;
- } else {
+ else
return false;
- }
}
};
- } catch (NumberFormatException e) {
- new MessageDialog (this,
- "warning this is not a number: " +
- greater_than_exons_text.getText ());
+ }
+ catch(NumberFormatException e)
+ {
+ new MessageDialog(this,
+ "warning this is not a number: " +
+ greater_than_exons_text.getText());
greater_than_exons_predicate = null;
}
- } else {
- greater_than_exons_predicate = null;
+ }
+
+
+ FeaturePredicate intron_pattern_predicate = null;
+ if(intron_pattern_button.isSelected())
+ {
+ intron_pattern_predicate = new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature feature)
+ {
+ if(feature.getSegments().size() < 2)
+ return false;
+
+ final Location location = feature.getLocation();
+ final RangeVector ranges = location.getRanges();
+ final Strand strand = feature.getStrand();
+ int pos1;
+ int pos2;
+ for(int i = 0; i < ranges.size () -1; ++i)
+ {
+ if(location.isComplement())
+ {
+ pos1 = ranges.size()-i-1;
+ pos2 = pos1-1;
+ }
+ else
+ {
+ pos1 = i;
+ pos2 = i+1;
+ }
+
+ final int end_of_range_1 =
+ ((Range)ranges.elementAt(pos1)).getEnd ();
+ final int start_of_range_2 =
+ ((Range)ranges.elementAt(pos2)).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())
+ bases = Bases.reverseComplement(strand.getRawSubSequenceC(feature_range));
+ else
+ bases = strand.getRawSubSequenceC(feature_range);
+
+ if(bases.length < 3)
+ return true;
+
+ if( bases[0] != 'g' ||
+ (bases[1] != 't' && bases[1] != 'c') ||
+ bases[bases.length-1] != 'g' ||
+ bases[bases.length-2] != 'a' )
+ {
+ return true;
+ }
+
+ }
+ catch(uk.ac.sanger.artemis.util.OutOfRangeException oore)
+ {
+ }
+ }
+
+ return false;
+ }
+ };
}
+
FeaturePredicate predicate = null;
-
- if (!by_key_button.isSelected () && !by_motif_button.isSelected ()) {
+ if(!by_key_button.isSelected() && !by_motif_button.isSelected())
+ {
// default to selecting all features
- predicate = new FeaturePredicate () {
- public boolean testPredicate (final Feature feature) {
+ predicate = new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature feature)
+ {
return true;
}
};
- } else {
- if (motif_predicate != null && key_and_qualifier_predicate != null) {
+ }
+ 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) {
+ new FeaturePredicateConjunction(key_and_qualifier_predicate,
+ motif_predicate,
+ FeaturePredicateConjunction.AND);
+ }
+ else
+ {
+ if(motif_predicate != null)
predicate = motif_predicate;
- } else {
+ else
predicate = key_and_qualifier_predicate;
- }
}
}
- if (less_than_bases_predicate != null) {
+ if(less_than_bases_predicate != null)
+ {
predicate =
- new FeaturePredicateConjunction (predicate,
- less_than_bases_predicate,
- FeaturePredicateConjunction.AND);
+ new FeaturePredicateConjunction(predicate,
+ less_than_bases_predicate,
+ FeaturePredicateConjunction.AND);
}
- if (greater_than_bases_predicate != null) {
+ if(greater_than_bases_predicate != null)
+ {
predicate =
- new FeaturePredicateConjunction (predicate,
+ new FeaturePredicateConjunction(predicate,
greater_than_bases_predicate,
FeaturePredicateConjunction.AND);
}
- if (less_than_exons_predicate != null) {
+ if(less_than_exons_predicate != null)
+ {
predicate =
- new FeaturePredicateConjunction (predicate,
- less_than_exons_predicate,
- FeaturePredicateConjunction.AND);
+ new FeaturePredicateConjunction(predicate,
+ less_than_exons_predicate,
+ FeaturePredicateConjunction.AND);
}
- if (greater_than_exons_predicate != null) {
+ if(greater_than_exons_predicate != null)
+ {
predicate =
- new FeaturePredicateConjunction (predicate,
- greater_than_exons_predicate,
- FeaturePredicateConjunction.AND);
+ new FeaturePredicateConjunction(predicate,
+ greater_than_exons_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(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();
- 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);
- }
+ 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);
}
}
}
@@ -844,50 +1002,17 @@ public class Selector extends JFrame
/**
* Return the Selection object that was passed to the constructor.
**/
- private Selection getSelection () {
+ private Selection getSelection()
+ {
return selection;
}
/**
* Return the EntryGroup object that was passed to the constructor.
**/
- private EntryGroup getEntryGroup () {
+ private EntryGroup getEntryGroup()
+ {
return entry_group;
}
- 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 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 JCheckBox partial_match_checkbox;
-
- /**
- * The EntryGroup object that was passed to the constructor.
- **/
- final EntryGroup entry_group;
-
- /**
- * This is the Selection that was passed to the constructor.
- **/
- final private Selection selection;
}