diff --git a/uk/ac/sanger/artemis/components/Navigator.java b/uk/ac/sanger/artemis/components/Navigator.java
index 7c8a0826465b7a2ab3e4b5119d54806be7b62bbc..22c1ab2c82207674905f1c04335ef2a4527e3a72 100644
--- a/uk/ac/sanger/artemis/components/Navigator.java
+++ b/uk/ac/sanger/artemis/components/Navigator.java
@@ -50,82 +50,90 @@ public class Navigator extends JFrame
private static final long serialVersionUID = 1L;
/** The JRadioButton that selects the goto base function. */
- final JRadioButton goto_base_button;
+ private final JRadioButton goto_base_button;
/** The JRadioButton that selects the goto base pattern function. */
- final JRadioButton goto_base_pattern_button;
+ private final JRadioButton goto_base_pattern_button =
+ new JRadioButton ("Find Base Pattern:", true);;
/** The JRadioButton that selects the find amino acid sequence function. */
- final JRadioButton goto_aa_pattern_button;
+ private final JRadioButton goto_aa_pattern_button =
+ new JRadioButton ("Find Amino Acid String:", true);;
/** The JRadioButton that selects the goto feature qualifier value function. */
- final JRadioButton goto_qualifier_button;
+ private final JRadioButton goto_qualifier_button;
/** The JRadioButton that selects the goto gene name function. */
- final JRadioButton goto_gene_name_button;
+ private final JRadioButton goto_gene_name_button;
/** The JRadioButton that selects the goto feature key function. */
- final JRadioButton goto_key_button;
+ private final JRadioButton goto_key_button;
/** This contains the pattern to search for if the user has selected the
goto base function. */
- final JTextField goto_base_text;
+ private final JTextField goto_base_text;
/** This contains the pattern to search for if the user has selected the
goto base pattern function. */
- final JTextField goto_base_pattern_text;
+ private final JTextField goto_base_pattern_text;
/** This contains the pattern to search for if the user has selected the
goto amino acid function. */
- final JTextField goto_aa_pattern_text;
+ private final JTextField goto_aa_pattern_text;
/** This contains the pattern to search for if the user has selected the
goto qualifier value function. */
- final JTextField goto_qualifier_textfield;
+ private final JTextField goto_qualifier_textfield;
/** This contains the pattern to search for if the user has selected the
goto gene name function. */
- final JTextField goto_gene_name_textfield;
+ private final JTextField goto_gene_name_textfield;
/** This contains the key to search for if the user has selected the
goto key function. */
- final JTextField goto_feature_key_textfield;
+ private final JTextField goto_feature_key_textfield;
/** The user selects this JRadioButton if the search should start at first/last
base or first/last feature (depending on the search type). */
- JRadioButton start_at_an_end_button;
+ private JRadioButton start_at_an_end_button;
/** The user selects this JRadioButton if the search should start at the
position of the current selection. */
- final JRadioButton start_at_selection_button;
+ private final JRadioButton start_at_selection_button;
/** If checked the search will go backwards. */
- final JCheckBox search_backward_button;
+ private final JCheckBox search_backward_button;
/** If checked the search will ignore the case of the query and subject. */
- final JCheckBox ignore_case_button;
+ private final JCheckBox ignore_case_button;
/** If checked the search text is allowed to match a substring of a
qualifier value. */
- final JCheckBox partial_match_button;
+ private final JCheckBox partial_match_button;
/** Check whether the match overlaps selected range */
- final JCheckBox overlaps_with_selection;
+ private final JCheckBox overlaps_with_selection;
+
+ /** Search fwd strand */
+ private final JCheckBox fwd_strand = new JCheckBox("Forward Strand ", true);;
+
+ /** Search bwd strand */
+ private final JCheckBox rev_strand = new JCheckBox("Reverse Strand", true);;
/**
* The GotoEventSource object that was passed to the constructor.
**/
- final GotoEventSource goto_event_source;
+ private final GotoEventSource goto_event_source;
/**
* The EntryGroup object that was passed to the constructor.
**/
- final EntryGroup entry_group;
+ private final EntryGroup entry_group;
/**
* This is the Selection that was passed to the constructor.
**/
- final private Selection selection;
+ private final Selection selection;
/**
* Create a new Navigator component.
@@ -262,8 +270,14 @@ public class Navigator extends JFrame
});
- goto_base_pattern_button =
- new JRadioButton ("Find Base Pattern:", true);
+ goto_base_pattern_button.addItemListener(new ItemListener() {
+ public void itemStateChanged(ItemEvent arg0) {
+ rev_strand.setEnabled(goto_aa_pattern_button.isSelected() ||
+ goto_base_pattern_button.isSelected());
+ fwd_strand.setEnabled(goto_aa_pattern_button.isSelected() ||
+ goto_base_pattern_button.isSelected());
+ }
+ });
button_group.add (goto_base_pattern_button);
final JPanel goto_base_pattern_panel = new JPanel (new FlowLayout (FlowLayout.LEFT));
@@ -286,8 +300,15 @@ public class Navigator extends JFrame
}
});
- goto_aa_pattern_button =
- new JRadioButton ("Find Amino Acid String:", true);
+
+ goto_aa_pattern_button.addItemListener(new ItemListener() {
+ public void itemStateChanged(ItemEvent arg0) {
+ rev_strand.setEnabled(goto_aa_pattern_button.isSelected() ||
+ goto_base_pattern_button.isSelected());
+ fwd_strand.setEnabled(goto_aa_pattern_button.isSelected() ||
+ goto_base_pattern_button.isSelected());
+ }
+ });
button_group.add (goto_aa_pattern_button);
final JPanel goto_aa_pattern_panel = new JPanel (new FlowLayout (FlowLayout.LEFT));
@@ -312,9 +333,7 @@ public class Navigator extends JFrame
goto_base_button.setSelected (true);
- final ButtonGroup start_position_button_group =
- new ButtonGroup ();
-
+ final ButtonGroup start_position_button_group = new ButtonGroup ();
final JPanel start_at_an_end_panel = new JPanel (new FlowLayout(FlowLayout.LEFT));
start_at_an_end_button =
@@ -350,7 +369,21 @@ public class Navigator extends JFrame
select_within_button_panel.add(overlaps_with_selection);
getContentPane ().add (select_within_button_panel, c);
+ //
+ // STRAND SELECTION
+ final JPanel strand_panel = new JPanel (new FlowLayout (FlowLayout.LEFT));
+ fwd_strand.setEnabled(goto_aa_pattern_button.isSelected() ||
+ goto_base_pattern_button.isSelected());
+ strand_panel.add(fwd_strand);
+
+ rev_strand.setEnabled(goto_aa_pattern_button.isSelected() ||
+ goto_base_pattern_button.isSelected());
+ strand_panel.add(rev_strand);
+ getContentPane ().add (strand_panel, c);
+
+ //
+ // OTHER OPTIONS
final JPanel option_button_panel = new JPanel (new FlowLayout (FlowLayout.LEFT));
search_backward_button = new JCheckBox ("Search Backward", false);
ignore_case_button = new JCheckBox ("Ignore Case", true);
@@ -364,7 +397,6 @@ public class Navigator extends JFrame
final JButton goto_button = new JButton ("Goto");
-
goto_button.addActionListener (new ActionListener () {
public void actionPerformed (ActionEvent e) {
doGoto ();
@@ -373,7 +405,6 @@ public class Navigator extends JFrame
final JButton clear_button = new JButton ("Clear");
-
clear_button.addActionListener (new ActionListener () {
public void actionPerformed (ActionEvent e) {
clear ();
@@ -382,7 +413,6 @@ public class Navigator extends JFrame
final JButton close_button = new JButton ("Close");
-
close_button.addActionListener (new ActionListener () {
public void actionPerformed (ActionEvent e) {
Navigator.this.dispose ();
@@ -390,10 +420,8 @@ public class Navigator extends JFrame
});
- final FlowLayout flow_layout =
- new FlowLayout (FlowLayout.CENTER, 15, 5);
-
- final JPanel close_and_goto_panel = new JPanel (flow_layout);
+ final JPanel close_and_goto_panel = new JPanel (
+ new FlowLayout (FlowLayout.CENTER, 15, 5));
close_and_goto_panel.add (goto_button);
close_and_goto_panel.add (clear_button);
@@ -413,11 +441,7 @@ public class Navigator extends JFrame
getEntryGroup ().addEntryGroupChangeListener (this);
pack ();
-
- final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- setLocation (new Point ((screen.width - getSize ().width) / 2,
- (screen.height - getSize ().height) / 2));
-
+ Utilities.centreFrame(this);
setVisible (true);
}
@@ -453,7 +477,9 @@ public class Navigator extends JFrame
final EntryGroup entry_group,
final Selection selection,
final boolean start_at_end,
- final boolean search_backwards) {
+ final boolean search_backwards,
+ final boolean search_fwd_strand,
+ final boolean search_bwd_strand) {
// if start_at_end is false we want to start the search at the selection
final Marker selection_base = selection.getLowestBaseOfSelection ();
@@ -470,7 +496,8 @@ public class Navigator extends JFrame
pattern.findMatch (entry_group.getBases (),
start_position,
entry_group.getSequenceLength (),
- search_backwards);
+ search_backwards,
+ search_fwd_strand, search_bwd_strand);
if (match_range == null) {
return null;
@@ -497,7 +524,9 @@ public class Navigator extends JFrame
final EntryGroup entry_group,
final Selection selection,
final boolean start_at_end,
- final boolean search_backwards) {
+ final boolean search_backwards,
+ final boolean search_fwd_strand,
+ final boolean search_bwd_strand) {
// if start_at_end is false we want to start the search at the selection
final Marker selection_base = selection.getLowestBaseOfSelection ();
@@ -510,19 +539,9 @@ public class Navigator extends JFrame
start_position = selection_base;
}
- final MarkerRange match_range;
-
- if (search_backwards) {
- match_range = sequence.findMatch (entry_group.getBases (),
- start_position,
- true);
- } else {
- match_range = sequence.findMatch (entry_group.getBases (),
- start_position,
- false);
- }
-
- return match_range;
+ return sequence.findMatch (entry_group.getBases (),
+ start_position, search_backwards,
+ search_fwd_strand, search_bwd_strand);
}
/**
@@ -530,17 +549,23 @@ public class Navigator extends JFrame
**/
private void doGoto () {
if (goto_base_button.isSelected ()) {
- doGotoBase ();
+ doGotoBase ();
return;
}
if (goto_base_pattern_button.isSelected ()) {
- doGotoBasePattern ();
+ if(!rev_strand.isSelected() && !fwd_strand.isSelected())
+ new MessageDialog (this, "Select a strand to search.");
+ else
+ doGotoBasePattern ();
return;
}
if (goto_aa_pattern_button.isSelected ()) {
- doGotoAAPattern ();
+ if(!rev_strand.isSelected() && !fwd_strand.isSelected())
+ new MessageDialog (this, "Select a strand to search.");
+ else
+ doGotoAAPattern ();
return;
}
@@ -633,11 +658,10 @@ public class Navigator extends JFrame
final boolean start_at_an_end = start_at_an_end_button.isSelected ();
final MarkerRange match_range =
- findBasePattern (pattern,
- getEntryGroup (),
- getSelection (),
- start_at_an_end,
- search_backward_button.isSelected ());
+ findBasePattern (pattern, getEntryGroup (),
+ getSelection (), start_at_an_end,
+ search_backward_button.isSelected (),
+ fwd_strand.isSelected(), rev_strand.isSelected());
if (match_range == null) {
new MessageDialog (this, "reached the end of sequence");
@@ -685,11 +709,10 @@ public class Navigator extends JFrame
final boolean search_backwards = search_backward_button.isSelected ();
final MarkerRange match_range =
- findAminoAcidSequence (pattern,
- getEntryGroup (),
- getSelection (),
- start_at_an_end,
- search_backwards);
+ findAminoAcidSequence (pattern, getEntryGroup (),
+ getSelection (), start_at_an_end,
+ search_backwards,
+ fwd_strand.isSelected(), rev_strand.isSelected());
if (match_range == null)
new MessageDialog (this, "reached the end of sequence");
diff --git a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
index 1d6d900567f205f96199a9c28d82efbf7a3b80c6..2b18c1ea1bb9f64310ac2fa6905e5b00d745a9ef 100644
--- a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
+++ b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
@@ -371,7 +371,9 @@ public class AminoAcidSequence
**/
public MarkerRange findMatch(final Bases bases,
final Marker search_start_marker,
- final boolean search_backwards)
+ final boolean search_backwards,
+ final boolean search_fwd_strand,
+ final boolean search_bwd_strand)
{
final String bases_string = bases.toString();
@@ -432,15 +434,21 @@ public class AminoAcidSequence
}
}
- final int forward_search_result =
- searchFor(bases_string,
- forward_search_start_index,
- search_backwards);
+ final int forward_search_result;
+ if(search_fwd_strand)
+ forward_search_result = searchFor(bases_string,
+ forward_search_start_index,
+ search_backwards);
+ else
+ forward_search_result = -1;
- final int complement_search_result =
- reverseComplementSearchFor(bases_string,
- complement_search_start_index,
- search_backwards);
+ final int complement_search_result;
+ if(search_bwd_strand)
+ complement_search_result = reverseComplementSearchFor(bases_string,
+ complement_search_start_index,
+ search_backwards);
+ else
+ complement_search_result = -1;
final int match_first_base;
final int match_last_base;
diff --git a/uk/ac/sanger/artemis/sequence/BasePattern.java b/uk/ac/sanger/artemis/sequence/BasePattern.java
index fe44fc669783576d1afba7238b7479ad4e423988..df8006fe08a6ac4cb3c6c3e6226c7ff705f5e61f 100644
--- a/uk/ac/sanger/artemis/sequence/BasePattern.java
+++ b/uk/ac/sanger/artemis/sequence/BasePattern.java
@@ -112,7 +112,9 @@ public class BasePattern {
public MarkerRange findMatch (final Bases bases,
final Marker search_start_marker,
final int search_end_position,
- final boolean search_backwards) {
+ final boolean search_backwards,
+ final boolean search_fwd_strand,
+ final boolean search_bwd_strand) {
final String bases_string = bases.toString ();
// search the bases_string forward for the pattern_string and its
@@ -157,17 +159,19 @@ public class BasePattern {
}
}
- final int forward_search_result =
- searchFor (bases_string,
- pattern_string,
- forward_search_start_index,
- search_backwards);
-
- final int complement_search_result =
- searchFor (bases_string,
- Bases.reverseComplement (pattern_string),
- complement_search_start_index,
- search_backwards);
+ final int forward_search_result;
+ if(search_fwd_strand)
+ forward_search_result = searchFor (bases_string, pattern_string,
+ forward_search_start_index, search_backwards);
+ else
+ forward_search_result = -1;
+
+ final int complement_search_result;
+ if(search_bwd_strand)
+ complement_search_result = searchFor (bases_string, Bases.reverseComplement (pattern_string),
+ complement_search_start_index, search_backwards);
+ else
+ complement_search_result = -1;
final int match_first_base;
final int match_last_base;
@@ -251,7 +255,7 @@ public class BasePattern {
while (true) {
final MarkerRange new_match_position =
- findMatch (bases, current_position_marker, search_end_position, false);
+ findMatch (bases, current_position_marker, search_end_position, false, true, true);
if (new_match_position == null) {
break;