diff --git a/uk/ac/sanger/artemis/components/ViewMenu.java b/uk/ac/sanger/artemis/components/ViewMenu.java
index 4b04a62f2112f33ed64ec21caf1f5ee6307d639f..75c2dd81f549b3a94bb6514ce41251961634bab3 100644
--- a/uk/ac/sanger/artemis/components/ViewMenu.java
+++ b/uk/ac/sanger/artemis/components/ViewMenu.java
@@ -20,7 +20,7 @@
* 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/ViewMenu.java,v 1.2 2004-12-14 15:53:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ViewMenu.java,v 1.3 2004-12-17 16:44:48 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import javax.swing.*;
* A popup menu with viewing commands.
*
* @author Kim Rutherford
- * @version $Id: ViewMenu.java,v 1.2 2004-12-14 15:53:11 tjc Exp $
+ * @version $Id: ViewMenu.java,v 1.3 2004-12-17 16:44:48 tjc Exp $
**/
public class ViewMenu extends SelectionMenu {
@@ -56,19 +56,20 @@ public class ViewMenu extends SelectionMenu {
* operate on.
* @param entry_group The EntryGroup object where new features/entries will
* be added.
- * @param goto_event_source The object that we will call makeBaseVisible ()
+ * @param goto_event_source The object that we will call makeBaseVisible()
* on.
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
* @param menu_name The name of the new menu.
**/
- public ViewMenu (final JFrame frame,
- final Selection selection,
- final GotoEventSource goto_event_source,
- final EntryGroup entry_group,
- final BasePlotGroup base_plot_group,
- final String menu_name) {
- super (frame, menu_name, selection);
+ public ViewMenu(final JFrame frame,
+ final Selection selection,
+ final GotoEventSource goto_event_source,
+ final EntryGroup entry_group,
+ final BasePlotGroup base_plot_group,
+ final String menu_name)
+ {
+ super(frame, menu_name, selection);
this.entry_group = entry_group;
this.selection = selection;
@@ -76,317 +77,352 @@ public class ViewMenu extends SelectionMenu {
this.base_plot_group = base_plot_group;
- plot_features_item = new JMenuItem ("Show Feature Plots");
- plot_features_item.setAccelerator (PLOT_FEATURES_KEY);
- plot_features_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- plotSelectedFeatures (getParentFrame (), getSelection ());
+ final JMenuItem plot_features_item = new JMenuItem("Show Feature Plots");
+ plot_features_item.setAccelerator(PLOT_FEATURES_KEY);
+ plot_features_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ plotSelectedFeatures(getParentFrame(), getSelection());
}
});
- view_feature_item = new JMenuItem ("View Selected Features");
- view_feature_item.setAccelerator (VIEW_FEATURES_KEY);
- view_feature_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewSelectedFeatures (getParentFrame (), getSelection ());
+ final JMenuItem view_feature_item = new JMenuItem("View Selected Features");
+ view_feature_item.setAccelerator(VIEW_FEATURES_KEY);
+ view_feature_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedFeatures(getParentFrame(), getSelection());
}
});
- view_selection_item = new JMenuItem ("View Selection");
- view_selection_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- new SelectionViewer (getSelection (), entry_group);
+ final JMenuItem view_selection_item = new JMenuItem("View Selection");
+ view_selection_item.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent event) {
+ new SelectionViewer(getSelection(), entry_group);
}
});
- feature_info_item = new JMenuItem ("Show Feature Statistics");
- feature_info_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewSelectedFeatureInfo ();
+ final JMenuItem feature_info_item = new JMenuItem("Show Feature Statistics");
+ feature_info_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedFeatureInfo();
}
});
- view_bases_item = new JMenuItem ("View Bases Of Selection");
- view_bases_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewSelectedBases (true);
+ final JMenuItem view_bases_item = new JMenuItem("View Bases Of Selection");
+ view_bases_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedBases(true);
}
});
- view_bases_as_fasta_item =
- new JMenuItem ("View Bases Of Selection As FASTA");
- view_bases_as_fasta_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewSelectedBases (false);
+ final JMenuItem view_bases_as_fasta_item =
+ new JMenuItem("View Bases Of Selection As FASTA");
+ view_bases_as_fasta_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedBases(false);
}
});
- view_aa_item = new JMenuItem ("View Amino Acids Of Selection");
- view_aa_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewSelectedAminoAcids (true);
+ final JMenuItem view_aa_item = new JMenuItem("View Amino Acids Of Selection");
+ view_aa_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedAminoAcids(true);
}
});
- view_aa_as_fasta_item =
- new JMenuItem ("View Amino Acids Of Selection As FASTA");
- view_aa_as_fasta_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewSelectedAminoAcids (false);
+ final JMenuItem view_aa_as_fasta_item =
+ new JMenuItem("View Amino Acids Of Selection As FASTA");
+ view_aa_as_fasta_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedAminoAcids(false);
}
});
- overview_item = new JMenuItem ("Show Overview");
- overview_item.setAccelerator (OVERVIEW_KEY);
- overview_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- new EntryGroupInfoDisplay (getParentFrame (), entry_group);
+ final JMenuItem overview_item = new JMenuItem("Show Overview");
+ overview_item.setAccelerator(OVERVIEW_KEY);
+ overview_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ new EntryGroupInfoDisplay(getParentFrame(), entry_group);
}
});
- forward_overview_item = new JMenuItem ("Show Forward Strand Overview");
- forward_overview_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- new EntryGroupInfoDisplay (getParentFrame (), entry_group,
- Bases.FORWARD);
+ final JMenuItem forward_overview_item = new JMenuItem("Show Forward Strand Overview");
+ forward_overview_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ new EntryGroupInfoDisplay(getParentFrame(), entry_group,
+ Bases.FORWARD);
}
});
- reverse_overview_item = new JMenuItem ("Show Reverse Strand Overview");
- reverse_overview_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- new EntryGroupInfoDisplay (getParentFrame (), entry_group,
- Bases.REVERSE);
+ final JMenuItem reverse_overview_item = new JMenuItem("Show Reverse Strand Overview");
+ reverse_overview_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ new EntryGroupInfoDisplay(getParentFrame(), entry_group,
+ Bases.REVERSE);
}
});
- view_cds_item = new JMenuItem ("Show CDS Genes And Products");
- view_cds_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
+ final JMenuItem view_cds_item = new JMenuItem("Show CDS Genes And Products");
+ view_cds_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
final FeaturePredicate feature_predicate =
- new FeatureKeyPredicate (Key.CDS);
+ new FeatureKeyPredicate(Key.CDS);
final String filter_name =
"CDS features (filtered from: " +
- getParentFrame ().getTitle () + ")";
+ getParentFrame().getTitle() + ")";
final FilteredEntryGroup filtered_entry_group =
- new FilteredEntryGroup (entry_group, feature_predicate, filter_name);
+ new FilteredEntryGroup(entry_group, feature_predicate, filter_name);
final FeatureListFrame feature_list_frame =
- new FeatureListFrame (filter_name,
+ new FeatureListFrame(filter_name,
selection, goto_event_source,
filtered_entry_group,
base_plot_group);
- feature_list_frame.getFeatureList ().setShowGenes (true);
- feature_list_frame.getFeatureList ().setShowProducts (true);
+ feature_list_frame.getFeatureList().setShowGenes(true);
+ feature_list_frame.getFeatureList().setShowProducts(true);
- feature_list_frame.setVisible (true);
+ feature_list_frame.setVisible(true);
}
});
JMenu search_results_menu = null;
- search_results_menu = new JMenu ("Search Results");
+ search_results_menu = new JMenu("Search Results");
final boolean sanger_options =
- Options.getOptions ().getPropertyTruthValue ("sanger_options");
+ Options.getOptions().getPropertyTruthValue("sanger_options");
final ExternalProgramVector external_programs =
- Options.getOptions ().getExternalPrograms ();
+ Options.getOptions().getExternalPrograms();
- final StringVector external_program_names = new StringVector ();
+ final StringVector external_program_names = new StringVector();
- for (int i = 0 ; i < external_programs.size () ; ++i) {
+ for(int i = 0 ; i < external_programs.size() ; ++i)
+ {
final ExternalProgram external_program =
- external_programs.elementAt (i);
+ external_programs.elementAt(i);
- final String new_name = external_program.getName ();
+ final String new_name = external_program.getName();
- if (!external_program_names.contains (new_name)) {
- external_program_names.add (new_name);
- }
+ if(!external_program_names.contains(new_name))
+ external_program_names.add(new_name);
}
- for (int i = 0 ; i < external_program_names.size () ; ++i) {
+ for(int i = 0 ; i < external_program_names.size() ; ++i)
+ {
final String external_program_name =
- external_program_names.elementAt (i);
+ external_program_names.elementAt(i);
final JMenuItem new_menu =
- makeSearchResultsMenu (external_program_name, false, sanger_options);
- search_results_menu.add (new_menu);
+ makeSearchResultsMenu(external_program_name, false, sanger_options);
+ search_results_menu.add(new_menu);
}
- if (sanger_options) {
- search_results_menu.addSeparator ();
+ if(sanger_options)
+ {
+ search_results_menu.addSeparator();
- for (int i = 0 ; i < external_program_names.size () ; ++i) {
+ for(int i = 0 ; i < external_program_names.size() ; ++i)
+ {
final String external_program_name =
- external_program_names.elementAt (i);
+ external_program_names.elementAt(i);
final JMenuItem new_menu =
- makeSearchResultsMenu (external_program_name, true, sanger_options);
- search_results_menu.add (new_menu);
+ makeSearchResultsMenu(external_program_name, true, sanger_options);
+ search_results_menu.add(new_menu);
}
}
final int MAX_FILTER_FEATURE_COUNT = 10000;
- final JMenu feature_filters_menu = new JMenu ("Feature Filters");
+ final JMenu feature_filters_menu = new JMenu("Feature Filters");
final JMenuItem bad_start_codons_item =
- new JMenuItem ("Suspicious Start Codons ...");
- bad_start_codons_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showBadStartCodons (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Suspicious Start Codons ...");
+ bad_start_codons_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showBadStartCodons(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem bad_stop_codons_item =
- new JMenuItem ("Suspicious Stop Codons ...");
- bad_stop_codons_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showBadStopCodons (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Suspicious Stop Codons ...");
+ bad_stop_codons_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showBadStopCodons(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem stop_codons_in_translation =
- new JMenuItem ("Stop Codons In Translation ...");
- stop_codons_in_translation.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showStopsInTranslation (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Stop Codons In Translation ...");
+ stop_codons_in_translation.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showStopsInTranslation(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem bad_feature_keys_item =
- new JMenuItem ("Non EMBL Keys ...");
- bad_feature_keys_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showNonEMBLKeys (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Non EMBL Keys ...");
+ bad_feature_keys_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showNonEMBLKeys(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem duplicated_keys_item =
- new JMenuItem ("Duplicated Features ...");
- duplicated_keys_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showDuplicatedFeatures (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Duplicated Features ...");
+ duplicated_keys_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showDuplicatedFeatures(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem overlapping_cds_features_item =
- new JMenuItem ("Overlapping CDS Features ...");
- overlapping_cds_features_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showOverlappingCDSs (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Overlapping CDS Features ...");
+ overlapping_cds_features_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showOverlappingCDSs(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem same_stop_cds_features_item =
- new JMenuItem ("CDSs Sharing Stop Codons ...");
- same_stop_cds_features_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showFeaturesWithSameStopCodons (getParentFrame (),
- selection, entry_group,
- goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("CDSs Sharing Stop Codons ...");
+ same_stop_cds_features_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showFeaturesWithSameStopCodons(getParentFrame(),
+ selection, entry_group,
+ goto_event_source,
+ base_plot_group);
}
});
final JMenuItem missing_qualifier_features_item =
- new JMenuItem ("Features Missing Required Qualifiers ...");
- missing_qualifier_features_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showMissingQualifierFeatures (getParentFrame (),
- selection,
- entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Features Missing Required Qualifiers ...");
+ missing_qualifier_features_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showMissingQualifierFeatures(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem filter_by_key_item =
- new JMenuItem ("Filter By Key ...");
- filter_by_key_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- if (checkEntryGroupSize (MAX_FILTER_FEATURE_COUNT)) {
- showFilterByKey (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
- }
+ new JMenuItem("Filter By Key ...");
+ filter_by_key_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ if(checkEntryGroupSize(MAX_FILTER_FEATURE_COUNT))
+ showFilterByKey(getParentFrame(), selection,
+ entry_group, goto_event_source,
+ base_plot_group);
}
});
final JMenuItem filter_by_selection_item =
- new JMenuItem ("Selected Features ...");
- filter_by_selection_item.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- showFilterBySelection (getParentFrame (),
- selection, entry_group, goto_event_source,
- base_plot_group);
+ new JMenuItem("Selected Features ...");
+ filter_by_selection_item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ showFilterBySelection(getParentFrame(),
+ selection, entry_group, goto_event_source,
+ base_plot_group);
}
});
- feature_filters_menu.add (bad_start_codons_item);
- feature_filters_menu.add (bad_stop_codons_item);
- feature_filters_menu.add (stop_codons_in_translation);
- feature_filters_menu.add (bad_feature_keys_item);
- feature_filters_menu.add (duplicated_keys_item);
- feature_filters_menu.add (overlapping_cds_features_item);
- feature_filters_menu.add (same_stop_cds_features_item);
- feature_filters_menu.add (missing_qualifier_features_item);
- feature_filters_menu.addSeparator ();
- feature_filters_menu.add (filter_by_key_item);
- feature_filters_menu.add (filter_by_selection_item);
-
- add (view_feature_item);
- add (view_selection_item);
- addSeparator ();
- if (search_results_menu != null) {
- add (search_results_menu);
- }
- add (view_cds_item);
- add (feature_filters_menu);
- addSeparator ();
- add (overview_item);
- add (forward_overview_item);
- add (reverse_overview_item);
- addSeparator ();
- add (view_bases_item);
- add (view_bases_as_fasta_item);
- add (view_aa_item);
- add (view_aa_as_fasta_item);
- addSeparator ();
- add (feature_info_item);
- add (plot_features_item);
+ feature_filters_menu.add(bad_start_codons_item);
+ feature_filters_menu.add(bad_stop_codons_item);
+ feature_filters_menu.add(stop_codons_in_translation);
+ feature_filters_menu.add(bad_feature_keys_item);
+ feature_filters_menu.add(duplicated_keys_item);
+ feature_filters_menu.add(overlapping_cds_features_item);
+ feature_filters_menu.add(same_stop_cds_features_item);
+ feature_filters_menu.add(missing_qualifier_features_item);
+ feature_filters_menu.addSeparator();
+ feature_filters_menu.add(filter_by_key_item);
+ feature_filters_menu.add(filter_by_selection_item);
+
+ add(view_feature_item);
+ add(view_selection_item);
+ addSeparator();
+ if(search_results_menu != null)
+ add(search_results_menu);
+
+ add(view_cds_item);
+ add(feature_filters_menu);
+ addSeparator();
+ add(overview_item);
+ add(forward_overview_item);
+ add(reverse_overview_item);
+ addSeparator();
+ add(view_bases_item);
+ add(view_bases_as_fasta_item);
+ add(view_aa_item);
+ add(view_aa_as_fasta_item);
+ addSeparator();
+ add(feature_info_item);
+ add(plot_features_item);
}
/**
@@ -396,17 +432,18 @@ public class ViewMenu extends SelectionMenu {
* operate on.
* @param entry_group The EntryGroup object where new features/entries will
* be added.
- * @param goto_event_source The object that we will call makeBaseVisible ()
+ * @param goto_event_source The object that we will call makeBaseVisible()
* on.
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public ViewMenu (final JFrame frame,
- final Selection selection,
- final GotoEventSource goto_event_source,
- final EntryGroup entry_group,
- final BasePlotGroup base_plot_group) {
- this (frame, selection, goto_event_source, entry_group,
+ public ViewMenu(final JFrame frame,
+ final Selection selection,
+ final GotoEventSource goto_event_source,
+ final EntryGroup entry_group,
+ final BasePlotGroup base_plot_group)
+ {
+ this(frame, selection, goto_event_source, entry_group,
base_plot_group, "View");
}
@@ -481,52 +518,43 @@ public class ViewMenu extends SelectionMenu {
* @param sanger_options true if the sanger_options is set to true in the
* options file.
**/
- private JMenuItem makeSearchResultsMenu (final String program_name,
+ private JMenuItem makeSearchResultsMenu(final String program_name,
final boolean send_to_browser,
- final boolean sanger_options) {
- final String new_menu_name;
-
- if (send_to_browser) {
- new_menu_name = program_name + " results (in browser)";
- } else {
- new_menu_name = program_name + " results";
- }
+ final boolean sanger_options)
+ {
+ final String suffix;
+ if(send_to_browser)
+ suffix = new String(" results (in browser)");
+ else
+ suffix = new String(" results");
- final JMenuItem new_menu;
+ final JMenuItem new_menu = new JMenuItem(program_name + suffix);
if ((sanger_options && send_to_browser || !sanger_options)
- && program_name.equals ("fasta")) {
- new_menu = new JMenuItem (new_menu_name);
+ && program_name.equals("fasta"))
new_menu.setAccelerator (FASTA_IN_BROWSER_KEY);
- } else {
+ else
+ {
if ((sanger_options && send_to_browser || !sanger_options)
- && program_name.equals ("blastp")) {
- new_menu = new JMenuItem (new_menu_name);
+ && program_name.equals("blastp"))
new_menu.setAccelerator (BLASTP_IN_BROWSER_KEY);
- } else {
- if (program_name.equals ("fasta")) {
- new_menu = new JMenuItem (new_menu_name);
+ else
+ {
+ if(program_name.equals("fasta"))
new_menu.setAccelerator (VIEW_FASTA_KEY);
- } else {
- if (program_name.equals ("blastp")) {
- new_menu = new JMenuItem (new_menu_name);
- new_menu.setAccelerator (VIEW_BLASTP_KEY);
- } else {
- if (program_name.equals ("hth")) {
- new_menu = new JMenuItem (new_menu_name);
- new_menu.setAccelerator (VIEW_HTH_KEY);
- } else {
- new_menu = new JMenuItem (new_menu_name);
- }
- }
- }
+ else if(program_name.equals("blastp"))
+ new_menu.setAccelerator (VIEW_BLASTP_KEY);
+ else if(program_name.equals("hth"))
+ new_menu.setAccelerator (VIEW_HTH_KEY);
}
}
- new_menu.addActionListener (new ActionListener () {
- public void actionPerformed (ActionEvent event) {
- viewExternalResults (getParentFrame (), getSelection (),
- program_name, send_to_browser);
+ new_menu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewExternalResults(getParentFrame(), getSelection(),
+ program_name, send_to_browser);
}
});
@@ -543,7 +571,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showBadStartCodons (final JFrame parent_frame,
+ protected static void showBadStartCodons (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -592,7 +620,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showBadStopCodons (final JFrame parent_frame,
+ protected static void showBadStopCodons (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -641,7 +669,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this Menu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showStopsInTranslation (final Frame parent_frame,
+ private static void showStopsInTranslation (final Frame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -691,7 +719,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showNonEMBLKeys (final JFrame parent_frame,
+ protected static void showNonEMBLKeys (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -734,7 +762,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showDuplicatedFeatures (final JFrame parent_frame,
+ protected static void showDuplicatedFeatures (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -789,7 +817,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showOverlappingCDSs (final JFrame parent_frame,
+ protected static void showOverlappingCDSs (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -854,7 +882,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void
+ private static void
showFeaturesWithSameStopCodons (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
@@ -927,14 +955,11 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showMissingQualifierFeatures (final JFrame parent_frame,
- final Selection selection,
- final EntryGroup
- entry_group,
- final GotoEventSource
- goto_source,
- final BasePlotGroup
- base_plot_group) {
+ protected static void showMissingQualifierFeatures(final JFrame parent_frame,
+ final Selection selection, final EntryGroup entry_group,
+ final GotoEventSource goto_source,
+ final BasePlotGroup base_plot_group)
+ {
final FeaturePredicate feature_predicate =
new FeaturePredicate () {
public boolean testPredicate (final Feature feature) {
@@ -972,7 +997,7 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showFilterByKey (final JFrame parent_frame,
+ private static void showFilterByKey (final JFrame parent_frame,
final Selection selection,
final EntryGroup entry_group,
final GotoEventSource goto_source,
@@ -1020,14 +1045,12 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showFilterByKeyHelper (final JFrame parent_frame,
- final Key key,
- final Selection selection,
- final EntryGroup entry_group,
- final GotoEventSource
- goto_source,
- final BasePlotGroup
- base_plot_group) {
+ private static void showFilterByKeyHelper (final JFrame parent_frame,
+ final Key key, final Selection selection,
+ final EntryGroup entry_group,
+ final GotoEventSource goto_source,
+ final BasePlotGroup base_plot_group)
+ {
final String filter_name =
"features with key: " + key + " (filtered from: " +
parent_frame.getTitle () + ")";
@@ -1055,13 +1078,11 @@ public class ViewMenu extends SelectionMenu {
* @param base_plot_group The BasePlotGroup associated with this JMenu -
* needed to call getCodonUsageAlgorithm()
**/
- public static void showFilterBySelection (final JFrame parent_frame,
- final Selection selection,
- final EntryGroup entry_group,
- final GotoEventSource
- goto_source,
- final BasePlotGroup
- base_plot_group) {
+ private static void showFilterBySelection (final JFrame parent_frame,
+ final Selection selection, final EntryGroup entry_group,
+ final GotoEventSource goto_source,
+ final BasePlotGroup base_plot_group)
+ {
final FeaturePredicate predicate =
new FeatureFromVectorPredicate (selection.getAllFeatures ());
@@ -1092,8 +1113,9 @@ public class ViewMenu extends SelectionMenu {
* @param frame The JFrame to use for MessageDialog components.
* @param selection The Selection containing the features to merge.
**/
- static void viewSelectedFeatures (final JFrame frame,
- final Selection selection) {
+ protected static void viewSelectedFeatures (final JFrame frame,
+ final Selection selection)
+ {
final FeatureVector features_to_view = selection.getAllFeatures ();
if (features_to_view.size () > MAXIMUM_SELECTED_FEATURES) {
@@ -1116,8 +1138,9 @@ public class ViewMenu extends SelectionMenu {
* @param frame The JFrame to use for MessageDialog components.
* @param selection The Selection containing the features to plot.
**/
- static void plotSelectedFeatures (final JFrame frame,
- final Selection selection) {
+ protected static void plotSelectedFeatures (final JFrame frame,
+ final Selection selection)
+ {
final FeatureVector features_to_plot = selection.getAllFeatures ();
if (features_to_plot.size () > MAXIMUM_SELECTED_FEATURES) {
@@ -1143,10 +1166,11 @@ public class ViewMenu extends SelectionMenu {
* @param send_to_browser if true the results should be sent straight to
* the web browser rather than using a SearchResultViewer object.
**/
- static void viewExternalResults (final JFrame frame,
+ protected static void viewExternalResults (final JFrame frame,
final Selection selection,
final String program_name,
- final boolean send_to_browser) {
+ final boolean send_to_browser)
+ {
final FeatureVector features_to_view = selection.getAllFeatures ();
if (features_to_view.size () > MAXIMUM_SELECTED_FEATURES) {
@@ -1263,7 +1287,8 @@ public class ViewMenu extends SelectionMenu {
* Open a FeatureInfo component for each of the selected features. The
* new component will listen for feature change events and update itself.
**/
- private void viewSelectedFeatureInfo () {
+ private void viewSelectedFeatureInfo ()
+ {
final FeatureVector features_to_view = getSelection ().getAllFeatures ();
if (features_to_view.size () > MAXIMUM_SELECTED_FEATURES) {
@@ -1393,24 +1418,11 @@ public class ViewMenu extends SelectionMenu {
/**
* Return the EntryGroup that was passed to the constructor.
**/
- private EntryGroup getEntryGroup () {
+ private EntryGroup getEntryGroup ()
+ {
return entry_group;
}
- private JMenuItem feature_info_item = null;
- private JMenuItem plot_features_item = null;
- private JMenuItem view_feature_item = null;
- private JMenuItem view_selection_item = null;
- private JMenuItem view_fasta_item = null;
- private JMenuItem view_bases_item = null;
- private JMenuItem view_bases_as_fasta_item = null;
- private JMenuItem view_aa_item = null;
- private JMenuItem view_aa_as_fasta_item = null;
- private JMenuItem overview_item = null;
- private JMenuItem forward_overview_item = null;
- private JMenuItem reverse_overview_item = null;
- private JMenuItem view_cds_item = null;
-
/**
* The EntryGroup that was passed to the constructor.
**/