From 61b3b004768ba36031bd26f5f3515decffd1fb74 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 22 May 2018 14:02:34 +0100 Subject: [PATCH] JAL-2629 method refactor and menu tidying --- src/jalview/gui/AlignFrame.java | 16 --- src/jalview/hmmer/HMMSearch.java | 21 +++- src/jalview/jbgui/GAlignFrame.java | 232 ++++++++++++++++-------------------- 3 files changed, 121 insertions(+), 148 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 3f74327..be765ec 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -5796,22 +5796,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void hmmerMenu_actionPerformed(ActionEvent e) - { - SequenceGroup grp = getViewport().getSelectionGroup(); - if (grp != null) - { - hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from " - + grp.getName()); - } - else - { - hmmBuild.setText(MessageManager.getString("label.hmmbuild") - + " from Alignment"); - } - } - - @Override protected void loadVcf_actionPerformed() { JalviewFileChooser chooser = new JalviewFileChooser( diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java index 4c5bfb3..a58b949 100644 --- a/src/jalview/hmmer/HMMSearch.java +++ b/src/jalview/hmmer/HMMSearch.java @@ -160,6 +160,25 @@ public class HMMSearch extends HmmerCommand List args = new ArrayList<>(); args.add(command); + buildArguments(args, searchOutputFile, hitsAlignmentFile, hmmFile); + + return runCommand(args); + } + + /** + * Appends command line arguments to the given list, to specify input and + * output files for the search, and any additional options that may have been + * passed from the parameters dialog + * + * @param args + * @param searchOutputFile + * @param hitsAlignmentFile + * @param hmmFile + * @throws IOException + */ + protected void buildArguments(List args, File searchOutputFile, + File hitsAlignmentFile, File hmmFile) throws IOException + { args.add("-o"); args.add(getFilePath(searchOutputFile)); args.add("-A"); @@ -282,8 +301,6 @@ public class HMMSearch extends HmmerCommand args.add(getFilePath(hmmFile)); args.add(getFilePath(databaseFile)); - - return runCommand(args); } /** diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 8226cee..bc71566 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -72,26 +72,6 @@ public class GAlignFrame extends JInternalFrame protected JMenu hmmerMenu = new JMenu(); - protected JMenu hmmAlign = new JMenu(); - - protected JMenuItem hmmAlignRun = new JMenuItem(); - - protected JMenuItem hmmAlignSettings = new JMenuItem(); - - protected JMenu hmmSearch = new JMenu(); - - protected JMenuItem hmmSearchRun = new JMenuItem(); - - protected JMenuItem hmmSearchSettings = new JMenuItem(); - - protected JMenuItem addDatabase = new JMenuItem(); - - protected JMenu hmmBuild = new JMenu(); - - protected JMenuItem hmmBuildRun = new JMenuItem(); - - protected JMenuItem hmmBuildSettings = new JMenuItem(); - protected JMenuItem webServiceNoServices; protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); @@ -280,7 +260,6 @@ public class GAlignFrame extends JInternalFrame private void jbInit() throws Exception { initColourMenu(); - initHMMERMenu(); JMenuItem saveAs = new JMenuItem( MessageManager.getString("action.save_as")); @@ -322,19 +301,8 @@ public class GAlignFrame extends JInternalFrame JMenu calculateMenu = new JMenu( MessageManager.getString("action.calculate")); webService.setText(MessageManager.getString("action.web_service")); - hmmerMenu.setText(MessageManager.getString("action.hmmer")); - hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); - hmmerMenu.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmerMenu_actionPerformed(e); - } - }); - hmmerMenu.add(hmmBuild); - hmmerMenu.add(hmmAlign); - hmmerMenu.add(hmmSearch); + + initHMMERMenu(); JMenuItem selectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.select_all")); @@ -1757,81 +1725,6 @@ public class GAlignFrame extends JInternalFrame selectHighlightedColumns_actionPerformed(actionEvent); } }; - hmmBuildRun.setText(MessageManager.formatMessage( - "label.action_with_default_settings", "hmmbuild")); - hmmBuildRun.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmBuild_actionPerformed(true); - } - }); - hmmBuildSettings.setText( - MessageManager.getString("label.edit_settings_and_run")); - hmmBuildSettings.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmBuild_actionPerformed(false); - } - }); - hmmAlignRun.setText(MessageManager.formatMessage( - "label.action_with_default_settings", "hmmalign")); - hmmAlignRun.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmAlign_actionPerformed(true); - } - }); - hmmAlignSettings.setText( - MessageManager.getString("label.edit_settings_and_run")); - hmmAlignSettings.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmAlign_actionPerformed(false); - } - }); - hmmSearchRun.setText(MessageManager.formatMessage( - "label.action_with_default_settings", "hmmsearch")); - hmmSearchRun.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmSearch_actionPerformed(true); - } - }); - hmmSearchSettings.setText( - MessageManager.getString("label.edit_settings_and_run")); - hmmSearchSettings.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmSearch_actionPerformed(false); - } - }); - addDatabase.setText(MessageManager.getString("label.add_database")); - addDatabase.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - try - { - addDatabase_actionPerformed(); - } catch (IOException e1) - { - e1.printStackTrace(); - } - } - }); selectHighlighted.addActionListener(al); JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); @@ -2014,40 +1907,119 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } - public void hmmerMenu_actionPerformed(ActionEvent e) - { - - } - /** - * Constructs the entries on the HMMER menu (does not add them to the menu). + * Constructs the entries on the HMMER menu */ protected void initHMMERMenu() { - hmmAlign = new JMenu(MessageManager.getString("label.hmmalign")); - hmmAlignSettings = new JMenuItem( - MessageManager.getString("label.edit_settings_and_run")); - hmmAlignRun = new JMenuItem(MessageManager.formatMessage( - "label.action_with_default_settings", "hmmalign")); - hmmAlign.add(hmmAlignSettings); - hmmAlign.add(hmmAlignRun); - hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild")); - hmmBuildSettings = new JMenuItem( + /* + * hmmbuild + */ + JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild")); + JMenuItem hmmBuildSettings = new JMenuItem( MessageManager.getString("label.edit_settings_and_run")); - hmmBuildRun = new JMenuItem(MessageManager.formatMessage( + hmmBuildSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmBuild_actionPerformed(false); + } + }); + JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage( "label.action_with_default_settings", "hmmbuild")); - hmmBuild.add(hmmBuildSettings); + hmmBuildRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmBuild_actionPerformed(true); + } + }); hmmBuild.add(hmmBuildRun); - hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch")); - hmmSearchSettings = new JMenuItem( + hmmBuild.add(hmmBuildSettings); + + /* + * hmmalign + */ + JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign")); + JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmalign")); + hmmAlignRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmAlign_actionPerformed(true); + } + }); + JMenuItem hmmAlignSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmAlignSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmAlign_actionPerformed(false); + } + }); + hmmAlign.add(hmmAlignRun); + hmmAlign.add(hmmAlignSettings); + + /* + * hmmsearch + */ + JMenu hmmSearch = new JMenu( + MessageManager.getString("label.hmmsearch")); + JMenuItem hmmSearchSettings = new JMenuItem( MessageManager.getString("label.edit_settings_and_run")); - hmmSearchRun = new JMenuItem(MessageManager.formatMessage( + hmmSearchSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmSearch_actionPerformed(false); + } + }); + JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage( "label.action_with_default_settings", "hmmsearch")); - addDatabase = new JMenuItem( + hmmSearchRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmSearch_actionPerformed(true); + } + }); + JMenuItem addDatabase = new JMenuItem( MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); hmmSearch.add(hmmSearchSettings); hmmSearch.add(hmmSearchRun); hmmSearch.add(addDatabase); + + /* + * top level menu + */ + hmmerMenu.setText(MessageManager.getString("action.hmmer")); + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + hmmerMenu.add(hmmBuild); + hmmerMenu.add(hmmAlign); + hmmerMenu.add(hmmSearch); + } protected void loadVcf_actionPerformed() -- 1.7.10.2