X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=25db31aab3246021583926c1e9b1902cd7c4daaf;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=0d6a03f3442af16edc02b5dd4c33e08b39518742;hpb=adcef27f5747b4e70e89a56c3735bc3afb8ce9bf;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 0d6a03f..25db31a 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -20,20 +20,6 @@ */ package jalview.jbgui; -import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.analysis.GeneticCodeI; -import jalview.analysis.GeneticCodes; -import jalview.api.SplitContainerI; -import jalview.bin.Cache; -import jalview.gui.JvSwingUtils; -import jalview.gui.Preferences; -import jalview.hmmer.HmmerCommand; -import jalview.io.FileFormatException; -import jalview.io.FileFormats; -import jalview.schemes.ResidueColourScheme; -import jalview.util.MessageManager; -import jalview.util.Platform; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.GridLayout; @@ -41,6 +27,7 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; +import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; @@ -64,6 +51,21 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.analysis.GeneticCodeI; +import jalview.analysis.GeneticCodes; +import jalview.api.SplitContainerI; +import jalview.bin.Cache; +import jalview.gui.JvSwingUtils; +import jalview.gui.Preferences; +import jalview.hmmer.HmmerCommand; +import jalview.io.FileFormatException; +import jalview.io.FileFormats; +import jalview.schemes.ResidueColourScheme; +import jalview.util.MessageManager; +import jalview.util.Platform; + + @SuppressWarnings("serial") public class GAlignFrame extends JInternalFrame { @@ -231,7 +233,8 @@ public class GAlignFrame extends JInternalFrame { // for Web-page embedding using id=align-frame-div - setName("jalview-alignment"); + setName(Platform.getAppID("alignment")); + jbInit(); setJMenuBar(alignFrameMenuBar); @@ -286,15 +289,12 @@ public class GAlignFrame extends JInternalFrame }; // FIXME getDefaultToolkit throws an exception in Headless mode - KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK, false); addMenuActionAndAccelerator(keyStroke, saveAs, al); closeMenuItem.setText(MessageManager.getString("action.close")); - keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -320,7 +320,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem selectAllSequenceMenuItem = new JMenuItem( MessageManager.getString("action.select_all")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -347,7 +347,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem invertSequenceMenuItem = new JMenuItem( MessageManager.getString("action.invert_sequence_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -383,7 +383,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem remove2LeftMenuItem = new JMenuItem( MessageManager.getString("action.remove_left")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -397,7 +397,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem remove2RightMenuItem = new JMenuItem( MessageManager.getString("action.remove_right")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -411,7 +411,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem removeGappedColumnMenuItem = new JMenuItem( MessageManager.getString("action.remove_empty_columns")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -425,8 +425,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem removeAllGapsMenuItem = new JMenuItem( MessageManager.getString("action.remove_all_gaps")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.SHIFT_DOWN_MASK, false); al = new ActionListener() { @@ -553,7 +553,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem removeRedundancyMenuItem = new JMenuItem( MessageManager.getString("action.remove_redundancy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -755,7 +755,7 @@ public class GAlignFrame extends JInternalFrame undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -769,7 +769,7 @@ public class GAlignFrame extends JInternalFrame redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -793,7 +793,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem printMenuItem = new JMenuItem( MessageManager.getString("action.print")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -819,7 +819,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem findMenuItem = new JMenuItem( MessageManager.getString("action.find")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.find_tip"))); al = new ActionListener() @@ -981,7 +981,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem deleteGroups = new JMenuItem( MessageManager.getString("action.undefine_groups")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1006,7 +1006,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem createGroup = new JMenuItem( MessageManager.getString("action.create_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1020,8 +1020,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem unGroup = new JMenuItem( MessageManager.getString("action.remove_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.SHIFT_DOWN_MASK, false); al = new ActionListener() { @@ -1035,7 +1035,7 @@ public class GAlignFrame extends JInternalFrame copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @@ -1049,7 +1049,7 @@ public class GAlignFrame extends JInternalFrame cut.setText(MessageManager.getString("action.cut")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1075,8 +1075,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem pasteNew = new JMenuItem( MessageManager.getString("label.to_new_alignment")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.SHIFT_DOWN_MASK, false); al = new ActionListener() { @@ -1098,7 +1098,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem pasteThis = new JMenuItem( MessageManager.getString("label.to_this_alignment")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1247,6 +1247,24 @@ public class GAlignFrame extends JInternalFrame @Override public void menuSelected(MenuEvent e) { + enableSortMenuOptions(); + } + + @Override + public void menuDeselected(MenuEvent e) + { + } + + @Override + public void menuCanceled(MenuEvent e) + { + } + }); + sortByTreeMenu.addMenuListener(new MenuListener() + { + @Override + public void menuSelected(MenuEvent e) + { buildTreeSortMenu(); } @@ -1628,8 +1646,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem invertColSel = new JMenuItem( MessageManager.getString("action.invert_column_selection")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() - | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, + Platform.SHORTCUT_KEY_MASK + | InputEvent.ALT_DOWN_MASK, false); al = new ActionListener() { @@ -1692,7 +1710,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1717,7 +1735,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem newView = new JMenuItem( MessageManager.getString("action.new_view")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + Platform.SHORTCUT_KEY_MASK, false); al = new ActionListener() { @Override @@ -1794,8 +1812,8 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem selectHighlighted = new JMenuItem( MessageManager.getString("action.select_highlighted_columns")); - selectHighlighted.setToolTipText( - MessageManager.getString("tooltip.select_highlighted_columns")); + selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.getString("tooltip.select_highlighted_columns"))); al = new ActionListener() { @Override @@ -2181,6 +2199,10 @@ public class GAlignFrame extends JInternalFrame } + protected void enableSortMenuOptions() + { + } + protected void loadVcf_actionPerformed() { } @@ -3019,4 +3041,6 @@ public class GAlignFrame extends JInternalFrame protected void showComplement_actionPerformed(boolean complement) { } + + }