X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=7daeb37454a764857c0a2be4ba519b7ac5c4bd68;hb=81d1b5ee333dee61382971eca41792d6a64a29fc;hp=6685c67c589abf56cf914af2d41a4089f1a0f1c9;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6685c67..7daeb37 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -20,18 +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.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; @@ -61,6 +49,18 @@ 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.io.FileFormats; +import jalview.schemes.ResidueColourScheme; +import jalview.util.MessageManager; +import jalview.util.Platform; + @SuppressWarnings("serial") public class GAlignFrame extends JInternalFrame { @@ -104,6 +104,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem copy = new JMenuItem(); + JMenuItem copyHighlighted = new JMenuItem(); + JMenuItem cut = new JMenuItem(); JMenu pasteMenu = new JMenu(); @@ -218,6 +220,7 @@ public class GAlignFrame extends JInternalFrame { try { + setFrameIcon(null); // for Web-page embedding using id=align-frame-div setName("jalview-alignment"); @@ -243,7 +246,7 @@ public class GAlignFrame extends JInternalFrame } } catch (Exception e) { - System.err.println(e.toString()); + jalview.bin.Console.errPrintln(e.toString()); } if (Platform.allowMnemonics()) // was "not mac and not JS" @@ -261,6 +264,7 @@ public class GAlignFrame extends JInternalFrame private void jbInit() throws Exception { + setFrameIcon(null); initColourMenu(); JMenuItem saveAs = new JMenuItem( @@ -283,7 +287,9 @@ public class GAlignFrame extends JInternalFrame closeMenuItem.setText(MessageManager.getString("action.close")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -306,7 +312,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -333,7 +341,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -369,7 +379,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -383,7 +395,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -397,7 +411,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -519,7 +535,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -694,7 +712,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -708,7 +728,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -732,7 +754,9 @@ public class GAlignFrame extends JInternalFrame JMenuItem printMenuItem = new JMenuItem( MessageManager.getString("action.print")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -758,7 +782,9 @@ public class GAlignFrame extends JInternalFrame JMenuItem findMenuItem = new JMenuItem( MessageManager.getString("action.find")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.find_tip"))); al = new ActionListener() @@ -919,7 +945,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -944,7 +972,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -973,7 +1003,9 @@ public class GAlignFrame extends JInternalFrame copy.setText(MessageManager.getString("action.copy")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @@ -987,7 +1019,9 @@ public class GAlignFrame extends JInternalFrame cut.setText(MessageManager.getString("action.cut")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -1029,7 +1063,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -1046,7 +1082,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - createPNG(null); + createPNG_actionPerformed(e); } }); createPNG.setActionCommand( @@ -1063,7 +1099,7 @@ public class GAlignFrame extends JInternalFrame }); seqLimits.setText( MessageManager.getString("label.show_sequence_limits")); - seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); + seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new ActionListener() { @Override @@ -1078,7 +1114,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - createEPS(null); + createEPS_actionPerformed(e); } }); @@ -1088,7 +1124,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - createSVG(null); + createSVG_actionPerformed(e); } }); @@ -1213,8 +1249,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("action.calculate_tree_pca")); padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); - padGapsMenuitem - .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { @Override @@ -1357,8 +1392,7 @@ public class GAlignFrame extends JInternalFrame }); autoCalculate.setText( MessageManager.getString("label.autocalculate_consensus")); - autoCalculate.setState( - jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { @Override @@ -1371,8 +1405,7 @@ public class GAlignFrame extends JInternalFrame MessageManager.getString("label.sort_alignment_new_tree")); sortByTree.setToolTipText("" + MessageManager.getString( "label.enable_automatically_sort_alignment_when_open_new_tree")); - sortByTree - .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); + sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { @Override @@ -1610,7 +1643,9 @@ public class GAlignFrame extends JInternalFrame JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -1635,7 +1670,9 @@ 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); + jalview.util.ShortcutKeyMaskExWrapper + .getMenuShortcutKeyMaskEx(), + false); al = new ActionListener() { @Override @@ -1723,6 +1760,26 @@ public class GAlignFrame extends JInternalFrame } }; selectHighlighted.addActionListener(al); + + copyHighlighted = new JMenuItem( + MessageManager.getString("action.copy_highlighted_regions")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); + copyHighlighted.setToolTipText( + MessageManager.getString("tooltip.copy_highlighted_regions")); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + copyHighlightedColumns_actionPerformed(actionEvent); + } + }; + addMenuActionAndAccelerator(keyStroke, copyHighlighted, al); + copyHighlighted.addActionListener(al); + JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); JMenu autoAnnMenu = new JMenu( @@ -1773,6 +1830,7 @@ public class GAlignFrame extends JInternalFrame editMenu.add(redoMenuItem); editMenu.add(cut); editMenu.add(copy); + editMenu.add(copyHighlighted); editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); @@ -1918,6 +1976,30 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + protected void createPNG_actionPerformed(ActionEvent object) + { + // TODO Auto-generated method stub + + } + + protected void createEPS_actionPerformed(ActionEvent object) + { + // TODO Auto-generated method stub + + } + + protected void createSVG_actionPerformed(ActionEvent object) + { + // TODO Auto-generated method stub + + } + + protected void copyHighlightedColumns_actionPerformed( + ActionEvent actionEvent) + { + + } + protected void loadVcf_actionPerformed() { } @@ -2095,7 +2177,7 @@ public class GAlignFrame extends JInternalFrame * @param forAlignment * update non-sequence-related annotations */ - protected void setAnnotationsVisibility(boolean visible, + public void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) { @@ -2405,10 +2487,6 @@ public class GAlignFrame extends JInternalFrame { } - public void createPNG(java.io.File f) - { - } - protected void font_actionPerformed(ActionEvent e) { } @@ -2422,15 +2500,6 @@ public class GAlignFrame extends JInternalFrame } - public void createEPS(java.io.File f) - { - } - - public void createSVG(java.io.File f) - { - - } - protected void loadTreeMenuItem_actionPerformed(ActionEvent e) {