X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;fp=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=ffa586e68eb0ff25ed85364274509fc9f579da2d;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=6aaba84b7596d7424cf15feaec4c3b7326879715;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6aaba84..ffa586e 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 { @@ -102,6 +102,8 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeatureCounts = new JCheckBoxMenuItem(); + JMenuItem copy = new JMenuItem(); JMenuItem cut = new JMenuItem(); @@ -283,7 +285,9 @@ 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 +310,9 @@ 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 +339,9 @@ 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 +377,9 @@ 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 +393,9 @@ 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 +409,9 @@ 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 +533,9 @@ 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 +710,9 @@ 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 +726,9 @@ 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 +752,9 @@ 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 +780,9 @@ 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() @@ -781,6 +805,16 @@ public class GAlignFrame extends JInternalFrame showSeqFeatures_actionPerformed(actionEvent); } }); + showSeqFeatureCounts.setText( + MessageManager.getString("label.show_sequence_feature_counts")); + showSeqFeatureCounts.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + showSeqFeatureCounts_actionPerformed(actionEvent); + } + }); /* * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); * showSeqFeaturesHeight.addActionListener(new ActionListener() { public @@ -919,7 +953,9 @@ 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 +980,9 @@ 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 +1011,9 @@ 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 +1027,9 @@ 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 +1071,9 @@ 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 @@ -1213,8 +1257,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("action.calculate_tree_pca")); padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); - padGapsMenuitem - .setState(Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { @Override @@ -1357,8 +1400,7 @@ public class GAlignFrame extends JInternalFrame }); autoCalculate.setText( MessageManager.getString("label.autocalculate_consensus")); - autoCalculate.setState( - Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { @Override @@ -1371,8 +1413,7 @@ 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(Cache.getDefault("SORT_BY_TREE", false)); + sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { @Override @@ -1610,7 +1651,9 @@ 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 +1678,9 @@ 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 @@ -1830,6 +1875,7 @@ public class GAlignFrame extends JInternalFrame autoAnnMenu.add(showAutoFirst); autoAnnMenu.add(showAutoLast); autoAnnMenu.addSeparator(); + autoAnnMenu.add(showSeqFeatureCounts); autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); @@ -1918,6 +1964,13 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + protected void showSeqFeatureCounts_actionPerformed( + ActionEvent actionEvent) + { + // TODO Auto-generated method stub + + } + protected void loadVcf_actionPerformed() { }