X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=37073437e703b65b3b3ad4bac5f22360023122de;hb=567c2595554096f10feab130153f97286f3f7d80;hp=dff20d3d76aa41d4411a7ce7852085a373ca7ecb;hpb=92bd4313e2f23a65df1eb965e836d178c1eacdd1;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index dff20d3..3707343 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -25,7 +25,7 @@ import jalview.api.SplitContainerI; import jalview.bin.Cache; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; -import jalview.io.FileFormat; +import jalview.io.FileFormats; import jalview.util.MessageManager; import jalview.util.Platform; @@ -65,8 +65,6 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem closeMenuItem = new JMenuItem(); - protected JMenu colourMenu = new JMenu(); - protected JMenu webService = new JMenu(); protected JMenuItem webServiceNoServices; @@ -81,8 +79,6 @@ public class GAlignFrame extends JInternalFrame protected JMenu outputTextboxMenu = new JMenu(); - protected JRadioButtonMenuItem textColour; - protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); @@ -93,14 +89,10 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem; - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem abovePIDThreshold; - public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); JMenuItem copy = new JMenuItem(); @@ -109,8 +101,6 @@ public class GAlignFrame extends JInternalFrame JMenu pasteMenu = new JMenu(); - protected JCheckBoxMenuItem applyToAllGroups; - protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); @@ -119,17 +109,27 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); - protected JMenuItem modifyPID; + protected JCheckBoxMenuItem applyToAllGroups; + + protected JMenu colourMenu = new JMenu(); + + protected JMenuItem textColour; + + protected JCheckBoxMenuItem conservationMenuItem; protected JMenuItem modifyConservation; + protected JCheckBoxMenuItem abovePIDThreshold; + + protected JMenuItem modifyPID; + protected JMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); protected JMenu sort = new JMenu(); - protected JMenu calculateTree = new JMenu(); + protected JMenuItem calculateTree = new JMenuItem(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); @@ -211,7 +211,7 @@ public class GAlignFrame extends JInternalFrame setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); @@ -533,26 +533,6 @@ public class GAlignFrame extends JInternalFrame PCAMenuItem_actionPerformed(e); } }); - JMenuItem averageDistanceTreeMenuItem = new JMenuItem( - MessageManager.getString("label.average_distance_identity")); - averageDistanceTreeMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); - JMenuItem neighbourTreeMenuItem = new JMenuItem( - MessageManager.getString("label.neighbour_joining_identity")); - neighbourTreeMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - neighbourTreeMenuItem_actionPerformed(e); - } - }); this.getContentPane().setLayout(new BorderLayout()); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); @@ -563,27 +543,6 @@ public class GAlignFrame extends JInternalFrame outputTextboxMenu.setText(MessageManager .getString("label.out_to_textbox")); - - JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem( - MessageManager.getString("label.average_distance_blosum62")); - avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - avTreeBlosumMenuItem_actionPerformed(e); - } - }); - JMenuItem njTreeBlosumMenuItem = new JMenuItem( - MessageManager.getString("label.neighbour_blosum62")); - njTreeBlosumMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - njTreeBlosumMenuItem_actionPerformed(e); - } - }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText(MessageManager .getString("label.show_annotations")); @@ -975,7 +934,7 @@ public class GAlignFrame extends JInternalFrame }); JMenuItem createGroup = new JMenuItem( - MessageManager.getString("action.create_groups")); + MessageManager.getString("action.create_group")); keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false); al = new ActionListener() @@ -1203,7 +1162,7 @@ public class GAlignFrame extends JInternalFrame @Override public void menuSelected(MenuEvent e) { - buildTreeMenu(); + buildTreeSortMenu(); } @Override @@ -1240,8 +1199,8 @@ public class GAlignFrame extends JInternalFrame }); sortByAnnotScore.setVisible(false); - calculateTree - .setText(MessageManager.getString("action.calculate_tree")); + calculateTree.setText(MessageManager + .getString("action.calculate_tree_pca")); padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); padGapsMenuitem.setState(jalview.bin.Cache @@ -1653,6 +1612,7 @@ public class GAlignFrame extends JInternalFrame formatMenu.setText(MessageManager.getString("action.format")); JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); + idRightAlign.setText(MessageManager .getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() @@ -1842,7 +1802,7 @@ public class GAlignFrame extends JInternalFrame calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); + // calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); calculateMenu.add(showReverse); @@ -1904,6 +1864,12 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + protected void configureSelectMenu() + { + // TODO Auto-generated method stub + + } + /** * Constructs the entries on the Colour menu (but does not add them to the * menu). @@ -1917,12 +1883,12 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - applyToAllGroups_actionPerformed(); + applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); } }); - textColour = new JRadioButtonMenuItem( - MessageManager.getString("action.set_text_colour")); + textColour = new JMenuItem( + MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { @Override @@ -1939,7 +1905,8 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(); + conservationMenuItem_actionPerformed(conservationMenuItem + .isSelected()); } }); @@ -1950,7 +1917,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - abovePIDThreshold_actionPerformed(); + abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); } }); modifyPID = new JMenuItem( @@ -2326,23 +2293,11 @@ public class GAlignFrame extends JInternalFrame { } - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - } - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - } - - protected void conservationMenuItem_actionPerformed() + protected void conservationMenuItem_actionPerformed(boolean selected) { } @@ -2358,7 +2313,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void abovePIDThreshold_actionPerformed() + protected void abovePIDThreshold_actionPerformed(boolean selected) { } @@ -2398,7 +2353,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void applyToAllGroups_actionPerformed() + protected void applyToAllGroups_actionPerformed(boolean selected) { } @@ -2626,7 +2581,7 @@ public class GAlignFrame extends JInternalFrame } - public void buildTreeMenu() + public void buildTreeSortMenu() { }