X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1b89d71c9848945444d28735db4be89efde76911;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=479eaaa1e54eef532b604baed83d6ad3087b8492;hpb=5672e0350c857fffd3932d7e3a385373ede46fd4;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 479eaaa..1b89d71 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -24,10 +24,6 @@ import javax.swing.*; import javax.swing.event.*; import jalview.schemes.*; -import java.awt.BorderLayout; - - - public class GAlignFrame extends JInternalFrame @@ -140,12 +136,15 @@ public class GAlignFrame JMenuItem invertColSel = new JMenuItem(); protected JTabbedPane tabbedPane = new JTabbedPane(); JMenuItem save = new JMenuItem(); - JMenuItem jMenuItem1 = new JMenuItem(); protected JMenuItem reload = new JMenuItem(); JMenuItem newView = new JMenuItem(); JMenuItem textColour = new JMenuItem(); - JMenu jMenu1 = new JMenu(); - JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem(); + JMenu formatMenu = new JMenu(); + JMenu selectMenu = new JMenu(); + protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); + protected JMenuItem gatherViews = new JMenuItem(); + protected JMenuItem expandViews = new JMenuItem(); + JMenuItem pageSetup = new JMenuItem(); public GAlignFrame() { try @@ -156,7 +155,8 @@ public class GAlignFrame // dynamically fill save as menu with available formats for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { - JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] ); + JMenuItem item = new JMenuItem(jalview.io.FormatAdapter. + WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { @@ -185,45 +185,49 @@ public class GAlignFrame reload.setMnemonic('R'); } - - if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { java.util.Enumeration userColours = jalview.gui.UserDefinedColours. getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours. + final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( + userColours. nextElement().toString()); radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - public void mousePressed(MouseEvent evt) + radioItem.removeActionListener(radioItem.getActionListeners()[0]); + + int option = JOptionPane.showInternalConfirmDialog(jalview.gui. + Desktop.desktop, + "Remove from default list?", + "Remove user defined colour", + JOptionPane.YES_NO_OPTION); + if (option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours.removeColourFromDefaults( + radioItem.getText()); + colourMenu.remove(radioItem); + } + else { - if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) + radioItem.addActionListener(new ActionListener() { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop, - "Remove from default list?", - "Remove user defined colour", - JOptionPane.YES_NO_OPTION); - if(option == JOptionPane.YES_OPTION) + public void actionPerformed(ActionEvent evt) { - jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText()); - colourMenu.remove(radioItem); + userDefinedColour_actionPerformed(evt); } - else - radioItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } + }); } - }); + } + } + }); radioItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -251,7 +255,6 @@ public class GAlignFrame setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); - } public void setColourSelected(String defaultColour) @@ -264,8 +267,8 @@ public class GAlignFrame switch (index) { case ColourSchemeProperty.NONE: - noColourmenuItem.setSelected(true); - break; + noColourmenuItem.setSelected(true); + break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -336,7 +339,8 @@ public class GAlignFrame saveAs.setText("Save As..."); saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. KeyEvent.VK_S, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false)); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | + java.awt.event.KeyEvent.SHIFT_MASK, false)); saveAs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -386,7 +390,7 @@ public class GAlignFrame invertSequenceMenuItem.setText("Invert Sequence Selection"); invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_I, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false)); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -396,7 +400,8 @@ public class GAlignFrame }); remove2LeftMenuItem.setText("Remove Left"); remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. - awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + awt.event.KeyEvent.VK_L, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -406,7 +411,8 @@ public class GAlignFrame }); remove2RightMenuItem.setText("Remove Right"); remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. - awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + awt.event.KeyEvent.VK_R, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -429,7 +435,8 @@ public class GAlignFrame removeAllGapsMenuItem.setText("Remove All Gaps"); removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_E, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false)); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | + java.awt.event.KeyEvent.SHIFT_MASK, false)); removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -481,7 +488,8 @@ public class GAlignFrame }); removeRedundancyMenuItem.setText("Remove Redundancy..."); removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + java.awt.event.KeyEvent.VK_D, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); removeRedundancyMenuItem.addActionListener(new java.awt.event. ActionListener() { @@ -641,7 +649,8 @@ public class GAlignFrame }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText("Show Annotations"); - annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true)); + annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault( + "SHOW_ANNOTATIONS", true)); annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -720,7 +729,7 @@ public class GAlignFrame wrapMenuItem_actionPerformed(e); } }); - printMenuItem.setText("Print"); + printMenuItem.setText("Print ..."); printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); printMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -821,7 +830,8 @@ public class GAlignFrame pasteNew.setText("To New Alignment"); pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_V, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.ALT_MASK, false)); + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | + java.awt.event.KeyEvent.SHIFT_MASK, false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -867,7 +877,7 @@ public class GAlignFrame }); seqLimits.setText("Show Sequence Limits"); - seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true)); + seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -939,11 +949,26 @@ public class GAlignFrame }); sortByTreeMenu.setText("By Tree Order"); sort.setText("Sort"); + sort.addMenuListener(new MenuListener() + { + public void menuSelected(MenuEvent e) + { + buildTreeMenu(); + } + + public void menuDeselected(MenuEvent e) + { + } + + public void menuCanceled(MenuEvent e) + { + } + }); calculate.setText("Calculate Tree"); jMenu2.setText("Export Image"); padGapsMenuitem.setText("Pad Gaps"); - padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -969,7 +994,6 @@ public class GAlignFrame } }); - featureSettings.setText("Feature Settings..."); featureSettings.addActionListener(new ActionListener() { @@ -1004,7 +1028,7 @@ public class GAlignFrame } }); autoCalculate.setText("Autocalculate Consensus"); - autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1098,7 +1122,10 @@ public class GAlignFrame }); invertColSel.setText("Invert Column Selection"); invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. - event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); + event.KeyEvent.VK_I, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() + | java.awt.event.KeyEvent.ALT_MASK, + false)); invertColSel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1108,12 +1135,12 @@ public class GAlignFrame }); tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { - public void stateChanged(ChangeEvent evt) - { - JTabbedPane pane = (JTabbedPane)evt.getSource(); - int sel = pane.getSelectedIndex(); - tabSelectionChanged(sel); - } + public void stateChanged(ChangeEvent evt) + { + JTabbedPane pane = (JTabbedPane) evt.getSource(); + int sel = pane.getSelectedIndex(); + tabSelectionChanged(sel); + } }); tabbedPane.addMouseListener(new MouseAdapter() { @@ -1159,7 +1186,8 @@ public class GAlignFrame } }); tabbedPane.setToolTipText(" Right-click to rename tab" - +"
Press X to eXpand tabs, G to reGroup."); + + + "
Press X to eXpand tabs, G to reGroup."); textColour.setText("Text Colour"); textColour.addActionListener(new ActionListener() { @@ -1168,13 +1196,52 @@ public class GAlignFrame textColour_actionPerformed(e); } }); - jMenu1.setText("Format"); - jCheckBoxMenuItem1.setText("Right Align Ids"); + formatMenu.setText("Format"); + selectMenu.setText("Select"); + idRightAlign.setText("Right Align Sequence Id"); + idRightAlign.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + idRightAlign_actionPerformed(e); + } + }); + gatherViews.setEnabled(false); + gatherViews.setText("Gather Views"); + gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_G, 0, false)); + gatherViews.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + gatherViews_actionPerformed(e); + } + }); + expandViews.setEnabled(false); + expandViews.setText("Expand Views"); + expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_X, 0, false)); + expandViews.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + expandViews_actionPerformed(e); + } + }); + pageSetup.setText("Page Setup ..."); + pageSetup.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pageSetup_actionPerformed(e); + } + }); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(selectMenu); alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(jMenu1); + alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); @@ -1186,6 +1253,7 @@ public class GAlignFrame fileMenu.add(save); fileMenu.add(saveAs); fileMenu.add(outputTextboxMenu); + fileMenu.add(pageSetup); fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(jMenu2); @@ -1202,14 +1270,6 @@ public class GAlignFrame editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(invertColSel); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(findMenuItem); - editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); editMenu.add(removeGappedColumnMenuItem); @@ -1218,6 +1278,8 @@ public class GAlignFrame editMenu.addSeparator(); editMenu.add(padGapsMenuitem); viewMenu.add(newView); + viewMenu.add(expandViews); + viewMenu.add(gatherViews); viewMenu.addSeparator(); viewMenu.add(jMenu3); viewMenu.add(hideMenu); @@ -1258,12 +1320,14 @@ public class GAlignFrame calculateMenu.addSeparator(); calculateMenu.add(showTranslation); calculateMenu.add(autoCalculate); - webServiceNoServices=new JMenuItem(""); - webService.add(webServiceNoServices);pasteMenu.add(pasteNew); + webServiceNoServices = new JMenuItem(""); + webService.add(webServiceNoServices); + pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); + sort.add(sortByTreeMenu); calculate.add(averageDistanceTreeMenuItem); calculate.add(neighbourTreeMenuItem); calculate.add(avDistanceTreeBlosumMenuItem); @@ -1281,18 +1345,26 @@ public class GAlignFrame jMenu3.add(showAllSeqs); hideMenu.add(hideSelColumns); hideMenu.add(hideSelSequences); - jMenu1.add(font); - jMenu1.addSeparator(); - jMenu1.add(seqLimits); - jMenu1.add(wrapMenuItem); - jMenu1.add(scaleAbove); - jMenu1.add(scaleLeft); - jMenu1.add(scaleRight); - jMenu1.add(hiddenMarkers); - jMenu1.add(viewBoxesMenuItem); - jMenu1.add(viewTextMenuItem); - jMenu1.add(colourTextMenuItem); - jMenu1.add(renderGapsMenuItem); + formatMenu.add(font); + formatMenu.addSeparator(); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(seqLimits); + formatMenu.add(idRightAlign); + formatMenu.add(hiddenMarkers); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); } protected void outputText_actionPerformed(ActionEvent e) @@ -1553,7 +1625,6 @@ public class GAlignFrame } - public void createEPS(java.io.File f) { } @@ -1586,8 +1657,6 @@ public class GAlignFrame { } - - protected void saveAs_actionPerformed(ActionEvent e) { } @@ -1596,7 +1665,6 @@ public class GAlignFrame { } - public void vamsasStore_actionPerformed(ActionEvent e) { @@ -1632,7 +1700,6 @@ public class GAlignFrame } - public void associatedData_actionPerformed(ActionEvent e) { @@ -1722,4 +1789,29 @@ public class GAlignFrame { } + + public void idRightAlign_actionPerformed(ActionEvent e) + { + + } + + public void expandViews_actionPerformed(ActionEvent e) + { + + } + + public void gatherViews_actionPerformed(ActionEvent e) + { + + } + + public void buildTreeMenu() + { + + } + + public void pageSetup_actionPerformed(ActionEvent e) + { + + } }