X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=304134cde86262ea031de344461a4c522cae2fb7;hb=0b23947e2cdcd704d3f313b23ba271e43d097344;hp=463bf70c67a424cfa6478c15297da1676f650a72;hpb=71a0d926b2dac39360d891f18271ae2100835166;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 463bf70..304134c 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) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -23,8 +23,11 @@ import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; -import jalview.gui.*; import jalview.schemes.*; +import java.awt.BorderLayout; + + + public class GAlignFrame extends JInternalFrame @@ -37,6 +40,7 @@ public class GAlignFrame protected JMenu colourMenu = new JMenu(); protected JMenu calculateMenu = new JMenu(); protected JMenu webService = new JMenu(); + protected JMenuItem webServiceNoServices; protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem invertSequenceMenuItem = new JMenuItem(); @@ -57,7 +61,7 @@ public class GAlignFrame protected JMenuItem clustalAlignMenuItem = new JMenuItem(); BorderLayout borderLayout1 = new BorderLayout(); public JLabel statusBar = new JLabel(); - protected JMenuItem saveAlignmentMenu = new JMenuItem(); + protected JMenuItem saveAs = new JMenuItem(); protected JMenu outputTextboxMenu = new JMenu(); protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); @@ -87,7 +91,7 @@ public class GAlignFrame JMenuItem findMenuItem = new JMenuItem(); JMenu searchMenu = new JMenu(); public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); JMenuItem deleteGroups = new JMenuItem(); JMenuItem delete = new JMenuItem(); @@ -99,26 +103,123 @@ public class GAlignFrame public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); JMenuItem createPNG = new JMenuItem(); protected JMenuItem font = new JMenuItem(); - public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem(); + public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); JMenuItem epsFile = new JMenuItem(); JMenuItem LoadtreeMenuItem = new JMenuItem(); - JMenuItem jnet = new JMenuItem(); public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); - JMenuItem modifyPID = new JMenuItem(); - JMenuItem modifyConservation = new JMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); protected JMenu sortByTreeMenu = new JMenu(); protected JMenu sort = new JMenu(); JMenu calculate = new JMenu(); - JMenuItem msaAlignMenuItem = new JMenuItem(); JMenu jMenu2 = new JMenu(); - JMenuItem padGapsMenuitem = new JMenuItem(); - JMenuItem ClustalRealign = new JMenuItem(); - + protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + protected ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JMenuItem showTranslation = new JMenuItem(); + public JMenuItem featureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); + protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem(); + JMenuItem annotationColour = new JMenuItem(); + JMenuItem associatedData = new JMenuItem(); + protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); + JMenu addSequenceMenu = new JMenu(); + JMenuItem addFromFile = new JMenuItem(); + JMenuItem addFromText = new JMenuItem(); + JMenuItem addFromURL = new JMenuItem(); + JMenuItem exportAnnotations = new JMenuItem(); + JMenuItem exportFeatures = new JMenuItem(); + protected JPanel statusPanel = new JPanel(); + GridLayout gridLayout1 = new GridLayout(); + JMenu jMenu3 = new JMenu(); + JMenuItem showAllSeqs = new JMenuItem(); + JMenuItem showAllColumns = new JMenuItem(); + JMenu hideMenu = new JMenu(); + JMenuItem hideSelSequences = new JMenuItem(); + JMenuItem hideSelColumns = new JMenuItem(); + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + JMenuItem invertColSel = new JMenuItem(); + protected JTabbedPane tabbedPane = new JTabbedPane(); + JMenuItem save = new JMenuItem(); public GAlignFrame() { - ButtonGroup colours = new ButtonGroup(); + try + { + jbInit(); + setJMenuBar(alignFrameMenuBar); + + // 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] ); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + } + catch (Exception e) + { + } + + + if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + 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)) + { + 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 + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + } + } + }); + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.insert(radioItem, 15); + colours.add(radioItem); + } + } colours.add(noColourmenuItem); colours.add(clustalColour); colours.add(zappoColour); @@ -133,9 +234,13 @@ public class GAlignFrame colours.add(BLOSUM62Colour); colours.add(nucleotideColour); - noColourmenuItem.setSelected(true); + setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); - String defaultColour = jalview.bin.Cache.getDefault("DEFAULT_COLOUR", null); + + } + + public void setColourSelected(String defaultColour) + { if (defaultColour != null) { @@ -143,6 +248,9 @@ public class GAlignFrame switch (index) { + case ColourSchemeProperty.NONE: + noColourmenuItem.setSelected(true); + break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -163,6 +271,10 @@ public class GAlignFrame break; + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; + case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); @@ -200,52 +312,26 @@ public class GAlignFrame } } - try - { - jbInit(); - setJMenuBar(alignFrameMenuBar); - - JMenuItem item; - - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) - { - item = new JMenuItem( (String) jalview.io.FormatAdapter.formats. - elementAt( - i)); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - outputText_actionPerformed(e); - } - }); - - outputTextboxMenu.add(item); - } - } - catch (Exception e) - { - } - } private void jbInit() throws Exception { - fileMenu.setMnemonic('F'); fileMenu.setText("File"); - saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save As"); - saveAlignmentMenu.addActionListener(new ActionListener() + saveAs.setText("Save As ..."); + saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. + KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false)); + saveAs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - saveAlignmentMenu_actionPerformed(e); + saveAs_actionPerformed(e); } }); closeMenuItem.setMnemonic('C'); closeMenuItem.setText("Close"); + closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_W, java.awt.event.KeyEvent.CTRL_MASK, false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -282,7 +368,10 @@ public class GAlignFrame deselectAllSequenceMenuItem_actionPerformed(e); } }); - invertSequenceMenuItem.setText("Invert Selection"); + invertSequenceMenuItem.setText("Invert Sequence Selection"); + invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_I, + java.awt.event.KeyEvent.SHIFT_MASK, false)); invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -291,6 +380,8 @@ public class GAlignFrame } }); remove2LeftMenuItem.setText("Remove Left"); + remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false)); remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -299,6 +390,8 @@ public class GAlignFrame } }); remove2RightMenuItem.setText("Remove Right"); + remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false)); remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -307,6 +400,9 @@ public class GAlignFrame } }); removeGappedColumnMenuItem.setText("Remove Empty Columns"); + removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke. + getKeyStroke(java.awt.event. + KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false)); removeGappedColumnMenuItem.addActionListener(new java.awt.event. ActionListener() { @@ -316,6 +412,8 @@ public class GAlignFrame } }); removeAllGapsMenuItem.setText("Remove All Gaps"); + removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false)); removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -366,6 +464,8 @@ public class GAlignFrame } }); removeRedundancyMenuItem.setText("Remove Redundancy..."); + removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( + java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false)); removeRedundancyMenuItem.addActionListener(new java.awt.event. ActionListener() { @@ -409,31 +509,8 @@ public class GAlignFrame neighbourTreeMenuItem_actionPerformed(e); } }); - clustalAlignMenuItem.setText("Clustal Alignment"); - clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalAlignMenuItem_actionPerformed(e); - } - }); this.getContentPane().setLayout(borderLayout1); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - alignFrameMenuBar.addAncestorListener(new AncestorListener() - { - public void ancestorAdded(AncestorEvent event) - { - alignFrameMenuBar_ancestorAdded(event); - } - - public void ancestorRemoved(AncestorEvent event) - { - } - - public void ancestorMoved(AncestorEvent event) - { - } - }); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); @@ -597,6 +674,8 @@ public class GAlignFrame redoMenuItem.setEnabled(false); redoMenuItem.setMnemonic('0'); redoMenuItem.setText("Redo"); + redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false)); redoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -629,6 +708,8 @@ public class GAlignFrame } }); printMenuItem.setText("Print"); + printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false)); printMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -666,12 +747,12 @@ public class GAlignFrame abovePIDThreshold_actionPerformed(e); } }); - sequenceFeatures.setText("Sequence Features"); - sequenceFeatures.addActionListener(new ActionListener() + showSeqFeatures.setText("Show Sequence Features"); + showSeqFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { - sequenceFeatures_actionPerformed(actionEvent); + showSeqFeatures_actionPerformed(actionEvent); } }); nucleotideColour.setText("Nucleotide"); @@ -683,6 +764,8 @@ public class GAlignFrame } }); deleteGroups.setText("Undefine groups"); + deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false)); deleteGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -745,7 +828,6 @@ public class GAlignFrame } }); applyToAllGroups.setText("Apply Colour To All Groups"); - applyToAllGroups.setState(true); applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -770,13 +852,14 @@ public class GAlignFrame font_actionPerformed(e); } }); - fullSeqId.setText("Show Full Sequence ID"); - fullSeqId.setState(true); - fullSeqId.addActionListener(new java.awt.event.ActionListener() + + seqLimits.setText("Show Sequence Limits"); + seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true)); + seqLimits.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - fullSeqId_actionPerformed(e); + seqLimit_actionPerformed(e); } }); epsFile.setText("EPS"); @@ -788,7 +871,7 @@ public class GAlignFrame } }); LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); - LoadtreeMenuItem.setText("Load Assocated Tree"); + LoadtreeMenuItem.setText("Load Associated Tree"); LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -796,14 +879,6 @@ public class GAlignFrame LoadtreeMenuItem_actionPerformed(e); } }); - jnet.setText("JNet"); - jnet.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - jpred_actionPerformed(e); - } - }); scaleAbove.setVisible(false); scaleAbove.setText("Scale Above"); scaleAbove.addActionListener(new java.awt.event.ActionListener() @@ -852,43 +927,235 @@ public class GAlignFrame sortByTreeMenu.setText("By Tree Order"); sort.setText("Sort"); calculate.setText("Calculate Tree"); - msaAlignMenuItem.setText("Muscle Alignment"); - msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() + + jMenu2.setText("Export Image"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + padGapsMenuitem_actionPerformed(e); + } + }); + vamsasStore.setVisible(false); + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - msaAlignMenuItem_actionPerformed(e); + vamsasStore_actionPerformed(e); } }); - jMenu2.setText("Export"); - padGapsMenuitem.setText("Pad Gaps"); - padGapsMenuitem.addActionListener(new ActionListener() + showTranslation.setText("Translate cDNA"); + showTranslation.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - padGapsMenuitem_actionPerformed(e); + showTranslation_actionPerformed(e); + } + }); + + + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + featureSettings_actionPerformed(e); + } + }); + fetchSequence.setText("Fetch Sequence(s)..."); + fetchSequence.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchSequence_actionPerformed(e); + } + }); + smoothFont.setText("Smooth Fonts"); + smoothFont.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + smoothFont_actionPerformed(e); + } + }); + + annotationColour.setText("By Annotation..."); + annotationColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(e); + } + }); + associatedData.setText("Load Features / Annotations"); + associatedData.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + associatedData_actionPerformed(e); + } + }); + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + autoCalculate_actionPerformed(e); + } + }); + addSequenceMenu.setText("Add Sequences"); + addFromFile.setText("From File"); + addFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromFile_actionPerformed(e); + } + }); + addFromText.setText("From Textbox"); + addFromText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromText_actionPerformed(e); + } + }); + addFromURL.setText("From URL"); + addFromURL.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromURL_actionPerformed(e); + } + }); + exportFeatures.setText("Export Features..."); + exportFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + exportFeatures_actionPerformed(e); + } + }); + exportAnnotations.setText("Export Annotations..."); + exportAnnotations.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + exportAnnotations_actionPerformed(e); + } + }); + statusPanel.setLayout(gridLayout1); + jMenu3.setText("Show"); + showAllSeqs.setText("All Sequences"); + showAllSeqs.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllSeqs_actionPerformed(e); + } + }); + showAllColumns.setText("All Columns"); + showAllColumns.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showAllColumns_actionPerformed(e); + } + }); + hideMenu.setText("Hide"); + hideSelSequences.setText("Selected Sequences"); + hideSelSequences.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSelSequences_actionPerformed(e); + } + }); + hideSelColumns.setText("Selected Columns"); + hideSelColumns.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSelColumns_actionPerformed(e); + } + }); + hiddenMarkers.setText("Hidden Markers"); + hiddenMarkers.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hiddenMarkers_actionPerformed(e); + } + }); + invertColSel.setText("Invert Column Selection"); + invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt. + event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false)); + invertColSel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertColSel_actionPerformed(e); + } + }); + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + JTabbedPane pane = (JTabbedPane)evt.getSource(); + int sel = pane.getSelectedIndex(); + tabSelectionChanged(sel); + } + }); + tabbedPane.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent e) + { + tabbedPane_mousePressed(e); + } + }); + tabbedPane.addFocusListener(new FocusAdapter() + { + public void focusGained(FocusEvent e) + { + tabbedPane_focusGained(e); } }); - ClustalRealign.setText("Clustal Realign"); - ClustalRealign.addActionListener(new ActionListener() + save.setText("Save"); + save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event. + KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false)); + save.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - ClustalRealign_actionPerformed(e); + save_actionPerformed(e); } }); + alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); - fileMenu.add(saveAlignmentMenu); - fileMenu.add(jMenu2); + alignFrameMenuBar.add(webService); + fileMenu.add(addSequenceMenu); + fileMenu.add(fetchSequence); + fileMenu.addSeparator(); + fileMenu.add(vamsasStore); + fileMenu.add(save); + fileMenu.add(saveAs); fileMenu.add(outputTextboxMenu); fileMenu.add(printMenuItem); fileMenu.addSeparator(); + fileMenu.add(jMenu2); + fileMenu.add(exportFeatures); + fileMenu.add(exportAnnotations); fileMenu.add(LoadtreeMenuItem); + fileMenu.add(associatedData); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); @@ -901,6 +1168,7 @@ public class GAlignFrame editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); + editMenu.add(invertColSel); editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); @@ -912,9 +1180,14 @@ public class GAlignFrame editMenu.add(padGapsMenuitem); searchMenu.add(findMenuItem); viewMenu.add(font); + viewMenu.add(smoothFont); + viewMenu.addSeparator(); + viewMenu.add(jMenu3); + viewMenu.add(hideMenu); + viewMenu.add(hiddenMarkers); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); - viewMenu.add(fullSeqId); + viewMenu.add(seqLimits); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); @@ -923,7 +1196,9 @@ public class GAlignFrame viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.add(sequenceFeatures); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); @@ -946,19 +1221,17 @@ public class GAlignFrame colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); + colourMenu.add(annotationColour); calculateMenu.add(sort); calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); - calculateMenu.add(webService); - webService.add(clustalAlignMenuItem); - webService.add(msaAlignMenuItem); - webService.add(jnet); - webService.add(ClustalRealign); - this.getContentPane().add(statusBar, BorderLayout.SOUTH); - jMenu1.add(pasteNew); + calculateMenu.add(showTranslation); + calculateMenu.add(autoCalculate); + webServiceNoServices=new JMenuItem(""); + webService.add(webServiceNoServices);jMenu1.add(pasteNew); jMenu1.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortGroupMenuItem); @@ -970,12 +1243,47 @@ public class GAlignFrame jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); + addSequenceMenu.add(addFromFile); + addSequenceMenu.add(addFromText); + addSequenceMenu.add(addFromURL); + this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); + statusPanel.add(statusBar, null); + this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); + jMenu3.add(showAllColumns); + jMenu3.add(showAllSeqs); + hideMenu.add(hideSelColumns); + hideMenu.add(hideSelSequences); } protected void outputText_actionPerformed(ActionEvent e) { } + public void addFromFile_actionPerformed(ActionEvent e) + { + + } + + public void addFromText_actionPerformed(ActionEvent e) + { + + } + + public void addFromURL_actionPerformed(ActionEvent e) + { + + } + + public void exportFeatures_actionPerformed(ActionEvent e) + { + + } + + public void exportAnnotations_actionPerformed(ActionEvent e) + { + + } + protected void htmlMenuItem_actionPerformed(ActionEvent e) { } @@ -1084,10 +1392,6 @@ public class GAlignFrame { } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) - { - } - protected void clustalColour_actionPerformed(ActionEvent e) { } @@ -1156,7 +1460,7 @@ public class GAlignFrame { } - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } @@ -1200,10 +1504,16 @@ public class GAlignFrame { } - protected void fullSeqId_actionPerformed(ActionEvent e) + protected void seqLimit_actionPerformed(ActionEvent e) { } + public void seqDBRef_actionPerformed(ActionEvent e) + { + + } + + public void createEPS(java.io.File f) { } @@ -1236,27 +1546,125 @@ public class GAlignFrame { } - protected void preferences_actionPerformed(ActionEvent e) + + + protected void saveAs_actionPerformed(ActionEvent e) { } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) + protected void padGapsMenuitem_actionPerformed(ActionEvent e) { } - protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) + + public void vamsasStore_actionPerformed(ActionEvent e) { + } - protected void saveAlignmentMenu_actionPerformed(ActionEvent e) + public void vamsasLoad_actionPerformed(ActionEvent e) { + } - protected void padGapsMenuitem_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(ActionEvent e) + { + + } + + public void featureSettings_actionPerformed(ActionEvent e) + { + + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + + } + + public void smoothFont_actionPerformed(ActionEvent e) { + } - protected void ClustalRealign_actionPerformed(ActionEvent e) + public void annotationColour_actionPerformed(ActionEvent e) { + + } + + + public void associatedData_actionPerformed(ActionEvent e) + { + + } + + public void autoCalculate_actionPerformed(ActionEvent e) + { + + } + + public void showAllSeqs_actionPerformed(ActionEvent e) + { + + } + + public void showAllColumns_actionPerformed(ActionEvent e) + { + + } + + public void hideSelSequences_actionPerformed(ActionEvent e) + { + + } + + public void hideSelColumns_actionPerformed(ActionEvent e) + { + + } + + public void hiddenMarkers_actionPerformed(ActionEvent e) + { + + } + + public void findPdbId_actionPerformed(ActionEvent e) + { + + } + + public void enterPdbId_actionPerformed(ActionEvent e) + { + + } + + public void pdbFile_actionPerformed(ActionEvent e) + { + + } + + public void invertColSel_actionPerformed(ActionEvent e) + { + + } + + public void tabSelectionChanged(int sel) + { + + } + + public void tabbedPane_mousePressed(MouseEvent e) + { + + } + + public void tabbedPane_focusGained(FocusEvent e) + { + requestFocus(); + } + + public void save_actionPerformed(ActionEvent e) + { + } }