X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=de46e5a9ee9a5837dfef2a96c33d670c8587d067;hb=009fc42205272de69744c96a04852241b9b03e85;hp=6c235a46c7328a3ec37febb5f3203d920cde8243;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6c235a4..de46e5a 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -23,7 +23,6 @@ import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; -import jalview.gui.*; import jalview.schemes.*; public class GAlignFrame @@ -37,6 +36,7 @@ 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(); @@ -102,23 +102,102 @@ public class GAlignFrame public JCheckBoxMenuItem fullSeqId = 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 ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem(); + protected JTabbedPane tabbedPane = new JTabbedPane(); + protected JMenuItem featureSettings = 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.formats.size(); i++) + { + JMenuItem 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) + { + } + + + 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 +212,13 @@ public class GAlignFrame colours.add(BLOSUM62Colour); colours.add(nucleotideColour); - noColourmenuItem.setSelected(true); + setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); - String defaultColour = Preferences.defaultColour; + + } + + public void setColourSelected(String defaultColour) + { if (defaultColour != null) { @@ -143,6 +226,9 @@ public class GAlignFrame switch (index) { + case ColourSchemeProperty.NONE: + noColourmenuItem.setSelected(true); + break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -163,6 +249,10 @@ public class GAlignFrame break; + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; + case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); @@ -200,35 +290,6 @@ 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) - { - e.printStackTrace(); - } - } private void jbInit() @@ -238,6 +299,8 @@ public class GAlignFrame fileMenu.setText("File"); saveAlignmentMenu.setMnemonic('L'); saveAlignmentMenu.setText("Save As"); + saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. + awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false)); saveAlignmentMenu.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -410,14 +473,6 @@ 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() @@ -550,7 +605,7 @@ public class GAlignFrame }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText("Show Annotations"); - annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation); + annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true)); annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -772,7 +827,7 @@ public class GAlignFrame } }); fullSeqId.setText("Show Full Sequence ID"); - fullSeqId.setState(true); + fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true)); fullSeqId.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -797,14 +852,6 @@ 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() @@ -853,29 +900,48 @@ 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"); + padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - msaAlignMenuItem_actionPerformed(e); + padGapsMenuitem_actionPerformed(e); } }); - jMenu2.setText("Export"); - padGapsMenuitem.setText("Pad Gaps"); - padGapsMenuitem.addActionListener(new ActionListener() + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - padGapsMenuitem_actionPerformed(e); + vamsasStore_actionPerformed(e); + } + }); + showTranslation.setText("Translate cDNA"); + showTranslation.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(e); } }); - ClustalRealign.setText("Clustal Realign"); - ClustalRealign.addActionListener(new ActionListener() + + tabbedPane.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent ece) + { + + tabSelected(); + } + }); +// featureSettings.setEnabled(false); + featureSettings.setText("Feature Settings..."); + featureSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - ClustalRealign_actionPerformed(e); + featureSettings_actionPerformed(e); } }); alignFrameMenuBar.add(fileMenu); @@ -884,6 +950,8 @@ public class GAlignFrame alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(vamsasStore); fileMenu.add(saveAlignmentMenu); fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); @@ -924,7 +992,9 @@ public class GAlignFrame viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); @@ -953,12 +1023,11 @@ public class GAlignFrame calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); - calculateMenu.add(webService); - webService.add(clustalAlignMenuItem); - webService.add(msaAlignMenuItem); - webService.add(jnet); - webService.add(ClustalRealign); + calculateMenu.add(showTranslation); + webServiceNoServices=new JMenuItem(""); + webService.add(webServiceNoServices); this.getContentPane().add(statusBar, BorderLayout.SOUTH); + this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); jMenu1.add(pasteNew); jMenu1.add(pasteThis); sort.add(sortIDMenuItem); @@ -1260,4 +1329,29 @@ public class GAlignFrame protected void ClustalRealign_actionPerformed(ActionEvent e) { } + + public void vamsasStore_actionPerformed(ActionEvent e) + { + + } + + public void vamsasLoad_actionPerformed(ActionEvent e) + { + + } + + public void showTranslation_actionPerformed(ActionEvent e) + { + + } + + public void tabSelected() + { + + } + + public void featureSettings_actionPerformed(ActionEvent e) + { + + } }