X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=bb69a54dba0d2ed06b16a5c5dfc07176f43b68c2;hb=4e66fcb33a56766f244dab68bc2087db29829efd;hp=26e532694dcd370d9bc31f703482a0b3cd452ea4;hpb=ef3333028b291ce92bdae34bd2f8487d35d0a0d3;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 26e5326..bb69a54 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,9 +21,7 @@ package jalview.jbgui; import java.awt.*; import java.awt.event.*; import javax.swing.*; -import javax.swing.event.*; -import jalview.gui.*; import jalview.schemes.*; public class GAlignFrame @@ -37,6 +35,7 @@ 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(); @@ -99,41 +98,28 @@ 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 ButtonGroup colours = new ButtonGroup(); + JMenuItem vamsasStore = new JMenuItem(); + protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem(); + //protected JTabbedPane tabbedPane = new JTabbedPane(); + public JMenuItem featureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); public GAlignFrame() { - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(nucleotideColour); - - setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); try @@ -141,12 +127,10 @@ public class GAlignFrame 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. + JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats. elementAt( i)); item.addActionListener(new java.awt.event.ActionListener() @@ -164,6 +148,73 @@ public class GAlignFrame { } + + 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); + colours.add(taylorColour); + colours.add(hydrophobicityColour); + colours.add(helixColour); + colours.add(strandColour); + colours.add(turnColour); + colours.add(buriedColour); + colours.add(userDefinedColour); + colours.add(PIDColour); + colours.add(BLOSUM62Colour); + colours.add(nucleotideColour); + + setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None")); + + } public void setColourSelected(String defaultColour) @@ -422,31 +473,8 @@ 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)); @@ -783,13 +811,14 @@ 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"); @@ -809,14 +838,6 @@ 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() @@ -865,29 +886,57 @@ 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.setVisible(false); + 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); + } + }); + + /* 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) + { + featureSettings_actionPerformed(e); } }); - ClustalRealign.setText("Clustal Realign"); - ClustalRealign.addActionListener(new ActionListener() + fetchSequence.setText("Fetch Sequence..."); + fetchSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - ClustalRealign_actionPerformed(e); + fetchSequence_actionPerformed(e); } }); alignFrameMenuBar.add(fileMenu); @@ -896,6 +945,9 @@ public class GAlignFrame alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(fetchSequence); + fileMenu.add(vamsasStore); fileMenu.add(saveAlignmentMenu); fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); @@ -927,7 +979,7 @@ public class GAlignFrame viewMenu.add(font); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); - viewMenu.add(fullSeqId); + viewMenu.add(seqLimits); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); @@ -936,7 +988,9 @@ 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); @@ -965,12 +1019,11 @@ 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); @@ -1097,10 +1150,6 @@ public class GAlignFrame { } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) - { - } - protected void clustalColour_actionPerformed(ActionEvent e) { } @@ -1213,10 +1262,16 @@ 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) { } @@ -1249,27 +1304,44 @@ public class GAlignFrame { } - protected void preferences_actionPerformed(ActionEvent e) + + + protected void saveAlignmentMenu_actionPerformed(ActionEvent e) + { + } + + protected void padGapsMenuitem_actionPerformed(ActionEvent e) { } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) + + public void vamsasStore_actionPerformed(ActionEvent e) { + } - protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) + public void vamsasLoad_actionPerformed(ActionEvent e) { + } - protected void saveAlignmentMenu_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(ActionEvent e) + { + + } + + public void tabSelected() { + } - protected void padGapsMenuitem_actionPerformed(ActionEvent e) + public void featureSettings_actionPerformed(ActionEvent e) { + } - protected void ClustalRealign_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed(ActionEvent e) { + } }