X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1cbe15c5dc274a5b6a56e0e49f50c2448d7311c2;hb=cb8ec179c020265666678572815ab056a024da22;hp=e4842ee9cf633e1142b03ffaf49afb86a2ccbb3a;hpb=c3ded07cf4a7708564e9878bf1763fe837e03ddc;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index e4842ee..1cbe15c 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(); @@ -87,7 +86,7 @@ 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 +98,113 @@ 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 JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem(); + //protected JTabbedPane tabbedPane = new JTabbedPane(); + public JMenuItem featureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); + protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem(); + JMenuItem annotationColour = new JMenuItem(); + JMenuItem fetchSeqFeatures = new JMenuItem(); + + + JMenuItem associatedData = new JMenuItem(); + protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); 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 +219,13 @@ 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 +233,9 @@ public class GAlignFrame switch (index) { + case ColourSchemeProperty.NONE: + noColourmenuItem.setSelected(true); + break; case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); @@ -163,6 +256,10 @@ public class GAlignFrame break; + case ColourSchemeProperty.TAYLOR: + taylorColour.setSelected(true); + break; + case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); @@ -200,34 +297,6 @@ 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) - { - } - } private void jbInit() @@ -237,6 +306,8 @@ 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) @@ -409,31 +480,8 @@ 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)); @@ -549,7 +597,7 @@ 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) @@ -666,12 +714,12 @@ 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"); @@ -770,13 +818,14 @@ 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 +837,7 @@ 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 +845,6 @@ 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() @@ -852,29 +893,98 @@ 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.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); + } + }); + smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false)); + annotationColour.setText("By Annotation..."); + annotationColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(e); + } + }); + fetchSeqFeatures.setText("Fetch Sequence Features"); + fetchSeqFeatures.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + fetchSeqFeatures_actionPerformed(e); + } + }); + associatedData.setText("Load Features / Annotations"); + associatedData.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + associatedData_actionPerformed(e); } }); - ClustalRealign.setText("Clustal Realign"); - ClustalRealign.addActionListener(new ActionListener() + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState(true); + autoCalculate.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - ClustalRealign_actionPerformed(e); + autoCalculate_actionPerformed(e); } }); alignFrameMenuBar.add(fileMenu); @@ -883,12 +993,17 @@ public class GAlignFrame alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + fileMenu.add(fetchSequence); + fileMenu.addSeparator(); + fileMenu.add(vamsasStore); fileMenu.add(saveAlignmentMenu); fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(LoadtreeMenuItem); + fileMenu.add(associatedData); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); @@ -912,9 +1027,10 @@ public class GAlignFrame editMenu.add(padGapsMenuitem); searchMenu.add(findMenuItem); viewMenu.add(font); + viewMenu.add(smoothFont); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); - viewMenu.add(fullSeqId); + viewMenu.add(seqLimits); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); @@ -923,7 +1039,10 @@ public class GAlignFrame viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.add(sequenceFeatures); + viewMenu.addSeparator(); + viewMenu.add(fetchSeqFeatures); + viewMenu.add(showSeqFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); @@ -946,18 +1065,19 @@ 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); + calculateMenu.add(showTranslation); + calculateMenu.add(autoCalculate); + 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); @@ -1084,10 +1204,6 @@ public class GAlignFrame { } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) - { - } - protected void clustalColour_actionPerformed(ActionEvent e) { } @@ -1156,7 +1272,7 @@ public class GAlignFrame { } - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } @@ -1200,10 +1316,16 @@ 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 +1358,64 @@ public class GAlignFrame { } - protected void preferences_actionPerformed(ActionEvent e) + + + protected void saveAlignmentMenu_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) { + } - protected void ClustalRealign_actionPerformed(ActionEvent e) + public void featureSettings_actionPerformed(ActionEvent e) { + + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + + } + + public void smoothFont_actionPerformed(ActionEvent e) + { + + } + + public void annotationColour_actionPerformed(ActionEvent e) + { + + } + + public void fetchSeqFeatures_actionPerformed(ActionEvent e) + { + + } + + public void associatedData_actionPerformed(ActionEvent e) + { + + } + + public void autoCalculate_actionPerformed(ActionEvent e) + { + } }