X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1cbe15c5dc274a5b6a56e0e49f50c2448d7311c2;hb=cb8ec179c020265666678572815ab056a024da22;hp=ddb2bcd954a15a1231874818257f579eb1a408ff;hpb=ab6be38b4baaf8fc26fc19b2e514a6c40d6118f3;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index ddb2bcd..1cbe15c 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -21,7 +21,6 @@ package jalview.jbgui; import java.awt.*; import java.awt.event.*; import javax.swing.*; -import javax.swing.event.*; import jalview.schemes.*; @@ -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(); @@ -99,7 +98,7 @@ 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(); public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); @@ -111,9 +110,21 @@ public class GAlignFrame protected JMenu sort = new JMenu(); JMenu calculate = new JMenu(); JMenu jMenu2 = new JMenu(); - JMenuItem padGapsMenuitem = 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() { @@ -471,21 +482,6 @@ public class GAlignFrame }); 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)); @@ -718,12 +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"); @@ -822,13 +818,14 @@ public class GAlignFrame font_actionPerformed(e); } }); - fullSeqId.setText("Show Full Sequence ID"); - fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",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"); @@ -840,7 +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) @@ -906,6 +903,90 @@ public class GAlignFrame padGapsMenuitem_actionPerformed(e); } }); + vamsasStore.setVisible(false); + vamsasStore.setText("VAMSAS store"); + vamsasStore.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent 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); + } + }); + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState(true); + autoCalculate.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + autoCalculate_actionPerformed(e); + } + }); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); @@ -913,12 +994,16 @@ public class GAlignFrame 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); @@ -942,9 +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); @@ -953,7 +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); @@ -976,14 +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(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); @@ -1110,10 +1204,6 @@ public class GAlignFrame { } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) - { - } - protected void clustalColour_actionPerformed(ActionEvent e) { } @@ -1182,7 +1272,7 @@ public class GAlignFrame { } - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } @@ -1226,10 +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) { } @@ -1262,27 +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) + { + + } + + public void showTranslation_actionPerformed(ActionEvent e) { + } - protected void padGapsMenuitem_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 fetchSeqFeatures_actionPerformed(ActionEvent e) + { + + } + + public void associatedData_actionPerformed(ActionEvent e) + { + + } + + public void autoCalculate_actionPerformed(ActionEvent e) + { + } }