X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1b03e19b687bceecb291538f7450a59184f6259e;hb=32a259190463ee06a81886db9d7843b565dea6df;hp=14975b746dcaa6c05310bb8000ae2ada0acdfbda;hpb=5874ca652d08909c74d422552eb03a996112316d;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 14975b7..1b03e19 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -23,6 +23,7 @@ import java.awt.event.*; import javax.swing.*; import jalview.schemes.*; +import java.awt.BorderLayout; public class GAlignFrame extends JInternalFrame @@ -113,22 +114,30 @@ public class GAlignFrame protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); protected ButtonGroup colours = new ButtonGroup(); JMenuItem vamsasStore = new JMenuItem(); - protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem(); - //protected JTabbedPane tabbedPane = new JTabbedPane(); + protected JMenuItem showTranslation = new JMenuItem(); 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(); 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 jMenu4 = new JMenu(); + JMenuItem hideSelSequences = new JMenuItem(); + JMenuItem hideSelColumns = new JMenuItem(); + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + JMenuItem invertColSel = new JMenuItem(); + public GAlignFrame() { @@ -139,11 +148,10 @@ public class GAlignFrame setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) + for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { - JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats. - elementAt( - i)); + JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] ); + item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -357,7 +365,7 @@ public class GAlignFrame deselectAllSequenceMenuItem_actionPerformed(e); } }); - invertSequenceMenuItem.setText("Invert Selection"); + invertSequenceMenuItem.setText("Invert Sequence Selection"); invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -967,14 +975,6 @@ public class GAlignFrame 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() { @@ -1017,6 +1017,75 @@ public class GAlignFrame 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); + } + }); + jMenu4.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.setState(true); + hiddenMarkers.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hiddenMarkers_actionPerformed(e); + } + }); + invertColSel.setText("Invert Column Selection"); + invertColSel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + invertColSel_actionPerformed(e); + } + }); + alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); @@ -1033,6 +1102,8 @@ public class GAlignFrame fileMenu.add(outputTextboxMenu); fileMenu.add(printMenuItem); fileMenu.addSeparator(); + fileMenu.add(exportFeatures); + fileMenu.add(exportAnnotations); fileMenu.add(LoadtreeMenuItem); fileMenu.add(associatedData); fileMenu.addSeparator(); @@ -1047,6 +1118,7 @@ public class GAlignFrame editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); + editMenu.add(invertColSel); editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); @@ -1060,6 +1132,10 @@ public class GAlignFrame viewMenu.add(font); viewMenu.add(smoothFont); viewMenu.addSeparator(); + viewMenu.add(jMenu3); + viewMenu.add(jMenu4); + viewMenu.add(hiddenMarkers); + viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); viewMenu.add(seqLimits); viewMenu.add(scaleAbove); @@ -1071,7 +1147,6 @@ public class GAlignFrame viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); viewMenu.addSeparator(); - viewMenu.add(fetchSeqFeatures); viewMenu.add(showSeqFeatures); viewMenu.add(featureSettings); viewMenu.addSeparator(); @@ -1106,10 +1181,7 @@ public class GAlignFrame 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); + webService.add(webServiceNoServices);jMenu1.add(pasteNew); jMenu1.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortGroupMenuItem); @@ -1124,12 +1196,43 @@ public class GAlignFrame addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); addSequenceMenu.add(addFromURL); + this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); + statusPanel.add(statusBar, null); + jMenu3.add(showAllColumns); + jMenu3.add(showAllSeqs); + jMenu4.add(hideSelColumns); + jMenu4.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) { } @@ -1438,32 +1541,58 @@ public class GAlignFrame } - public void fetchSeqFeatures_actionPerformed(ActionEvent e) + + public void associatedData_actionPerformed(ActionEvent e) { } - public void associatedData_actionPerformed(ActionEvent e) + public void autoCalculate_actionPerformed(ActionEvent e) { } - public void autoCalculate_actionPerformed(ActionEvent e) + public void showAllSeqs_actionPerformed(ActionEvent e) { } - public void addFromFile_actionPerformed(ActionEvent e) + public void showAllColumns_actionPerformed(ActionEvent e) { } - public void addFromText_actionPerformed(ActionEvent e) + public void hideSelSequences_actionPerformed(ActionEvent e) { } - public void addFromURL_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) { }