X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=237cf4c53ce7eeeb1d41c652451e1528ac2d510c;hb=7749f0e593d610c517dfd6796cf6087191b189ad;hp=ddb2bcd954a15a1231874818257f579eb1a408ff;hpb=ab6be38b4baaf8fc26fc19b2e514a6c40d6118f3;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index ddb2bcd..237cf4c 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -24,6 +24,10 @@ import javax.swing.*; import javax.swing.event.*; import jalview.schemes.*; +import java.awt.BorderLayout; + + + public class GAlignFrame extends JInternalFrame @@ -87,7 +91,7 @@ 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 +103,7 @@ 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(); @@ -111,24 +115,45 @@ 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 JMenuItem showTranslation = new JMenuItem(); + public JMenuItem featureSettings = new JMenuItem(); + JMenuItem fetchSequence = new JMenuItem(); + protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem(); + JMenuItem annotationColour = 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 hideMenu = new JMenu(); + JMenuItem hideSelSequences = new JMenuItem(); + JMenuItem hideSelColumns = new JMenuItem(); + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + JMenuItem invertColSel = new JMenuItem(); + protected JTabbedPane tabbedPane = new JTabbedPane(); public GAlignFrame() { - - try { jbInit(); 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) @@ -342,7 +367,7 @@ 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) @@ -471,21 +496,6 @@ 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 +728,12 @@ 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 +832,14 @@ 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 +851,7 @@ 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) @@ -899,6 +910,7 @@ public class GAlignFrame jMenu2.setText("Export"); padGapsMenuitem.setText("Pad Gaps"); + padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -906,6 +918,192 @@ 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); + } + }); + associatedData.setText("Load Features / Annotations"); + associatedData.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + associatedData_actionPerformed(e); + } + }); + autoCalculate.setText("Autocalculate Consensus"); + autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + autoCalculate_actionPerformed(e); + } + }); + addSequenceMenu.setText("Add Sequences"); + addFromFile.setText("From File"); + addFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromFile_actionPerformed(e); + } + }); + addFromText.setText("From Textbox"); + addFromText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addFromText_actionPerformed(e); + } + }); + addFromURL.setText("From URL"); + addFromURL.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + 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); + } + }); + hideMenu.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); + } + }); + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + JTabbedPane pane = (JTabbedPane)evt.getSource(); + int sel = pane.getSelectedIndex(); + tabSelectionChanged(sel); + } + }); + tabbedPane.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent e) + { + tabbedPane_mousePressed(e); + } + }); + alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); @@ -913,12 +1111,19 @@ public class GAlignFrame alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); + fileMenu.add(addSequenceMenu); + fileMenu.add(fetchSequence); + fileMenu.addSeparator(); + fileMenu.add(vamsasStore); fileMenu.add(saveAlignmentMenu); fileMenu.add(jMenu2); fileMenu.add(outputTextboxMenu); fileMenu.add(printMenuItem); fileMenu.addSeparator(); + fileMenu.add(exportFeatures); + fileMenu.add(exportAnnotations); fileMenu.add(LoadtreeMenuItem); + fileMenu.add(associatedData); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); @@ -931,6 +1136,7 @@ public class GAlignFrame editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); + editMenu.add(invertColSel); editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); @@ -942,9 +1148,14 @@ public class GAlignFrame editMenu.add(padGapsMenuitem); searchMenu.add(findMenuItem); viewMenu.add(font); + viewMenu.add(smoothFont); + viewMenu.addSeparator(); + viewMenu.add(jMenu3); + viewMenu.add(hideMenu); + viewMenu.add(hiddenMarkers); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); - viewMenu.add(fullSeqId); + viewMenu.add(seqLimits); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); @@ -953,7 +1164,9 @@ public class GAlignFrame viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.add(sequenceFeatures); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); @@ -976,15 +1189,17 @@ 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); - jMenu1.add(pasteNew); + webService.add(webServiceNoServices);jMenu1.add(pasteNew); jMenu1.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortGroupMenuItem); @@ -996,12 +1211,47 @@ public class GAlignFrame jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); + addSequenceMenu.add(addFromFile); + addSequenceMenu.add(addFromText); + addSequenceMenu.add(addFromURL); + this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); + statusPanel.add(statusBar, null); + this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); + jMenu3.add(showAllColumns); + jMenu3.add(showAllSeqs); + hideMenu.add(hideSelColumns); + hideMenu.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) { } @@ -1110,10 +1360,6 @@ public class GAlignFrame { } - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) - { - } - protected void clustalColour_actionPerformed(ActionEvent e) { } @@ -1182,7 +1428,7 @@ public class GAlignFrame { } - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } @@ -1226,10 +1472,16 @@ 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 +1514,115 @@ 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) + { + + } + + public void featureSettings_actionPerformed(ActionEvent e) { + + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + } - protected void ClustalRealign_actionPerformed(ActionEvent e) + public void smoothFont_actionPerformed(ActionEvent e) { + + } + + public void annotationColour_actionPerformed(ActionEvent e) + { + + } + + + public void associatedData_actionPerformed(ActionEvent e) + { + + } + + public void autoCalculate_actionPerformed(ActionEvent e) + { + + } + + public void showAllSeqs_actionPerformed(ActionEvent e) + { + + } + + public void showAllColumns_actionPerformed(ActionEvent e) + { + + } + + public void hideSelSequences_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) + { + + } + + public void tabSelectionChanged(int sel) + { + + } + + public void tabbedPane_mousePressed(MouseEvent e) + { + } }