X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=4bf8176572a1f4a1c13c68b9ba5bb034bf72af6e;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=d3154c7408f4ff0ebbf1844e9dd3ced60d788157;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index d3154c7..4bf8176 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -20,6 +20,10 @@ */ package jalview.jbgui; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.bin.Cache; +import jalview.gui.JvSwingUtils; +import jalview.gui.Preferences; import jalview.schemes.ColourSchemeProperty; import jalview.util.MessageManager; @@ -63,6 +67,8 @@ public class GAlignFrame extends JInternalFrame protected JMenu viewMenu = new JMenu(); + protected JMenu annotationsMenu = new JMenu(); + protected JMenu colourMenu = new JMenu(); protected JMenu calculateMenu = new JMenu(); @@ -208,6 +214,10 @@ public class GAlignFrame extends JInternalFrame JMenuItem createPNG = new JMenuItem(); + JMenuItem createBioJS = new JMenuItem(); + + JMenuItem createSVG = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); @@ -302,6 +312,18 @@ public class GAlignFrame extends JInternalFrame JMenuItem showAllhidden = new JMenuItem(); + protected JMenuItem showAllSeqAnnotations = new JMenuItem(); + + protected JMenuItem hideAllSeqAnnotations = new JMenuItem(); + + protected JMenuItem showAllAlAnnotations = new JMenuItem(); + + protected JMenuItem hideAllAlAnnotations = new JMenuItem(); + + protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); JMenuItem invertColSel = new JMenuItem(); @@ -354,8 +376,16 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(); + private JMenuItem grpsFromSelection = new JMenuItem(); + private SequenceAnnotationOrder annotationSortOrder; + + private boolean showAutoCalculatedAbove = false; + public GAlignFrame() { try @@ -371,6 +401,7 @@ public class GAlignFrame extends JInternalFrame item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -381,6 +412,7 @@ public class GAlignFrame extends JInternalFrame } } catch (Exception e) { + System.err.println(e.toString()); } if (!new jalview.util.Platform().isAMac()) @@ -407,6 +439,7 @@ public class GAlignFrame extends JInternalFrame radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() @@ -431,6 +464,7 @@ public class GAlignFrame extends JInternalFrame { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -442,6 +476,7 @@ public class GAlignFrame extends JInternalFrame }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -580,6 +615,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.SHIFT_MASK, false)); saveAs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { saveAs_actionPerformed(e); @@ -591,6 +627,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { closeMenuItem_actionPerformed(false); @@ -598,6 +635,7 @@ public class GAlignFrame extends JInternalFrame }); editMenu.setText(MessageManager.getString("action.edit")); viewMenu.setText(MessageManager.getString("action.view")); + annotationsMenu.setText(MessageManager.getString("action.annotations")); colourMenu.setText(MessageManager.getString("action.colour")); calculateMenu.setText(MessageManager.getString("action.calculate")); webService.setText(MessageManager.getString("action.web_service")); @@ -609,6 +647,7 @@ public class GAlignFrame extends JInternalFrame selectAllSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { selectAllSequenceMenuItem_actionPerformed(e); @@ -621,6 +660,7 @@ public class GAlignFrame extends JInternalFrame deselectAllSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { deselectAllSequenceMenuItem_actionPerformed(e); @@ -634,6 +674,7 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertSequenceMenuItem_actionPerformed(e); @@ -643,6 +684,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.make_groups_selection")); grpsFromSelection.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); @@ -668,6 +710,7 @@ public class GAlignFrame extends JInternalFrame remove2LeftMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { remove2LeftMenuItem_actionPerformed(e); @@ -681,6 +724,7 @@ public class GAlignFrame extends JInternalFrame remove2RightMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { remove2RightMenuItem_actionPerformed(e); @@ -694,6 +738,7 @@ public class GAlignFrame extends JInternalFrame removeGappedColumnMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { removeGappedColumnMenuItem_actionPerformed(e); @@ -708,6 +753,7 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { removeAllGapsMenuItem_actionPerformed(e); @@ -718,6 +764,7 @@ public class GAlignFrame extends JInternalFrame justifyLeftMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { justifyLeftMenuItem_actionPerformed(e); @@ -728,6 +775,7 @@ public class GAlignFrame extends JInternalFrame justifyRightMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { justifyRightMenuItem_actionPerformed(e); @@ -737,6 +785,7 @@ public class GAlignFrame extends JInternalFrame viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { viewBoxesMenuItem_actionPerformed(e); @@ -746,6 +795,7 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem.setState(true); viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { viewTextMenuItem_actionPerformed(e); @@ -757,6 +807,7 @@ public class GAlignFrame extends JInternalFrame showNonconservedMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showUnconservedMenuItem_actionPerformed(e); @@ -767,6 +818,7 @@ public class GAlignFrame extends JInternalFrame sortPairwiseMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortPairwiseMenuItem_actionPerformed(e); @@ -775,6 +827,7 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem.setText(MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortIDMenuItem_actionPerformed(e); @@ -785,6 +838,7 @@ public class GAlignFrame extends JInternalFrame sortLengthMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortLengthMenuItem_actionPerformed(e); @@ -793,19 +847,21 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem.setText(MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortGroupMenuItem_actionPerformed(e); } }); removeRedundancyMenuItem.setText(MessageManager - .getString("action.remove_redundancy")); + .getString("action.remove_redundancy").concat("...")); removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); removeRedundancyMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { removeRedundancyMenuItem_actionPerformed(e); @@ -816,6 +872,7 @@ public class GAlignFrame extends JInternalFrame pairwiseAlignmentMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pairwiseAlignmentMenuItem_actionPerformed(e); @@ -825,6 +882,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PCAMenuItem_actionPerformed(e); @@ -835,6 +893,7 @@ public class GAlignFrame extends JInternalFrame averageDistanceTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { averageDistanceTreeMenuItem_actionPerformed(e); @@ -845,6 +904,7 @@ public class GAlignFrame extends JInternalFrame neighbourTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { neighbourTreeMenuItem_actionPerformed(e); @@ -862,6 +922,7 @@ public class GAlignFrame extends JInternalFrame clustalColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(e); @@ -870,6 +931,7 @@ public class GAlignFrame extends JInternalFrame zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { zappoColour_actionPerformed(e); @@ -878,6 +940,7 @@ public class GAlignFrame extends JInternalFrame taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { taylorColour_actionPerformed(e); @@ -888,6 +951,7 @@ public class GAlignFrame extends JInternalFrame hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(e); @@ -896,6 +960,7 @@ public class GAlignFrame extends JInternalFrame helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { helixColour_actionPerformed(e); @@ -905,6 +970,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(e); @@ -913,6 +979,7 @@ public class GAlignFrame extends JInternalFrame turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { turnColour_actionPerformed(e); @@ -921,6 +988,7 @@ public class GAlignFrame extends JInternalFrame buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { buriedColour_actionPerformed(e); @@ -930,6 +998,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { userDefinedColour_actionPerformed(e); @@ -939,6 +1008,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(e); @@ -948,6 +1018,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("label.blosum62_score")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { BLOSUM62Colour_actionPerformed(e); @@ -956,6 +1027,7 @@ public class GAlignFrame extends JInternalFrame nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideColour_actionPerformed(e); @@ -967,6 +1039,7 @@ public class GAlignFrame extends JInternalFrame purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(e); @@ -977,6 +1050,7 @@ public class GAlignFrame extends JInternalFrame RNAInteractionColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { RNAInteractionColour_actionPerformed(e); @@ -994,6 +1068,7 @@ public class GAlignFrame extends JInternalFrame avDistanceTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { avTreeBlosumMenuItem_actionPerformed(e); @@ -1004,6 +1079,7 @@ public class GAlignFrame extends JInternalFrame njTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { njTreeBlosumMenuItem_actionPerformed(e); @@ -1012,21 +1088,103 @@ public class GAlignFrame extends JInternalFrame annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText(MessageManager .getString("label.show_annotations")); - annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault( - "SHOW_ANNOTATIONS", true)); - annotationPanelMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotationPanelMenuItem_actionPerformed(e); - } - }); + annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS", + true)); + annotationPanelMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + annotationPanelMenuItem_actionPerformed(e); + } + }); + showAllAlAnnotations.setText(MessageManager + .getString("label.show_all_al_annotations")); + final boolean isAnnotationPanelShown = annotationPanelMenuItem + .getState(); + showAllAlAnnotations.setEnabled(isAnnotationPanelShown); + showAllAlAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllAnnotations_actionPerformed(false, true); + } + }); + hideAllAlAnnotations.setText(MessageManager + .getString("label.hide_all_al_annotations")); + hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); + hideAllAlAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideAllAnnotations_actionPerformed(false, true); + } + }); + showAllSeqAnnotations.setText(MessageManager + .getString("label.show_all_seq_annotations")); + showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); + showAllSeqAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllAnnotations_actionPerformed(true, false); + } + }); + hideAllSeqAnnotations.setText(MessageManager + .getString("label.hide_all_seq_annotations")); + hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); + hideAllSeqAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideAllAnnotations_actionPerformed(true, false); + } + }); + SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder + .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + sortAnnBySequence.setText(MessageManager + .getString("label.sort_annotations_by_sequence")); + sortAnnBySequence + .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + sortAnnBySequence.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + boolean newState = sortAnnBySequence.getState(); + sortAnnByLabel.setSelected(false); + setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL + : SequenceAnnotationOrder.NONE); + sortAnnotations_actionPerformed(); + } + }); + sortAnnByLabel.setText(MessageManager + .getString("label.sort_annotations_by_label")); + sortAnnByLabel + .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + sortAnnByLabel.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + boolean newState = sortAnnByLabel.getState(); + sortAnnBySequence.setSelected(false); + setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE + : SequenceAnnotationOrder.NONE); + sortAnnotations_actionPerformed(); + } + }); colourTextMenuItem.setText(MessageManager .getString("label.colour_text")); colourTextMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { colourTextMenuItem_actionPerformed(e); @@ -1035,15 +1193,30 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem.setText(MessageManager.getString("label.html")); htmlMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { htmlMenuItem_actionPerformed(e); } }); + + // TODO uncomment when supported by MassageManager + // createBioJS.setText(MessageManager.getString("label.biojs_html_export")); + createBioJS.setText("BioJS"); + createBioJS.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + bioJSMenuItem_actionPerformed(e); + } + }); + overviewMenuItem.setText(MessageManager .getString("label.overview_window")); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { overviewMenuItem_actionPerformed(e); @@ -1056,6 +1229,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); undoMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { undoMenuItem_actionPerformed(e); @@ -1068,6 +1242,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); redoMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { redoMenuItem_actionPerformed(e); @@ -1078,6 +1253,7 @@ public class GAlignFrame extends JInternalFrame conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(e); @@ -1086,6 +1262,7 @@ public class GAlignFrame extends JInternalFrame noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(e); @@ -1094,6 +1271,7 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { wrapMenuItem_actionPerformed(e); @@ -1105,6 +1283,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); printMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { printMenuItem_actionPerformed(e); @@ -1116,6 +1295,7 @@ public class GAlignFrame extends JInternalFrame renderGapsMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { renderGapsMenuItem_actionPerformed(e); @@ -1125,8 +1305,11 @@ public class GAlignFrame extends JInternalFrame findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); + findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.find_tip"))); findMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { findMenuItem_actionPerformed(e); @@ -1136,6 +1319,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.above_identity_threshold")); abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { abovePIDThreshold_actionPerformed(e); @@ -1145,6 +1329,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.show_sequence_features")); showSeqFeatures.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { showSeqFeatures_actionPerformed(actionEvent); @@ -1161,6 +1346,7 @@ public class GAlignFrame extends JInternalFrame showDbRefsMenuitem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showDbRefs_actionPerformed(e); @@ -1172,6 +1358,7 @@ public class GAlignFrame extends JInternalFrame showNpFeatsMenuitem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showNpFeats_actionPerformed(e); @@ -1183,6 +1370,7 @@ public class GAlignFrame extends JInternalFrame showGroupConservation.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showGroupConservation_actionPerformed(e); @@ -1195,6 +1383,7 @@ public class GAlignFrame extends JInternalFrame showGroupConsensus.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showGroupConsensus_actionPerformed(e); @@ -1206,6 +1395,7 @@ public class GAlignFrame extends JInternalFrame showConsensusHistogram.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showConsensusHistogram_actionPerformed(e); @@ -1217,6 +1407,7 @@ public class GAlignFrame extends JInternalFrame showSequenceLogo.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showSequenceLogo_actionPerformed(e); @@ -1228,6 +1419,7 @@ public class GAlignFrame extends JInternalFrame normaliseSequenceLogo.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { normaliseSequenceLogo_actionPerformed(e); @@ -1240,17 +1432,45 @@ public class GAlignFrame extends JInternalFrame applyAutoAnnotationSettings.setVisible(true); applyAutoAnnotationSettings.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { applyAutoAnnotationSettings_actionPerformed(e); } + }); + ButtonGroup buttonGroup = new ButtonGroup(); + buttonGroup.add(showAutoFirst); + buttonGroup.add(showAutoLast); + showAutoFirst.setText(MessageManager.getString("label.show_first")); + showAutoFirst.setSelected(Cache.getDefault( + Preferences.SHOW_AUTOCALC_ABOVE, + false)); + showAutoFirst.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + setShowAutoCalculatedAbove(showAutoFirst.isSelected()); + sortAnnotations_actionPerformed(); + } + }); + showAutoLast.setText(MessageManager.getString("label.show_last")); + showAutoLast.setSelected(!showAutoFirst.isSelected()); + showAutoLast.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + setShowAutoCalculatedAbove(!showAutoLast.isSelected()); + sortAnnotations_actionPerformed(); + } }); nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideColour_actionPerformed(e); @@ -1276,6 +1496,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); deleteGroups.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { deleteGroups_actionPerformed(e); @@ -1287,6 +1508,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); createGroup.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createGroup_actionPerformed(e); @@ -1299,6 +1521,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.SHIFT_MASK, false)); unGroup.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { unGroup_actionPerformed(e); @@ -1311,6 +1534,7 @@ public class GAlignFrame extends JInternalFrame copy.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(e); @@ -1322,16 +1546,16 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); cut.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(e); } }); delete.setText(MessageManager.getString("action.delete")); - delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false)); delete.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { delete_actionPerformed(e); @@ -1345,6 +1569,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.SHIFT_MASK, false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pasteNew_actionPerformed(e); @@ -1356,6 +1581,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); pasteThis.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pasteThis_actionPerformed(e); @@ -1365,6 +1591,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.apply_colour_to_all_groups")); applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { applyToAllGroups_actionPerformed(e); @@ -1372,6 +1599,7 @@ public class GAlignFrame extends JInternalFrame }); createPNG.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createPNG(null); @@ -1380,20 +1608,22 @@ public class GAlignFrame extends JInternalFrame createPNG.setActionCommand(MessageManager .getString("label.save_png_image")); createPNG.setText("PNG"); + font.setText(MessageManager.getString("action.font")); font.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { font_actionPerformed(e); } }); - seqLimits.setText(MessageManager .getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { seqLimit_actionPerformed(e); @@ -1402,17 +1632,30 @@ public class GAlignFrame extends JInternalFrame epsFile.setText("EPS"); epsFile.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createEPS(null); } }); + + createSVG.setText("SVG"); + createSVG.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createSVG(null); + } + }); + LoadtreeMenuItem.setActionCommand(MessageManager .getString("label.load_tree_for_sequence_set")); LoadtreeMenuItem.setText(MessageManager .getString("label.load_associated_tree")); LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { LoadtreeMenuItem_actionPerformed(e); @@ -1423,6 +1666,7 @@ public class GAlignFrame extends JInternalFrame scaleAbove.setText(MessageManager.getString("action.scale_above")); scaleAbove.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { scaleAbove_actionPerformed(e); @@ -1433,6 +1677,7 @@ public class GAlignFrame extends JInternalFrame scaleLeft.setText(MessageManager.getString("action.scale_left")); scaleLeft.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { scaleLeft_actionPerformed(e); @@ -1443,6 +1688,7 @@ public class GAlignFrame extends JInternalFrame scaleRight.setText(MessageManager.getString("action.scale_right")); scaleRight.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { scaleRight_actionPerformed(e); @@ -1455,6 +1701,7 @@ public class GAlignFrame extends JInternalFrame centreColumnLabelsMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { centreColumnLabels_actionPerformed(e); @@ -1467,6 +1714,7 @@ public class GAlignFrame extends JInternalFrame followHighlightMenuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { followHighlight_actionPerformed(); @@ -1478,6 +1726,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.modify_identity_thereshold")); modifyPID.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { modifyPID_actionPerformed(e); @@ -1488,6 +1737,7 @@ public class GAlignFrame extends JInternalFrame modifyConservation .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { modifyConservation_actionPerformed(e); @@ -1498,15 +1748,18 @@ public class GAlignFrame extends JInternalFrame sort.setText(MessageManager.getString("action.sort")); sort.addMenuListener(new MenuListener() { + @Override public void menuSelected(MenuEvent e) { buildTreeMenu(); } + @Override public void menuDeselected(MenuEvent e) { } + @Override public void menuCanceled(MenuEvent e) { } @@ -1514,17 +1767,20 @@ public class GAlignFrame extends JInternalFrame sortByAnnotScore.setText(MessageManager .getString("label.sort_by_score")); sort.add(sortByAnnotScore); - sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() + sort.addMenuListener(new javax.swing.event.MenuListener() { + @Override public void menuCanceled(MenuEvent e) { } + @Override public void menuDeselected(MenuEvent e) { } + @Override public void menuSelected(MenuEvent e) { buildSortByAnnotationScoresMenu(); @@ -1541,6 +1797,7 @@ public class GAlignFrame extends JInternalFrame .getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { padGapsMenuitem_actionPerformed(e); @@ -1550,6 +1807,7 @@ public class GAlignFrame extends JInternalFrame vamsasStore.setText(MessageManager.getString("label.vamsas_store")); vamsasStore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { vamsasStore_actionPerformed(e); @@ -1559,6 +1817,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.translate_cDNA")); showTranslation.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showTranslation_actionPerformed(e); @@ -1568,6 +1827,7 @@ public class GAlignFrame extends JInternalFrame + "..."); extractScores.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { extractScores_actionPerformed(e); @@ -1586,6 +1846,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { featureSettings_actionPerformed(e); @@ -1595,6 +1856,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("label.fetch_sequences")); fetchSequence.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fetchSequence_actionPerformed(e); @@ -1605,6 +1867,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.by_annotation")); annotationColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotationColour_actionPerformed(e); @@ -1615,6 +1878,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.by_rna_helixes")); rnahelicesColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { rnahelicesColour_actionPerformed(e); @@ -1625,6 +1889,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { associatedData_actionPerformed(e); @@ -1636,6 +1901,7 @@ public class GAlignFrame extends JInternalFrame "AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { autoCalculate_actionPerformed(e); @@ -1651,6 +1917,7 @@ public class GAlignFrame extends JInternalFrame .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortByTreeOption_actionPerformed(e); @@ -1666,6 +1933,7 @@ public class GAlignFrame extends JInternalFrame listenToViewSelections.setState(false); listenToViewSelections.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { listenToViewSelections_actionPerformed(e); @@ -1677,6 +1945,7 @@ public class GAlignFrame extends JInternalFrame addFromFile.setText(MessageManager.getString("label.from_file")); addFromFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { addFromFile_actionPerformed(e); @@ -1685,6 +1954,7 @@ public class GAlignFrame extends JInternalFrame addFromText.setText(MessageManager.getString("label.from_textbox")); addFromText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { addFromText_actionPerformed(e); @@ -1693,6 +1963,7 @@ public class GAlignFrame extends JInternalFrame addFromURL.setText(MessageManager.getString("label.from_url")); addFromURL.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { addFromURL_actionPerformed(e); @@ -1702,6 +1973,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.export_features")); exportFeatures.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { exportFeatures_actionPerformed(e); @@ -1711,6 +1983,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.export_annotations")); exportAnnotations.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { exportAnnotations_actionPerformed(e); @@ -1723,6 +1996,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_sequence_visibility")); showAllSeqs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showAllSeqs_actionPerformed(e); @@ -1733,6 +2007,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_columns_visibility")); showAllColumns.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showAllColumns_actionPerformed(e); @@ -1745,6 +2020,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_sequence_visibility")); hideSelSequences.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSelSequences_actionPerformed(e); @@ -1756,6 +2032,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_columns_visibility")); hideSelColumns.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSelColumns_actionPerformed(e); @@ -1765,6 +2042,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.selected_region")); hideAllSelection.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideAllSelection_actionPerformed(e); @@ -1775,6 +2053,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.all_but_selected_region")); hideAllButSelection.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideAllButSelection_actionPerformed(e); @@ -1786,16 +2065,17 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggles_visibility_hidden_selected_regions")); showAllhidden.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showAllhidden_actionPerformed(e); } }); - hiddenMarkers.setText(MessageManager .getString("action.show_hidden_markers")); hiddenMarkers.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hiddenMarkers_actionPerformed(e); @@ -1809,6 +2089,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.ALT_MASK, false)); invertColSel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertColSel_actionPerformed(e); @@ -1816,6 +2097,7 @@ public class GAlignFrame extends JInternalFrame }); tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { JTabbedPane pane = (JTabbedPane) evt.getSource(); @@ -1825,6 +2107,7 @@ public class GAlignFrame extends JInternalFrame }); tabbedPane.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { tabbedPane_mousePressed(e); @@ -1832,6 +2115,7 @@ public class GAlignFrame extends JInternalFrame }); tabbedPane.addFocusListener(new FocusAdapter() { + @Override public void focusGained(FocusEvent e) { tabbedPane_focusGained(e); @@ -1843,6 +2127,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); save.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save_actionPerformed(e); @@ -1852,6 +2137,7 @@ public class GAlignFrame extends JInternalFrame reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { reload_actionPerformed(e); @@ -1863,6 +2149,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); newView.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { newView_actionPerformed(e); @@ -1875,6 +2162,7 @@ public class GAlignFrame extends JInternalFrame + "..."); textColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(e); @@ -1886,6 +2174,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { idRightAlign_actionPerformed(e); @@ -1897,6 +2186,7 @@ public class GAlignFrame extends JInternalFrame java.awt.event.KeyEvent.VK_G, 0, false)); gatherViews.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { gatherViews_actionPerformed(e); @@ -1908,6 +2198,7 @@ public class GAlignFrame extends JInternalFrame java.awt.event.KeyEvent.VK_X, 0, false)); expandViews.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { expandViews_actionPerformed(e); @@ -1917,6 +2208,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("action.page_setup") + "..."); pageSetup.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pageSetup_actionPerformed(e); @@ -1926,6 +2218,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.alignment_props") + "..."); alignmentProperties.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { alignmentProperties(); @@ -1939,6 +2232,7 @@ public class GAlignFrame extends JInternalFrame alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(annotationsMenu); alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); @@ -1988,7 +2282,19 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(hideMenu); viewMenu.addSeparator(); viewMenu.add(followHighlightMenuItem); - viewMenu.add(annotationPanelMenuItem); + annotationsMenu.add(annotationPanelMenuItem); + annotationsMenu.addSeparator(); + annotationsMenu.add(showAllAlAnnotations); + annotationsMenu.add(hideAllAlAnnotations); + annotationsMenu.addSeparator(); + annotationsMenu.add(showAllSeqAnnotations); + annotationsMenu.add(hideAllSeqAnnotations); + annotationsMenu.add(sortAnnBySequence); + annotationsMenu.add(sortAnnByLabel); + annotationsMenu.addSeparator(); + autoAnnMenu.add(showAutoFirst); + autoAnnMenu.add(showAutoLast); + autoAnnMenu.addSeparator(); autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); @@ -1996,7 +2302,7 @@ public class GAlignFrame extends JInternalFrame autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); - viewMenu.add(autoAnnMenu); + annotationsMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); // viewMenu.add(showSeqFeaturesHeight); @@ -2061,6 +2367,8 @@ public class GAlignFrame extends JInternalFrame jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); + jMenu2.add(createBioJS); + jMenu2.add(createSVG); addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); addSequenceMenu.add(addFromURL); @@ -2107,6 +2415,59 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + /** + * Action on clicking sort annotations by type. + * + * @param sortOrder + */ + protected void sortAnnotations_actionPerformed() + { + } + + /** + * Action on clicking Show all annotations. + * + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + protected void showAllAnnotations_actionPerformed(boolean forSequences, + boolean forAlignment) + { + setAnnotationsVisibility(true, forSequences, forAlignment); + } + + /** + * Action on clicking Hide all annotations. + * + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + protected void hideAllAnnotations_actionPerformed(boolean forSequences, + boolean forAlignment) + { + setAnnotationsVisibility(false, forSequences, forAlignment); + } + + /** + * Set the visibility of annotations to true or false. Can act on + * sequence-related annotations, or alignment-related, or both. + * + * @param visible + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + protected void setAnnotationsVisibility(boolean visible, + boolean forSequences, boolean forAlignment) + { + + } + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub @@ -2265,6 +2626,11 @@ public class GAlignFrame extends JInternalFrame { } + protected void bioJSMenuItem_actionPerformed(ActionEvent e) + { + + } + protected void closeMenuItem_actionPerformed(boolean b) { } @@ -2518,6 +2884,10 @@ public class GAlignFrame extends JInternalFrame { } + public void createSVG(java.io.File f) + { + + } protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { @@ -2751,4 +3121,24 @@ public class GAlignFrame extends JInternalFrame // TODO Auto-generated method stub } + + protected boolean isShowAutoCalculatedAbove() + { + return showAutoCalculatedAbove; + } + + protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove) + { + this.showAutoCalculatedAbove = showAutoCalculatedAbove; + } + + protected SequenceAnnotationOrder getAnnotationSortOrder() + { + return annotationSortOrder; + } + + protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder) + { + this.annotationSortOrder = annotationSortOrder; + } }