X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=439a67d88c676180ce0fd46b1074d096fae00978;hb=bbfdb203ce3a889600caa52478478b75ab03809f;hp=04955e32785318abf1e502ea3b7b492734cfeb86;hpb=9d4857e06cfe5d96edb50bf702fffc58139b7aab;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 04955e3..439a67d 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.jbgui;
@@ -114,6 +113,13 @@ public class GAlignFrame extends JInternalFrame
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -122,7 +128,7 @@ public class GAlignFrame extends JInternalFrame
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
JMenuItem htmlMenuItem = new JMenuItem();
@@ -147,9 +153,8 @@ public class GAlignFrame extends JInternalFrame
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+ public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
@@ -196,7 +201,9 @@ public class GAlignFrame extends JInternalFrame
JMenu jMenu2 = new JMenu();
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
protected ButtonGroup colours = new ButtonGroup();
@@ -215,10 +222,16 @@ public class GAlignFrame extends JInternalFrame
JMenuItem annotationColour = new JMenuItem();
+ protected JMenuItem rnahelicesColour = new JMenuItem();
+
JMenuItem associatedData = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
JMenu addSequenceMenu = new JMenu();
JMenuItem addFromFile = new JMenuItem();
@@ -236,7 +249,7 @@ public class GAlignFrame extends JInternalFrame
GridLayout gridLayout1 = new GridLayout();
JMenu jMenu3 = new JMenu();
-
+
JMenuItem showAllSeqs = new JMenuItem();
JMenuItem showAllColumns = new JMenuItem();
@@ -247,6 +260,12 @@ public class GAlignFrame extends JInternalFrame
JMenuItem hideSelColumns = new JMenuItem();
+ JMenuItem hideAllButSelection = new JMenuItem();
+
+ JMenuItem hideAllSelection = new JMenuItem();
+
+ JMenuItem showAllhidden = new JMenuItem();
+
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
JMenuItem invertColSel = new JMenuItem();
@@ -270,7 +289,7 @@ public class GAlignFrame extends JInternalFrame
protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
-
+
protected JMenuItem gatherViews = new JMenuItem();
protected JMenuItem expandViews = new JMenuItem();
@@ -278,17 +297,29 @@ public class GAlignFrame extends JInternalFrame
JMenuItem pageSetup = new JMenuItem();
JMenuItem alignmentProperties = new JMenuItem();
-
+
JMenu tooltipSettingsMenu = new JMenu();
- private JMenuItem justifyLeftMenuItem=new JMenuItem();
+ private JMenuItem justifyLeftMenuItem = new JMenuItem();
+
+ private JMenuItem justifyRightMenuItem = new JMenuItem();
+
+ JMenu autoAnnMenu = new JMenu();
+
+ protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
- private JMenuItem justifyRightMenuItem=new JMenuItem();
-
- protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private JMenuItem grpsFromSelection = new JMenuItem();
+
public GAlignFrame()
{
try
@@ -345,8 +376,7 @@ public class GAlignFrame extends JInternalFrame
if (evt.isControlDown()
|| SwingUtilities.isRightMouseButton(evt))
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
@@ -396,6 +426,8 @@ public class GAlignFrame extends JInternalFrame
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
@@ -412,9 +444,6 @@ public class GAlignFrame extends JInternalFrame
switch (index)
{
- case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
case ColourSchemeProperty.CLUSTAL:
clustalColour.setSelected(true);
@@ -469,10 +498,25 @@ public class GAlignFrame extends JInternalFrame
break;
+ case ColourSchemeProperty.PURINEPYRIMIDINE:
+ purinePyrimidineColour.setSelected(true);
+
+ break;
+ /*
+ * case ColourSchemeProperty.COVARIATION:
+ * covariationColour.setSelected(true);
+ *
+ * break;
+ */
case ColourSchemeProperty.USER_DEFINED:
userDefinedColour.setSelected(true);
break;
+ case ColourSchemeProperty.NONE:
+ default:
+ noColourmenuItem.setSelected(true);
+ break;
+
}
}
@@ -550,7 +594,7 @@ public class GAlignFrame extends JInternalFrame
public void actionPerformed(ActionEvent e)
{
makeGrpsFromSelection_actionPerformed(e);
- }
+ }
});
remove2LeftMenuItem.setText("Remove Left");
@@ -603,21 +647,23 @@ public class GAlignFrame extends JInternalFrame
}
});
justifyLeftMenuItem.setText("Left Justify Alignment");
- justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- justifyLeftMenuItem_actionPerformed(e);
- }
- });
+ justifyLeftMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
+ });
justifyRightMenuItem.setText("Right Justify Alignment");
- justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- justifyRightMenuItem_actionPerformed(e);
- }
- });
+ justifyRightMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
+ });
viewBoxesMenuItem.setText("Boxes");
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -636,15 +682,16 @@ public class GAlignFrame extends JInternalFrame
viewTextMenuItem_actionPerformed(e);
}
});
- showUnconservedMenuItem.setText("Show Unconserved");
- showUnconservedMenuItem.setState(false);
- showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showUnconservedMenuItem_actionPerformed(e);
- }
- });
+ showNonconservedMenuItem.setText("Show nonconserved");
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
sortPairwiseMenuItem.setText("by Pairwise Identity");
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
@@ -663,13 +710,14 @@ public class GAlignFrame extends JInternalFrame
}
});
sortLengthMenuItem.setText("By Length");
- sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortLengthMenuItem_actionPerformed(e);
- }
- });
+ sortLengthMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortLengthMenuItem_actionPerformed(e);
+ }
+ });
sortGroupMenuItem.setText("by Group");
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
@@ -823,6 +871,31 @@ public class GAlignFrame extends JInternalFrame
BLOSUM62Colour_actionPerformed(e);
}
});
+ nucleotideColour.setText("Nucleotide");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(e); } });
+ */
+
avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
@@ -975,14 +1048,12 @@ public class GAlignFrame extends JInternalFrame
showSeqFeatures_actionPerformed(actionEvent);
}
});
- showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
- showSeqFeaturesHeight.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- showSeqFeaturesHeight_actionPerformed(actionEvent);
- }
- });
+ /*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+ * void actionPerformed(ActionEvent actionEvent) {
+ * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+ */
showDbRefsMenuitem.setText("Show Database Refs");
showDbRefsMenuitem.addActionListener(new ActionListener()
{
@@ -991,7 +1062,7 @@ public class GAlignFrame extends JInternalFrame
{
showDbRefs_actionPerformed(e);
}
-
+
});
showNpFeatsMenuitem.setText("Show Non-Positional Features");
showNpFeatsMenuitem.addActionListener(new ActionListener()
@@ -1001,7 +1072,7 @@ public class GAlignFrame extends JInternalFrame
{
showNpFeats_actionPerformed(e);
}
-
+
});
showGroupConservation.setText("Group Conservation");
showGroupConservation.addActionListener(new ActionListener()
@@ -1011,7 +1082,7 @@ public class GAlignFrame extends JInternalFrame
{
showGroupConservation_actionPerformed(e);
}
-
+
});
showGroupConsensus.setText("Group Consensus");
@@ -1022,7 +1093,49 @@ public class GAlignFrame extends JInternalFrame
{
showGroupConsensus_actionPerformed(e);
}
-
+
+ });
+ showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ normaliseSequenceLogo.setText("Normalise Consensus Logo");
+ normaliseSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ normaliseSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+
});
nucleotideColour.setText("Nucleotide");
@@ -1203,9 +1316,9 @@ public class GAlignFrame extends JInternalFrame
{
followHighlight_actionPerformed();
}
-
+
});
-
+
modifyPID.setText("Modify Identity Threshold...");
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
@@ -1299,7 +1412,7 @@ public class GAlignFrame extends JInternalFrame
}
});
extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
- // score extraction
+ // score extraction
showProducts.setText("Get Cross References");
/*
* showProducts.addActionListener(new ActionListener() {
@@ -1332,6 +1445,16 @@ public class GAlignFrame extends JInternalFrame
annotationColour_actionPerformed(e);
}
});
+
+ rnahelicesColour.setText("By RNA helices");
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_actionPerformed(e);
+ }
+ });
+
associatedData.setText("Load Features / Annotations");
associatedData.addActionListener(new ActionListener()
{
@@ -1350,6 +1473,29 @@ public class GAlignFrame extends JInternalFrame
autoCalculate_actionPerformed(e);
}
});
+ sortByTree.setText("Sort Alignment With New Tree");
+ sortByTree.setToolTipText("Enable this to automatically sort
the alignment when you open
a new tree.");
+ sortByTree.setState(jalview.bin.Cache.getDefault(
+ "SORT_BY_TREE", false));
+ sortByTree.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortByTreeOption_actionPerformed(e);
+ }
+ });
+
+ listenToViewSelections.setText("Listen for selections");
+ listenToViewSelections.setToolTipText("When selected, selections in this view will mirror
selections made on the same sequences in other views.");
+ listenToViewSelections.setState(false);
+ listenToViewSelections.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ listenToViewSelections_actionPerformed(e);
+ }
+ });
+
addSequenceMenu.setText("Add Sequences");
addFromFile.setText("From File");
addFromFile.addActionListener(new ActionListener()
@@ -1394,6 +1540,7 @@ public class GAlignFrame extends JInternalFrame
statusPanel.setLayout(gridLayout1);
jMenu3.setText("Show");
showAllSeqs.setText("All Sequences");
+ showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
showAllSeqs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1402,6 +1549,7 @@ public class GAlignFrame extends JInternalFrame
}
});
showAllColumns.setText("All Columns");
+ showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
showAllColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1411,6 +1559,7 @@ public class GAlignFrame extends JInternalFrame
});
hideMenu.setText("Hide");
hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
hideSelSequences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1419,6 +1568,7 @@ public class GAlignFrame extends JInternalFrame
}
});
hideSelColumns.setText("Selected Columns");
+ hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
hideSelColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1426,6 +1576,34 @@ public class GAlignFrame extends JInternalFrame
hideSelColumns_actionPerformed(e);
}
});
+ hideAllSelection.setText("Selected Region");
+ hideAllSelection.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllSelection_actionPerformed(e);
+ }
+ });
+ // TODO: should be hidden if no selection exists.
+ hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
+ hideAllButSelection.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllButSelection_actionPerformed(e);
+ }
+ });
+ showAllhidden.setText("All Sequences and Columns");
+ showAllhidden
+ .setToolTipText("H toggles visibility of hidden or selected regions.");
+ showAllhidden.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllhidden_actionPerformed(e);
+ }
+ });
+
hiddenMarkers.setText("Show Hidden Markers");
hiddenMarkers.addActionListener(new ActionListener()
{
@@ -1559,6 +1737,7 @@ public class GAlignFrame extends JInternalFrame
}
});
tooltipSettingsMenu.setText("Sequence ID Tooltip");
+ autoAnnMenu.setText("Autocalculated Annotation");
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
@@ -1599,9 +1778,10 @@ public class GAlignFrame extends JInternalFrame
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
// dont add these yet in the CVS build - they cannot be undone!
- editMenu.add(justifyLeftMenuItem);
- editMenu.add(justifyRightMenuItem);
- editMenu.addSeparator();
+ // Excluded from Jalview 2.5 release - undo needs to be implemented.
+ // editMenu.add(justifyLeftMenuItem);
+ // editMenu.add(justifyRightMenuItem);
+ // editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
viewMenu.add(newView);
viewMenu.add(expandViews);
@@ -1612,12 +1792,18 @@ public class GAlignFrame extends JInternalFrame
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
viewMenu.add(annotationPanelMenuItem);
- viewMenu.add(showGroupConservation);
- viewMenu.add(showGroupConsensus);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
- viewMenu.add(showSeqFeaturesHeight);
-
+ // viewMenu.add(showSeqFeaturesHeight);
+
viewMenu.add(featureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
tooltipSettingsMenu.add(showNpFeatsMenuitem);
@@ -1641,6 +1827,8 @@ public class GAlignFrame extends JInternalFrame
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
@@ -1648,6 +1836,7 @@ public class GAlignFrame extends JInternalFrame
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
@@ -1657,6 +1846,7 @@ public class GAlignFrame extends JInternalFrame
calculateMenu.add(showTranslation);
calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
webServiceNoServices = new JMenuItem("");
@@ -1683,8 +1873,12 @@ public class GAlignFrame extends JInternalFrame
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
jMenu3.add(showAllColumns);
jMenu3.add(showAllSeqs);
+ jMenu3.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
@@ -1699,7 +1893,7 @@ public class GAlignFrame extends JInternalFrame
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelsMenuItem);
- formatMenu.add(showUnconservedMenuItem);
+ formatMenu.add(showNonconservedMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
@@ -1708,67 +1902,118 @@ public class GAlignFrame extends JInternalFrame
selectMenu.add(invertColSel);
selectMenu.add(deleteGroups);
selectMenu.add(grpsFromSelection);
+ // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
+ //selectMenu.addSeparator();
+ //selectMenu.add(listenToViewSelections);
}
- protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
- protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
+ protected void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showSeqFeaturesHeight_actionPerformed(
ActionEvent actionEvent)
{
// TODO Auto-generated method stub
-
+
}
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void followHighlight_actionPerformed()
{
// TODO Auto-generated method stub
-
+
}
protected void showNpFeats_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showDbRefs_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void centreColumnLabels_actionPerformed(ActionEvent e)
@@ -1972,6 +2217,14 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
@@ -2124,6 +2377,11 @@ public class GAlignFrame extends JInternalFrame
}
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void associatedData_actionPerformed(ActionEvent e)
{
@@ -2134,6 +2392,11 @@ public class GAlignFrame extends JInternalFrame
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_actionPerformed(ActionEvent e)
{