X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d3154c7408f4ff0ebbf1844e9dd3ced60d788157;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=16e78f546ed8babed9b14fa2452476c9b44215c8;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 16e78f5..d3154c7 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -142,7 +142,7 @@ public class GAlignFrame extends JInternalFrame
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
+
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
@@ -187,8 +187,9 @@ public class GAlignFrame extends JInternalFrame
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
-
+
JMenuItem createGroup = new JMenuItem();
+
JMenuItem unGroup = new JMenuItem();
JMenuItem delete = new JMenuItem();
@@ -246,7 +247,7 @@ public class GAlignFrame extends JInternalFrame
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem extractScores = new JMenuItem();
-
+
protected JMenuItem expandAlignment = new JMenuItem();
protected JMenu showProducts = new JMenu();
@@ -415,8 +416,10 @@ public class GAlignFrame extends JInternalFrame
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
@@ -542,11 +545,11 @@ public class GAlignFrame extends JInternalFrame
purinePyrimidineColour.setSelected(true);
break;
-
+
case ColourSchemeProperty.RNAINTERACTION:
- RNAInteractionColour.setSelected(true);
+ RNAInteractionColour.setSelected(true);
- break;
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
@@ -598,7 +601,8 @@ public class GAlignFrame extends JInternalFrame
colourMenu.setText(MessageManager.getString("action.colour"));
calculateMenu.setText(MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
- selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
+ selectAllSequenceMenuItem.setText(MessageManager
+ .getString("action.select_all"));
selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -610,7 +614,8 @@ public class GAlignFrame extends JInternalFrame
selectAllSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
+ deselectAllSequenceMenuItem.setText(MessageManager
+ .getString("action.deselect_all"));
deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
deselectAllSequenceMenuItem
@@ -621,7 +626,8 @@ public class GAlignFrame extends JInternalFrame
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.setText(MessageManager
+ .getString("action.invert_sequence_selection"));
invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -633,7 +639,8 @@ public class GAlignFrame extends JInternalFrame
invertSequenceMenuItem_actionPerformed(e);
}
});
- grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.setText(MessageManager
+ .getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -641,16 +648,20 @@ public class GAlignFrame extends JInternalFrame
makeGrpsFromSelection_actionPerformed(e);
}
});
- expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
- expandAlignment.setToolTipText(MessageManager.getString("label.view_flanking_regions"));
- expandAlignment.addActionListener(new java.awt.event.ActionListener() {
+ expandAlignment.setText(MessageManager
+ .getString("action.view_flanking_regions"));
+ expandAlignment.setToolTipText(MessageManager
+ .getString("label.view_flanking_regions"));
+ expandAlignment.addActionListener(new java.awt.event.ActionListener()
+ {
@Override
public void actionPerformed(ActionEvent e)
{
expand_newalign(e);
}
});
- remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.setText(MessageManager
+ .getString("action.remove_left"));
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
@@ -662,7 +673,8 @@ public class GAlignFrame extends JInternalFrame
remove2LeftMenuItem_actionPerformed(e);
}
});
- remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.setText(MessageManager
+ .getString("action.remove_right"));
remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
@@ -674,7 +686,8 @@ public class GAlignFrame extends JInternalFrame
remove2RightMenuItem_actionPerformed(e);
}
});
- removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setText(MessageManager
+ .getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -686,7 +699,8 @@ public class GAlignFrame extends JInternalFrame
removeGappedColumnMenuItem_actionPerformed(e);
}
});
- removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.setText(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
@@ -699,7 +713,8 @@ public class GAlignFrame extends JInternalFrame
removeAllGapsMenuItem_actionPerformed(e);
}
});
- justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.setText(MessageManager
+ .getString("action.left_justify_alignment"));
justifyLeftMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -708,7 +723,8 @@ public class GAlignFrame extends JInternalFrame
justifyLeftMenuItem_actionPerformed(e);
}
});
- justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
+ justifyRightMenuItem.setText(MessageManager
+ .getString("action.right_justify_alignment"));
justifyRightMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -735,7 +751,8 @@ public class GAlignFrame extends JInternalFrame
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+ showNonconservedMenuItem.setText(MessageManager
+ .getString("label.show_non_conversed"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem
.addActionListener(new java.awt.event.ActionListener()
@@ -745,7 +762,8 @@ public class GAlignFrame extends JInternalFrame
showUnconservedMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.setText(MessageManager
+ .getString("action.by_pairwise_id"));
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -762,7 +780,8 @@ public class GAlignFrame extends JInternalFrame
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+ sortLengthMenuItem
+ .setText(MessageManager.getString("action.by_length"));
sortLengthMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -779,7 +798,8 @@ public class GAlignFrame extends JInternalFrame
sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.setText(MessageManager
+ .getString("action.remove_redundancy"));
removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -791,7 +811,8 @@ public class GAlignFrame extends JInternalFrame
removeRedundancyMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.setText(MessageManager
+ .getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -800,7 +821,8 @@ public class GAlignFrame extends JInternalFrame
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.setText(MessageManager
+ .getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -808,8 +830,8 @@ public class GAlignFrame extends JInternalFrame
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem
- .setText(MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.setText(MessageManager
+ .getString("label.average_distance_identity"));
averageDistanceTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -818,7 +840,8 @@ public class GAlignFrame extends JInternalFrame
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.setText(MessageManager
+ .getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -833,7 +856,8 @@ public class GAlignFrame extends JInternalFrame
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
+ outputTextboxMenu.setText(MessageManager
+ .getString("label.out_to_textbox"));
clustalColour.setText(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
@@ -859,7 +883,8 @@ public class GAlignFrame extends JInternalFrame
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -876,7 +901,8 @@ public class GAlignFrame extends JInternalFrame
helixColour_actionPerformed(e);
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -900,7 +926,8 @@ public class GAlignFrame extends JInternalFrame
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -908,7 +935,8 @@ public class GAlignFrame extends JInternalFrame
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -916,7 +944,8 @@ public class GAlignFrame extends JInternalFrame
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour
+ .setText(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -933,7 +962,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
@@ -942,13 +972,14 @@ public class GAlignFrame extends JInternalFrame
purinePyrimidineColour_actionPerformed(e);
}
});
-
+
RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+ RNAInteractionColour
+ .addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- RNAInteractionColour_actionPerformed(e);
+ RNAInteractionColour_actionPerformed(e);
}
});
/*
@@ -958,7 +989,8 @@ public class GAlignFrame extends JInternalFrame
* covariationColour_actionPerformed(e); } });
*/
- avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.setText(MessageManager
+ .getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -967,7 +999,8 @@ public class GAlignFrame extends JInternalFrame
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.setText(MessageManager
+ .getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -977,7 +1010,8 @@ public class GAlignFrame extends JInternalFrame
}
});
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem.setText(MessageManager
+ .getString("label.show_annotations"));
annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
"SHOW_ANNOTATIONS", true));
annotationPanelMenuItem
@@ -988,7 +1022,8 @@ public class GAlignFrame extends JInternalFrame
annotationPanelMenuItem_actionPerformed(e);
}
});
- colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.setText(MessageManager
+ .getString("label.colour_text"));
colourTextMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1005,7 +1040,8 @@ public class GAlignFrame extends JInternalFrame
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.setText(MessageManager
+ .getString("label.overview_window"));
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1037,7 +1073,8 @@ public class GAlignFrame extends JInternalFrame
redoMenuItem_actionPerformed(e);
}
});
- conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1073,7 +1110,8 @@ public class GAlignFrame extends JInternalFrame
printMenuItem_actionPerformed(e);
}
});
- renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem
+ .setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem
.addActionListener(new java.awt.event.ActionListener()
@@ -1094,7 +1132,8 @@ public class GAlignFrame extends JInternalFrame
findMenuItem_actionPerformed(e);
}
});
- abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1102,7 +1141,8 @@ public class GAlignFrame extends JInternalFrame
abovePIDThreshold_actionPerformed(e);
}
});
- showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
+ showSeqFeatures.setText(MessageManager
+ .getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
@@ -1116,7 +1156,8 @@ public class GAlignFrame extends JInternalFrame
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
+ showDbRefsMenuitem.setText(MessageManager
+ .getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
@@ -1126,7 +1167,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(MessageManager
+ .getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
@@ -1136,7 +1178,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
+ showGroupConservation.setText(MessageManager
+ .getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
@@ -1147,7 +1190,8 @@ public class GAlignFrame extends JInternalFrame
});
- showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
+ showGroupConsensus.setText(MessageManager
+ .getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
@@ -1157,7 +1201,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(MessageManager
+ .getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
@@ -1167,7 +1212,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
+ showSequenceLogo.setText(MessageManager
+ .getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
@@ -1177,7 +1223,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.setText(MessageManager
+ .getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
@@ -1187,7 +1234,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setText(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
@@ -1221,7 +1269,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
+ deleteGroups
+ .setText(MessageManager.getString("action.undefine_groups"));
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask(), false));
@@ -1245,8 +1294,9 @@ public class GAlignFrame extends JInternalFrame
});
unGroup.setText(MessageManager.getString("action.remove_group"));
unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+ java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
unGroup.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1311,7 +1361,8 @@ public class GAlignFrame extends JInternalFrame
pasteThis_actionPerformed(e);
}
});
- applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setText(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1326,7 +1377,8 @@ public class GAlignFrame extends JInternalFrame
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
+ createPNG.setActionCommand(MessageManager
+ .getString("label.save_png_image"));
createPNG.setText("PNG");
font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
@@ -1337,7 +1389,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
+ seqLimits.setText(MessageManager
+ .getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new java.awt.event.ActionListener()
{
@@ -1354,8 +1407,10 @@ public class GAlignFrame extends JInternalFrame
createEPS(null);
}
});
- LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
- LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
+ 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()
{
public void actionPerformed(ActionEvent e)
@@ -1395,7 +1450,8 @@ public class GAlignFrame extends JInternalFrame
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.setText(MessageManager
+ .getString("label.centre_column_labels"));
centreColumnLabelsMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1406,7 +1462,8 @@ public class GAlignFrame extends JInternalFrame
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
+ followHighlightMenuItem.setText(MessageManager
+ .getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
@@ -1417,7 +1474,8 @@ public class GAlignFrame extends JInternalFrame
});
- modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1425,7 +1483,8 @@ public class GAlignFrame extends JInternalFrame
modifyPID_actionPerformed(e);
}
});
- modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_thereshold"));
modifyConservation
.addActionListener(new java.awt.event.ActionListener()
{
@@ -1434,7 +1493,8 @@ public class GAlignFrame extends JInternalFrame
modifyConservation_actionPerformed(e);
}
});
- sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
+ sortByTreeMenu
+ .setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
sort.addMenuListener(new MenuListener()
{
@@ -1451,7 +1511,8 @@ public class GAlignFrame extends JInternalFrame
{
}
});
- sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
+ sortByAnnotScore.setText(MessageManager
+ .getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
{
@@ -1471,7 +1532,8 @@ public class GAlignFrame extends JInternalFrame
});
sortByAnnotScore.setVisible(false);
- calculateTree.setText(MessageManager.getString("action.calculate_tree"));
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree"));
jMenu2.setText(MessageManager.getString("label.export_image"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
@@ -1493,7 +1555,8 @@ public class GAlignFrame extends JInternalFrame
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1501,7 +1564,8 @@ public class GAlignFrame extends JInternalFrame
showTranslation_actionPerformed(e);
}
});
- extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
+ extractScores.setText(MessageManager.getString("label.extract_scores")
+ + "...");
extractScores.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1518,7 +1582,8 @@ public class GAlignFrame extends JInternalFrame
* public void actionPerformed(ActionEvent e) {
* showProducts_actionPerformed(e); } });
*/
- openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
+ openFeatureSettings.setText(MessageManager
+ .getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1526,7 +1591,8 @@ public class GAlignFrame extends JInternalFrame
featureSettings_actionPerformed(e);
}
});
- fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
+ fetchSequence
+ .setText(MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1535,7 +1601,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- annotationColour.setText(MessageManager.getString("action.by_annotation"));
+ annotationColour.setText(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1544,7 +1611,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
+ rnahelicesColour.setText(MessageManager
+ .getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1553,7 +1621,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- associatedData.setText(MessageManager.getString("label.load_features_annotations"));
+ associatedData.setText(MessageManager
+ .getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1561,7 +1630,8 @@ public class GAlignFrame extends JInternalFrame
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
autoCalculate.setState(jalview.bin.Cache.getDefault(
"AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
@@ -1571,9 +1641,12 @@ public class GAlignFrame extends JInternalFrame
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setText(MessageManager
+ .getString("label.sort_alignment_new_tree"));
sortByTree
- .setToolTipText("" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+ .setToolTipText(""
+ + MessageManager
+ .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
@@ -1584,9 +1657,12 @@ public class GAlignFrame extends JInternalFrame
}
});
- listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
+ listenToViewSelections.setText(MessageManager
+ .getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+ .setToolTipText(""
+ + MessageManager
+ .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
@@ -1596,7 +1672,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+ addSequenceMenu
+ .setText(MessageManager.getString("label.add_sequences"));
addFromFile.setText(MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
@@ -1621,7 +1698,8 @@ public class GAlignFrame extends JInternalFrame
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText(MessageManager.getString("label.export_features"));
+ exportFeatures.setText(MessageManager
+ .getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1629,7 +1707,8 @@ public class GAlignFrame extends JInternalFrame
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
+ exportAnnotations.setText(MessageManager
+ .getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1640,7 +1719,8 @@ public class GAlignFrame extends JInternalFrame
statusPanel.setLayout(gridLayout1);
jMenu3.setText(MessageManager.getString("action.show"));
showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
- showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+ showAllSeqs.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1649,7 +1729,8 @@ public class GAlignFrame extends JInternalFrame
}
});
showAllColumns.setText(MessageManager.getString("label.all_columns"));
- showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+ showAllColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1658,8 +1739,10 @@ public class GAlignFrame extends JInternalFrame
}
});
hideMenu.setText(MessageManager.getString("action.hide"));
- hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
- hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+ hideSelSequences.setText(MessageManager
+ .getString("label.selected_sequences"));
+ hideSelSequences.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1667,8 +1750,10 @@ public class GAlignFrame extends JInternalFrame
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+ hideSelColumns.setText(MessageManager
+ .getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1676,7 +1761,8 @@ public class GAlignFrame extends JInternalFrame
hideSelColumns_actionPerformed(e);
}
});
- hideAllSelection.setText(MessageManager.getString("label.selected_region"));
+ hideAllSelection.setText(MessageManager
+ .getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1685,7 +1771,8 @@ public class GAlignFrame extends JInternalFrame
}
});
// TODO: should be hidden if no selection exists.
- hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
+ hideAllButSelection.setText(MessageManager
+ .getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1693,9 +1780,10 @@ public class GAlignFrame extends JInternalFrame
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
- showAllhidden
- .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
+ showAllhidden.setText(MessageManager
+ .getString("label.all_sequences_columns"));
+ showAllhidden.setToolTipText(MessageManager
+ .getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1704,7 +1792,8 @@ public class GAlignFrame extends JInternalFrame
}
});
- hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(MessageManager
+ .getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1712,7 +1801,8 @@ public class GAlignFrame extends JInternalFrame
hiddenMarkers_actionPerformed(e);
}
});
- invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
+ invertColSel.setText(MessageManager
+ .getString("action.invert_column_selection"));
invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
.getMenuShortcutKeyMask()
@@ -1778,8 +1868,11 @@ public class GAlignFrame extends JInternalFrame
newView_actionPerformed(e);
}
});
- tabbedPane.setToolTipText("" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "");
- textColour.setText(MessageManager.getString("label.colour_text") + "...");
+ tabbedPane.setToolTipText(""
+ + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ + "");
+ textColour.setText(MessageManager.getString("label.colour_text")
+ + "...");
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1789,7 +1882,8 @@ public class GAlignFrame extends JInternalFrame
});
formatMenu.setText(MessageManager.getString("action.format"));
selectMenu.setText(MessageManager.getString("action.select"));
- idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
+ idRightAlign.setText(MessageManager
+ .getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1819,7 +1913,8 @@ public class GAlignFrame extends JInternalFrame
expandViews_actionPerformed(e);
}
});
- pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
+ pageSetup
+ .setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1827,7 +1922,8 @@ public class GAlignFrame extends JInternalFrame
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
+ alignmentProperties.setText(MessageManager
+ .getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
@@ -1835,8 +1931,10 @@ public class GAlignFrame extends JInternalFrame
alignmentProperties();
}
});
- tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
- autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
+ tooltipSettingsMenu.setText(MessageManager
+ .getString("label.sequence_id_tooltip"));
+ autoAnnMenu.setText(MessageManager
+ .getString("label.autocalculated_annotation"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
@@ -1937,7 +2035,7 @@ public class GAlignFrame extends JInternalFrame
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
@@ -1950,7 +2048,8 @@ public class GAlignFrame extends JInternalFrame
calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
- webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
@@ -2321,11 +2420,10 @@ public class GAlignFrame extends JInternalFrame
protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
}
-
+
protected void RNAInteractionColour_actionPerformed(ActionEvent e)
{
}
-
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
@@ -2366,11 +2464,11 @@ public class GAlignFrame extends JInternalFrame
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
-
+
protected void createGroup_actionPerformed(ActionEvent e)
{
}
-
+
protected void unGroup_actionPerformed(ActionEvent e)
{
}
@@ -2651,6 +2749,6 @@ public class GAlignFrame extends JInternalFrame
protected void expand_newalign(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
}