/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
+import jalview.schemes.RNAInteractionColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import java.util.Vector;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+ ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
+
public AlignmentPanel alignPanel;
public AlignViewport viewport;
{
ex.printStackTrace();
}
-
+ // need to get window geometry before we calculate alignment layout
+ if (applet != null)
+ {
+ String param;
+ try
+ {
+ param = applet.getParameter("windowWidth");
+ if (param != null)
+ {
+ int width = Integer.parseInt(param);
+ DEFAULT_WIDTH = width;
+ }
+ param = applet.getParameter("windowHeight");
+ if (param != null)
+ {
+ int height = Integer.parseInt(param);
+ DEFAULT_HEIGHT = height;
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
showSequenceLogo.setState(viewport.isShowSequenceLogo());
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
seqLimits.setState(viewport.showJVSuffix);
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
- try
- {
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
- {
- }
}
if (viewport.getAlignment().isNucleotide())
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true);
- statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
+ statusBar.setText(MessageManager
+ .getString("label.successfully_added_features_alignment"));
}
return featuresFile;
}
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
+ {
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
}
}
break;
-
+
case KeyEvent.VK_U:
if (evt.isControlDown())
{
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
- 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 400, 250);
}
else if (source == overviewMenuItem)
{
{
changeColour(new PurinePyrimidineColourScheme());
}
+ else if (source == RNAInteractionColour)
+ {
+ changeColour(new RNAInteractionColourScheme());
+ }
else if (source == RNAHelixColour)
{
new RNAHelicesColourChooser(viewport, alignPanel);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.input_cut_paste"), 500, 500);
}
protected void outputText_actionPerformed(ActionEvent e)
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.showJVSuffix));
public void loadAnnotations()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
+ cap.setText(MessageManager
+ .getString("label.paste_features_annotations_Tcoffee_here"));
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.paste_annotations"), 400, 300);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
else
{
if (features == null)
+ {
features = "";
+ }
}
return features;
{
undoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ undoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.undo_command", new String[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(true);
CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ redoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.redo_command", new String[]
+ { command.getDescription() }));
}
else
{
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
.size()]);
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = invertGroup.elementAt(i);
+ }
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
if (newAlignment)
{
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
+ String newtitle = MessageManager.getString("label.copied_sequences");
+ if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
- newtitle = newtitle.concat("- from " + getTitle());
+ newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
}
// !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
protected void makeGrpsFromSelection_actionPerformed()
{
- if (avc.makeGroupsFromSelection()) {
+ if (avc.makeGroupsFromSelection())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
{
avc.createGroup();
}
+
protected void unGroup_actionPerformed()
{
if (avc.unGroup())
alignPanel.alignmentChanged();
}
}
+
protected void deleteGroups_actionPerformed()
{
if (avc.deleteGroups())
viewport.getSelectionGroup());
}
- statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : viewport.getAlignment().getGroups())
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns", new String[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
- overview.getPreferredSize().width,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[]
+ { this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
{
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
+ cs, "Background"));
}
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs.setConservationApplied(true);
+ viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
-
}
else
{
- cs.setConservation(null);
+ cs.setConservationApplied(false);
}
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
-
}
viewport.setGlobalColourScheme(cs);
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
}
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.paste_newick_file"), 400, 300);
}
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile,
+ MessageManager.getString("label.load_tree_from_file"), tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
.sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[]
+ { title }), oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
+ g.drawString(MessageManager.formatMessage(
+ "label.jalviewLite_release", new String[]
+ { version }), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
+ g.drawString(MessageManager.formatMessage(
+ "label.jaview_build_date", new String[]
+ { builddate }), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString(
- MessageManager.getString("label.jalview_authors_1"),
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
x, y += fh * 1.5);
- g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
- g.drawString(
- MessageManager.getString("label.jalview_dev_managers"),
- x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
g.drawString(
- MessageManager.getString("label.jalview_distribution_lists"),
- x, y += fh);
- g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
+ MessageManager.getString("label.jalview_dev_managers"), x,
+ y += fh);
+ g.drawString(MessageManager
+ .getString("label.jalview_distribution_lists"), x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"),
+ x, y += fh + 8);
g.drawString(
MessageManager.getString("label.jalview_cite_1_authors"),
x, y += fh);
g.drawString(
- MessageManager.getString("label.jalview_cite_1_title"),
- x, y += fh);
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
}
Menu fileMenu = new Menu(MessageManager.getString("action.file"));
- MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
- MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
- MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
- MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features").concat("..."));
- MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations").concat("..."));
- MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
- Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
- MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
- MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
- MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
+ MenuItem invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
MenuItem remove2LeftMenuItem = new MenuItem();
MenuItem purinePyrimidineColour = new MenuItem();
+ MenuItem RNAInteractionColour = new MenuItem();
+
MenuItem RNAHelixColour = new MenuItem();
MenuItem userDefinedColour = new MenuItem();
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
MenuItem overviewMenuItem = new MenuItem();
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
+ remove2LeftMenuItem.setLabel(MessageManager
+ .getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
+ remove2RightMenuItem.setLabel(MessageManager
+ .getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setLabel(MessageManager
+ .getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.setLabel(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.setLabel(MessageManager
+ .getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
+ sortLengthMenuItem.setLabel(MessageManager
+ .getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy").concat("..."));
removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem
- .setLabel(MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ outputTextboxMenu.setLabel(MessageManager
+ .getString("label.out_to_textbox"));
clustalColour.setLabel(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(this);
zappoColour.addActionListener(this);
taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
+ RNAInteractionColour.setLabel(MessageManager
+ .getString("label.rna_interaction"));
+ RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager
+ .getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
// provided
tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem
- .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
- overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
undoMenuItem.setEnabled(false);
undoMenuItem.setLabel(MessageManager.getString("action.undo"));
redoMenuItem.setEnabled(false);
redoMenuItem.setLabel(MessageManager.getString("action.redo"));
redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.setLabel(MessageManager
+ .getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
findMenuItem.setLabel(MessageManager.getString("action.find"));
findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
- deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.setLabel(MessageManager
+ .getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
unGroup.setLabel(MessageManager.getString("action.remove_group"));
pasteNew.addActionListener(this);
pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
font.setLabel(MessageManager.getString("action.font"));
scaleRight.setState(true);
scaleRight.setLabel(MessageManager.getString("action.scale_right"));
scaleRight.addItemListener(this);
- modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(this);
- modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_thereshold"));
modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
sort.setLabel(MessageManager.getString("action.sort"));
calculate.setLabel(MessageManager.getString("action.calculate_tree"));
autoCalculate.addItemListener(this);
sortByTree.addItemListener(this);
- inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
helpMenu.setLabel(MessageManager.getString("action.help"));
documentation.setLabel(MessageManager.getString("label.documentation"));
about.setLabel(MessageManager.getString("label.about"));
about.addActionListener(this);
seqLimits.setState(true);
- seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
- featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
+ featureSettings.setLabel(MessageManager
+ .getString("label.feature_settings"));
featureSettings.addActionListener(this);
- sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
- annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
- invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
menu1.setLabel(MessageManager.getString("action.show"));
showColumns.setLabel(MessageManager.getString("label.all_columns"));
showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
- menu2.setLabel(MessageManager.getString("aciton.hide"));
- hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
- hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
- hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
- hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
- showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
- showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
- showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
- showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
- showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
- normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
- applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
+ menu2.setLabel(MessageManager.getString("action.hide"));
+ hideColumns
+ .setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager
+ .getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager
+ .getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager
+ .getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager
+ .getString("label.all_sequences_columns"));
+ showGroupConsensus.setLabel(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager
+ .getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager
+ .getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager
+ .getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
+ autoAnnMenu.setLabel(MessageManager
+ .getString("label.autocalculated_annotation"));
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
}
+ public void setStatus(String string)
+ {
+ statusBar.setText(string);
+ };
+
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Remove Seperator
embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
- Font.PLAIN, 10, false); // use our own fonts.
+ Font.PLAIN, 11, false); // use our own fonts.
// and actually add the components to the applet area
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
}
}
return true;
git://source.jalview.org / jalview.git / blobdiff