X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=31809936357340eb6083ef7f524a680ef1d02ba4;hb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;hp=d992233ce52d93580dd71bbe150e21d8cddca11b;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d992233..3180993 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -32,6 +34,7 @@ import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
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;
@@ -54,7 +57,7 @@ import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
-import jalview.io.HTMLOutput;
+import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
@@ -151,9 +154,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public AlignmentPanel alignPanel;
AlignViewport viewport;
-
+
public AlignViewControllerI avc;
-
Vector alignPanels = new Vector();
@@ -262,21 +264,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
- viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
-
- alignPanel = new AlignmentPanel(this, viewport);
if (al.getDataset() == null)
{
al.setDataset(null);
}
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+
addAlignmentPanel(alignPanel, true);
init();
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
@@ -297,7 +301,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
@@ -330,6 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
+
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
@@ -341,7 +347,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
addKeyListener();
-
+
}
/**
@@ -372,7 +378,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ {
+ alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
@@ -384,38 +392,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_DOWN:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(false);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, 1);
+ }
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(true);
+ }
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
+ {
+ alignPanel.getSeqPanel().moveCursor(0, -1);
+ }
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(-1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ {
+ slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
+ }
else
- alignPanel.seqPanel.moveCursor(1, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
break;
@@ -439,7 +463,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
|| evt.isShiftDown() || evt.isAltDown());
}
@@ -448,19 +472,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_S:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRow();
+ alignPanel.getSeqPanel().setCursorRow();
}
break;
case KeyEvent.VK_C:
if (viewport.cursorMode && !evt.isControlDown())
{
- alignPanel.seqPanel.setCursorColumn();
+ alignPanel.getSeqPanel().setCursorColumn();
}
break;
case KeyEvent.VK_P:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorPosition();
+ alignPanel.getSeqPanel().setCursorPosition();
}
break;
@@ -468,45 +492,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
case KeyEvent.VK_COMMA:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setCursorRowAndColumn();
+ alignPanel.getSeqPanel().setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
}
break;
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;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+ alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
}
- alignPanel.seqPanel.seqCanvas.repaint();
+ alignPanel.getSeqPanel().seqCanvas.repaint();
break;
case KeyEvent.VK_F1:
try
{
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
- "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
+ Help.showHelpWindow();
} catch (Exception ex)
{
ex.printStackTrace();
@@ -551,14 +570,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
}
}
@@ -568,7 +591,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
- avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
alignPanels.addElement(ap);
@@ -714,14 +738,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
- idRightAlign.setSelected(av.rightAlignIds);
+ idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
renderGapsMenuItem.setSelected(av.renderGaps);
wrapMenuItem.setSelected(av.wrapAlignment);
scaleAbove.setVisible(av.wrapAlignment);
scaleLeft.setVisible(av.wrapAlignment);
scaleRight.setVisible(av.wrapAlignment);
- annotationPanelMenuItem.setState(av.showAnnotation);
+ annotationPanelMenuItem.setState(av.isShowAnnotation());
+ /*
+ * Show/hide annotations only enabled if annotation panel is shown
+ */
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -812,14 +843,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
{
- throw new Error(
- "call setProgressBar before registering the progress bar's handler.");
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
if (handler.canCancel())
{
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
cancel.addActionListener(new ActionListener()
{
@@ -828,10 +859,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(
- "Cancelled "
- + ((JLabel) progressPanel.getComponent(0))
- .getText(), id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
@@ -853,9 +881,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
@Override
- public void setStatus(String text) {
+ public void setStatus(String text)
+ {
statusBar.setText(text);
};
+
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
@@ -866,7 +896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureRenderer getFeatureRenderer()
{
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
}
@Override
@@ -992,8 +1022,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText(MessageManager.getString("action.save"));
+ chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -1002,9 +1032,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
currentFileFormat = chooser.getSelectedFormat();
if (currentFileFormat == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager
+ .getString("label.file_format_not_specified"),
+ JOptionPane.WARNING_MESSAGE);
value = chooser.showSaveDialog(this);
return;
}
@@ -1040,8 +1075,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
success = new Jalview2XML().SaveAlignment(this, file, shortName);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
-
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new String[]
+ { fileName, format }));
}
else
@@ -1062,8 +1098,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.save_omit_hidden_columns"),
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
@@ -1093,7 +1131,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new String[]
+ { fileName, format }));
} catch (Exception ex)
{
success = false;
@@ -1104,8 +1145,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
- MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new String[]
+ { fileName }), MessageManager
+ .getString("label.error_saving_file"),
+ JOptionPane.WARNING_MESSAGE);
}
return success;
@@ -1142,8 +1186,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("label.alignment_contains_hidden_columns"),
- MessageManager.getString("action.save_omit_hidden_columns"),
+ MessageManager
+ .getString("label.alignment_contains_hidden_columns"),
+ MessageManager
+ .getString("action.save_omit_hidden_columns"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
@@ -1161,8 +1207,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
viewport.getAlignment(), omitHidden,
viewport.getColumnSelection()));
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1180,9 +1227,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel,
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ // new HTMLOutput(alignPanel,
+ // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+ // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ new HtmlSvgOutput(alignPanel);
}
public void createImageMap(File file, String image)
@@ -1214,6 +1262,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.makeEPS(f);
}
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
@@ -1245,7 +1297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportAnnotations(alignPanel,
- viewport.showAnnotation ? viewport.getAlignment()
+ viewport.isShowAnnotation() ? viewport.getAlignment()
.getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), ((Alignment) viewport
.getAlignment()).alignmentProperties);
@@ -1258,8 +1310,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));
- chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(MessageManager
+ .getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
@@ -1358,8 +1412,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+ CommandI command = viewport.historyList.peek();
+ undoMenuItem.setText(MessageManager.formatMessage(
+ "label.undo_command", new String[]
+ { command.getDescription() }));
}
else
{
@@ -1371,8 +1427,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+ CommandI command = viewport.redoList.peek();
+ redoMenuItem.setText(MessageManager.formatMessage(
+ "label.redo_command", new String[]
+ { command.getDescription() }));
}
else
{
@@ -1430,8 +1488,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
+ {
return;
- CommandI command = (CommandI) viewport.historyList.pop();
+ }
+ CommandI command = viewport.historyList.pop();
viewport.redoList.push(command);
command.undoCommand(getViewAlignments());
@@ -1470,7 +1530,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
+ CommandI command = viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand(getViewAlignments());
@@ -1563,7 +1623,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ alignPanel.getSeqPanel().seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() != viewport
@@ -1583,37 +1643,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = (SequenceI) 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);
+ {
+ alignPanel.getSeqPanel().moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(-size, 0);
+ {
+ alignPanel.getSeqPanel().moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
@@ -1634,7 +1710,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
@@ -1705,7 +1783,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.jalviewClipboard = new Object[]
{ seqs, viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", new String[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
@@ -1912,7 +1992,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
@@ -1967,7 +2049,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
AlignmentAnnotation sann[] = sequences[i].getAnnotation();
if (sann == null)
+ {
continue;
+ }
for (int avnum = 0; avnum < alview.length; avnum++)
{
if (alview[avnum] != alignment)
@@ -2028,9 +2112,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
@@ -2063,59 +2147,61 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+
@Override
protected void expand_newalign(ActionEvent e)
{
- try {
- AlignmentI alignment = AlignmentUtils.expandContext(getViewport().getAlignment(), -1);
- AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- String newtitle = new String("Flanking alignment");
-
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ try
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
+ .getAlignment(), -1);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Flanking alignment");
+
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
{
- int[] region = (int[]) hc.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];
+ for (int i = 0; i < hc.size(); i++)
+ {
+ int[] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
}
- }
- // >>>This is a fix for the moment, until a better solution is
- // found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
- .transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
- // TODO: maintain provenance of an alignment, rather than just make the
- // title a concatenation of operations.
- {
- if (title.startsWith("Copied sequences"))
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
{
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
}
- }
- Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
} catch (Exception ex)
{
ex.printStackTrace();
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
- }
- catch (OutOfMemoryError oom)
+ } catch (OutOfMemoryError oom)
{
new OOMWarning("Viewing flanking region of alignment", oom);
}
}
+
/**
* DOCUMENT ME!
*
@@ -2145,17 +2231,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- Vector seqs = new Vector();
+ List seqs = new ArrayList(sg.getSize());
SequenceI seq;
for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
+ seqs.add(seq);
}
- // If the cut affects all sequences, remove highlighted columns
+ // If the cut affects all sequences, warn, remove highlighted columns
if (sg.getSize() == viewport.getAlignment().getHeight())
{
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
@@ -2163,14 +2259,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceI[] cut = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
- cut[i] = (SequenceI) seqs.elementAt(i);
+ cut[i] = seqs.get(i);
}
/*
* //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);
@@ -2199,7 +2296,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
- if (avc.deleteGroups()) {
+ if (avc.deleteGroups())
+ {
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
@@ -2240,14 +2338,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (viewport.cursorMode)
{
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
+ alignPanel.getSeqPanel().keyboardNo1 = null;
+ alignPanel.getSeqPanel().keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+ alignPanel.getIdPanel().getIdCanvas().searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
@@ -2357,7 +2455,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -2405,7 +2505,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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
@@ -2568,7 +2670,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
boolean addFirstIndex = false;
if (viewTitle == null || viewTitle.trim().length() == 0)
{
- viewTitle = "View";
+ viewTitle = MessageManager.getString("action.view");
addFirstIndex = true;
}
else
@@ -2600,7 +2702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addAlignmentPanel(newap, true);
newap.alignmentChanged();
-
+
if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
@@ -2644,7 +2746,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+ alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
.calculateIdWidth());
alignPanel.paintAlignment(true);
}
@@ -2652,7 +2754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
- viewport.rightAlignIds = idRightAlign.isSelected();
+ viewport.setRightAlignIds(idRightAlign.isSelected());
alignPanel.paintAlignment(true);
}
@@ -2674,7 +2776,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
{
alignPanel.scrollToPosition(
- alignPanel.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.getSeqPanel().seqCanvas.searchResults, false);
}
}
@@ -2995,16 +3097,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * DOCUMENT ME!
+ * Action on toggle of the 'Show annotations' menu item. This shows or hides
+ * the annotations panel as a whole.
+ *
+ * The options to show/hide all annotations should be enabled when the panel
+ * is shown, and disabled when the panel is hidden.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ final boolean setVisible = annotationPanelMenuItem.isSelected();
+ viewport.setShowAnnotation(setVisible);
+ alignPanel.setAnnotationVisible(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
}
@Override
@@ -3014,11 +3124,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
- editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
+ editPane.setText(MessageManager.formatMessage("label.html_content",
+ new String[]
+ { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);
+ Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[]
+ { getTitle() }), 500, 400);
}
/**
@@ -3038,8 +3152,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
- frame.getWidth(), frame.getHeight());
+ Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[]
+ { this.getTitle() }), frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -3421,7 +3536,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
new UserDefinedColours(alignPanel, null);
}
@@ -3470,8 +3586,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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)
{
@@ -3622,15 +3740,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
+ JOptionPane.showInternalMessageDialog(this, MessageManager
+ .getString("label.you_must_select_least_two_sequences"),
+ MessageManager.getString("label.invalid_selection"),
JOptionPane.WARNING_MESSAGE);
}
else
{
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
@@ -3648,10 +3769,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane.showInternalMessageDialog(this,
- MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager.getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showInternalMessageDialog(
+ this,
+ MessageManager
+ .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
@@ -3752,8 +3877,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.you_need_more_two_sequences_selected_build_tree"),
+ MessageManager
+ .getString("label.not_enough_sequences"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
@@ -3767,8 +3895,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
- MessageManager.getString("label.sequences_selection_not_aligned"),
+ MessageManager
+ .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager
+ .getString("label.sequences_selection_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -3786,8 +3916,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JOptionPane
.showMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
- MessageManager.getString("label.sequences_not_aligned"),
+ MessageManager
+ .getString("label.sequences_must_be_aligned_before_creating_tree"),
+ MessageManager
+ .getString("label.sequences_not_aligned"),
JOptionPane.WARNING_MESSAGE);
return;
@@ -3824,7 +3956,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem("by " + title);
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
@@ -3942,15 +4074,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
calculateTree.removeAll();
// build the calculate menu
-
- for (final String type:new String[] {"NJ", "AV"})
+
+ for (final String type : new String[]
+ { "NJ", "AV" })
{
- String treecalcnm = MessageManager.getString("label.tree_calc_"+type.toLowerCase());
- for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + type.toLowerCase());
+ for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
{
JMenuItem tm = new JMenuItem();
ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isProtein()==!viewport.getAlignment().isNucleotide())
+ if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
{
String smn = MessageManager.getStringOrReturn(
"label.score_model_", sm.getName());
@@ -3959,6 +4093,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
tm.setText(title);//
tm.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
NewTreePanel(type, (String) pwtype, title);
@@ -4050,6 +4185,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
msa = viewport.getAlignmentView(true);
}
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
+ {
+ int option = JOptionPane
+ .showConfirmDialog(
+this,
+ "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.",
+ "Invalid selection",
+ JOptionPane.OK_CANCEL_OPTION);
+ if (option == JOptionPane.OK_OPTION)
+ {
+ msa = viewport.getAlignmentView(false);
+ }
+
+ }
else
{
/*
@@ -4113,8 +4263,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));
- chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_newick_like_tree_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
int value = chooser.showOpenDialog(null);
@@ -4129,14 +4280,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), MessageManager
+ .getString("label.possible_problem_with_tree_file"),
JOptionPane.WARNING_MESSAGE);
}
}
@@ -4241,7 +4398,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
- final List legacyItems=new ArrayList();
+ final List legacyItems = new ArrayList();
try
{
System.err.println("Building ws menu again "
@@ -4264,6 +4421,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
+ // final JMenu msawsmenu = new
+ // JMenu(MessageManager.getString("label.alignment"));
+ // final JMenu secstrmenu = new
+ // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+ // final JMenu seqsrchmenu = new
+ // JMenu(MessageManager.getString("label.sequence_database_search"));
+ // final JMenu analymenu = new
+ // JMenu(MessageManager.getString("label.analysis"));
+ // final JMenu dismenu = new
+ // JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4274,7 +4441,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// be
// stored or retrieved from elsewhere
// No MSAWS used any more:
- // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ // Vector msaws = null; // (Vector)
+ // Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
@@ -4286,17 +4454,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
- int p=secstrmenu.getItemCount();
+ int p = secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- int q=secstrmenu.getItemCount();
- for (int litm=p;litm"+MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new String[]
+ { Integer.valueOf(
+ filesnotmatched
+ .size())
+ .toString() })+"