/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import java.awt.Canvas;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
import java.awt.Menu;
import java.awt.MenuBar;
import java.awt.MenuItem;
+import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
annotationPanelMenuItem.setState(viewport.isShowAnnotation());
- showAlignmentAnnotations.setState(viewport.isShowAnnotation());
- showSequenceAnnotations.setState(viewport.isShowAnnotation());
+ showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAlignmentAnnotations.setState(true);
+ showSequenceAnnotations.setState(false);
seqLimits.setState(viewport.getShowJVSuffix());
alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
alignPanel.alabels.addKeyListener(this);
+ setAnnotationsVisibility();
+
if (addToDisplay)
{
addToDisplay(embedded);
}
else if (source == annotationPanelMenuItem)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ boolean showAnnotations = annotationPanelMenuItem.getState();
+ showAlignmentAnnotations.setEnabled(showAnnotations);
+ showSequenceAnnotations.setEnabled(showAnnotations);
+ viewport.setShowAnnotation(showAnnotations);
+ alignPanel.setAnnotationVisible(showAnnotations);
}
else if (source == sequenceFeatures)
{
/**
* Set the visibility state of sequence-related and/or alignment-related
- * annotations depending on checkbox selections. Repaint after calling.
+ * annotations depending on checkbox selections, and repaint.
*
* @param visible
*/
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- // TODO need to trigger a repaint of the complementary panel - how?
- // would prefer to handle in SplitFrame but it is not overriding key
- // listener chiz
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
}
}
seqs.addElement(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())
{
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
+ {
+ String title = MessageManager.getString("label.delete_all");
+ Panel infoPanel = new Panel();
+ infoPanel.setLayout(new FlowLayout());
+ infoPanel
+ .add(new Label(MessageManager.getString("warn.delete_all")));
+
+ final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+ dialog.setMainPanel(infoPanel);
+ dialog.ok.setLabel(MessageManager.getString("action.ok"));
+ dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+ dialog.setVisible(true);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+ }
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
MessageManager.getString("label.sort_annotations_by_label"));
showAutoFirst = new CheckboxMenuItem(
MessageManager.getString("label.show_first"));
+ showAutoFirst.setState(false); // pending applet parameter
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
showAutoLast = new CheckboxMenuItem(
MessageManager.getString("label.show_last"));
+ showAutoLast.setState(!showAutoFirst.getState());
showAlignmentAnnotations.addItemListener(this);
showSequenceAnnotations.addItemListener(this);
sortAnnBySequence.addItemListener(this);