/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.BufferedImage;
-
-import jalview.datamodel.*;
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Vector;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import jalview.util.ParseHtmlBodyAndLinks;
public class AnnotationLabels extends Panel implements ActionListener,
this.av = av;
}
- public void setScrollOffset(int y)
+ public void setScrollOffset(int y, boolean repaint)
{
scrollOffset = y;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
/**
int getSelectedRow(int y)
{
int row = -2;
- AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (aa == null)
{
}
}
+ refresh();
+ }
+
+ /**
+ * Adjust size and repaint
+ */
+ protected void refresh()
+ {
ap.annotationPanel.adjustPanelHeight();
setSize(getSize().width, ap.annotationPanel.getSize().height);
ap.validate();
return true;
}
else
+ {
return false;
+ }
}
if (row > -1)
{
- ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(av.getAlignment().getAlignmentAnnotation()[row].getDescription(true), true, "\n");
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+ av.getAlignment().getAlignmentAnnotation()[row]
+ .getDescription(true),
+ true, "\n");
if (tooltip == null)
{
tooltip = new Tooltip(phb.getNonHtmlContent(), this);
.getSize(), f = ap.seqPanelHolder.getSize();
int dif = evt.getY() - oldY;
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
if ((d.height - dif) > 20 && (f.height + dif) > 20)
{
int end = getSelectedRow(evt.getY() + scrollOffset);
- if (start>-1 && start != end)
+ if (start > -1 && start != end)
{
// Swap these annotations
AlignmentAnnotation startAA = ap.av.getAlignment()
{
return;
}
- dragCancelled=false;
+ dragCancelled = false;
// todo: move below to mouseClicked ?
selectedRow = getSelectedRow(evt.getY() + scrollOffset);
- AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- PopupMenu popup = new PopupMenu("Annotations");
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
MenuItem item = new MenuItem(ADDNEW);
item.addActionListener(this);
item = new MenuItem(HIDE);
item.addActionListener(this);
popup.add(item);
+
+ /*
+ * Hide all <label>:
+ */
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ final String label = aa[selectedRow].label;
+ MenuItem hideType = new MenuItem(
+ MessageManager.getString("label.hide_all") + " " + label);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ refresh();
+ }
+ });
+ popup.add(hideType);
+ }
+ }
+
if (hasHiddenRows)
{
item = new MenuItem(SHOWALL);
{
popup.addSeparator();
final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus",
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
+ .isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
{
}
else
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
ap.paintAlignment(true);
}
if (aaa.groupRef != null)
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- "Show Group Histogram",
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
});
popup.add(chist);
final CheckboxMenuItem cprofl = new CheckboxMenuItem(
- "Show Group Logo",
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addItemListener(new ItemListener()
{
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
+
popup.add(cprofl);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(true);
+ aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
}
else
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.showConsensusHistogram.setState(chist
+ .getState()); // TODO: implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for applet
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
popup.add(chist);
final CheckboxMenuItem cprof = new CheckboxMenuItem(
- "Show Logo", av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
cprof.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
// can be
// updated.
av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
popup.add(cprof);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
+ av.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
}
item = new MenuItem(COPYCONS_SEQ);
}
else if (aa[selectedRow].sequenceRef != null)
{
- Vector sr = new Vector();
- sr.addElement(aa[selectedRow].sequenceRef);
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+ ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+ .asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg!=null)
+ {
+ // we make a copy rather than edit the current selection if no modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(evt.isControlDown() || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ } else {
+ if (evt.isControlDown())
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ } else {
+ // notionally, we should also add intermediate sequences from last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ } else {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
ap.av.setSelectionGroup(sg);
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
if (av.hasHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(i);
-
jalview.appletgui.AlignFrame.copiedHiddenColumns
.addElement(new int[]
{ region[0], region[1] });
{
int w = getSize().width;
int h = getSize().height;
- if (image == null || w != image.getWidth(this) || h!=image.getHeight(this) )
+ if (image == null || w != image.getWidth(this)
+ || h != image.getHeight(this))
{
image = createImage(w, ap.annotationPanel.getSize().height);
}
dragEvent.getY());
}
- if ((aa == null) || (aa.length < 1))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
g.setColor(Color.black);
- g.drawString("Right click", 2, 8);
- g.drawString("to add annotation", 2, 18);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
}