/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 jalview.datamodel.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.util.ParseHtmlBodyAndLinks;
-public class AnnotationLabels extends Panel implements ActionListener,
- MouseListener, MouseMotionListener
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Cursor;
+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;
+
+public class AnnotationLabels extends Panel
+ implements ActionListener, MouseListener, MouseMotionListener
{
Image image;
+ /**
+ * width in pixels within which height adjuster arrows are shown and active
+ */
+ private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
+ /**
+ * height in pixels for allowing height adjuster to be active
+ */
+ private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
boolean active = false;
AlignmentPanel ap;
this.ap = ap;
this.av = ap.av;
setLayout(null);
-
- /**
- * this retrieves the adjustable height glyph from resources. we don't use
- * it at the moment. java.net.URL url =
- * getClass().getResource("/images/idwidth.gif"); Image temp = null;
- *
- * if (url != null) { temp =
- * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
- *
- * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
- * mt.waitForID(0); } catch (Exception ex) { }
- *
- * BufferedImage bi = new BufferedImage(temp.getHeight(this),
- * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
- * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
- * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
- */
addMouseListener(this);
addMouseMotionListener(this);
}
return row;
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
ap.alignFrame);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
- + " - " + aa[selectedRow].label, 500, 100);
+ jalview.bin.JalviewLite.addFrame(frame,
+ ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+ 100);
cap.setText(aa[selectedRow].toString());
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
}
}
+ refresh();
+ }
+
+ /**
+ * Adjust size and repaint
+ */
+ protected void refresh()
+ {
ap.annotationPanel.adjustPanelHeight();
setSize(getSize().width, ap.annotationPanel.getSize().height);
ap.validate();
- ap.paintAlignment(true);
+ // TODO: only paint if we needed to
+ ap.paintAlignment(true, true);
}
boolean editLabelDescription(AlignmentAnnotation annotation)
{
- Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
- + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+ Checkbox padGaps = new Checkbox(
+ "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
+ annotation.padGaps);
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Label",
return true;
}
else
+ {
return false;
+ }
}
boolean resizePanel = false;
+ @Override
public void mouseMoved(MouseEvent evt)
{
- resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+ && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
int row = getSelectedRow(evt.getY() + scrollOffset);
if (row > -1)
dragCancelled = true;
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (dragCancelled)
if (resizePanel)
{
- Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
- .getSize(), f = ap.seqPanelHolder.getSize();
+ Dimension d = ap.annotationPanelHolder.getSize(),
+ e = ap.annotationSpaceFillerHolder.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)
{
ap.annotationPanel.setSize(d.width, d.height - dif);
setSize(new Dimension(e.width, d.height - dif));
- ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- d.height - dif));
- ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
- - dif));
+ ap.annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, d.height - dif));
+ ap.annotationPanelHolder
+ .setSize(new Dimension(d.width, d.height - dif));
ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
av.calcPanelHeight());
f.height += dif;
ap.seqPanelHolder.setPreferredSize(f);
- ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+ ap.setScrollValues(av.getRanges().getStartRes(),
+ av.getRanges().getStartSeq());
ap.validate();
// ap.paintAlignment(true);
ap.addNotify();
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (!resizePanel && !dragCancelled)
resizePanel = false;
dragEvent = null;
dragCancelled = false;
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
repaint();
ap.annotationPanel.repaint();
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
if (evt.getY() < 10 && evt.getX() < 14)
resizePanel = true;
repaint();
}
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
}
+ @Override
public void mouseExited(MouseEvent evt)
{
dragCancelled = false;
repaint();
}
+ @Override
public void mousePressed(MouseEvent evt)
{
oldY = evt.getY();
.getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- PopupMenu popup = new PopupMenu(MessageManager.getString("label.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",
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
if (aaa.groupRef != null)
}
else
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
});
popup.add(cbmi);
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()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
});
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()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
popup.add(cprofl);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- "Normalise Group Logo",
+ MessageManager
+ .getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
else
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.showConsensusHistogram.setState(chist
- .getState()); // TODO: implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for applet
+ 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()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
});
popup.add(cprof);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- "Normalise Logo", av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
// can be
// updated.
av.setShowSequenceLogo(true);
- ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
- // implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for
- // applet
+ 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());
// todo: make the ap scroll to the selection - not necessary, first
// click highlights/scrolls, second selects
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- ap.av.sendSelection();
- ap.paintAlignment(false);
+ // process modifiers
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
+ {
+ if (jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown())
+ {
+ // clone a new selection group from the associated group
+ ap.av.setSelectionGroup(
+ new SequenceGroup(aa[selectedRow].groupRef));
+ }
+ else
+ {
+ // set selection to the associated group so it can be edited
+ ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+ }
+ }
+ else
+ {
+ // modify current selection with associated group
+ int remainToAdd = aa[selectedRow].groupRef.getSize();
+ for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(sgs, --remainToAdd == 0);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(sgs, --remainToAdd == 0);
+ }
+ }
+ }
+ ap.paintAlignment(false, false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
}
else
{
- ap.seqPanel.ap.idPanel
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
+ ap.seqPanel.ap.idPanel.highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
}
return;
}
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 (!(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ else
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ 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);
+ ap.paintAlignment(false, false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
return;
}
jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
- jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
- + sq.getStart() + "\t" + sq.getEnd() + "\t"
- + sq.getSequenceAsString() + "\n");
+ jalview.appletgui.AlignFrame.copiedSequences
+ .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
+ + "\t" + sq.getSequenceAsString() + "\n");
if (av.hasHiddenColumns())
{
- jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
- {
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(i);
-
- jalview.appletgui.AlignFrame.copiedHiddenColumns
- .addElement(new int[]
- { region[0], region[1] });
- }
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
int w = getSize().width;
}
}
g.translate(0, +scrollOffset);
- if (resizePanel)
- {
- g.setColor(Color.red);
- g.setPaintMode();
- g.drawLine(2, 8, 5, 2);
- g.drawLine(5, 2, 8, 8);
- }
- else if (!dragCancelled && dragEvent != null && aa != null)
+
+ if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
dragEvent.getY());
}
- if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
g.setColor(Color.black);
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
}
git://source.jalview.org / jalview.git / blobdiff