/*
- * 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.gui;
-import java.util.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
import java.util.regex.Pattern;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
- static String TOGGLE_LABELSCALE = "Scale Label to Column";
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+ .compile("<");
- static String ADDNEW = "Add New Row";
+ String TOGGLE_LABELSCALE = MessageManager
+ .getString("label.scale_label_to_column");
- static String EDITNAME = "Edit Label/Description";
+ String ADDNEW = MessageManager.getString("label.add_new_row");
- static String HIDE = "Hide This Row";
+ String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
- static String DELETE = "Delete This Row";
+ String HIDE = MessageManager.getString("label.hide_row");
- static String SHOWALL = "Show All Hidden Rows";
+ String DELETE = MessageManager.getString("label.delete_row");
- static String OUTPUT_TEXT = "Export Annotation";
+ String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
+ String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+
+ String COPYCONS_SEQ = MessageManager
+ .getString("label.copy_consensus_sequence");
boolean resizePanel = false;
int selectedRow;
- int scrollOffset = 0;
+ private int scrollOffset = 0;
Font font = new Font("Arial", Font.PLAIN, 11);
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
- image = (Image) bi;
+ image = bi;
addMouseListener(this);
addMouseMotionListener(this);
+ addMouseWheelListener(ap.getAnnotationPanel());
}
public AnnotationLabels(AlignViewport av)
void getSelectedRow(int y)
{
int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
selectedRow = -2;
if (aa != null)
{
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ boolean fullRepaint = false;
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
- null, new Annotation[ap.av.alignment.getWidth()]);
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
if (!editLabelDescription(newAnnotation))
{
return;
}
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(EDITNAME))
{
+ String name = aa[selectedRow].label;
editLabelDescription(aa[selectedRow]);
- repaint();
+ if (!name.equalsIgnoreCase(aa[selectedRow].label))
+ {
+ fullRepaint = true;
+ }
}
else if (evt.getActionCommand().equals(HIDE))
{
}
else if (evt.getActionCommand().equals(DELETE))
{
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+ ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(SHOWALL))
{
aa[i].visible = true;
}
}
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
- new AlignmentAnnotation[]
- { aa[selectedRow] }, null, null);
+ new AlignmentAnnotation[] { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- ap.validateAnnotationDimensions(false);
+ refresh(fullRepaint);
+
+ }
+
+ /**
+ * Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
+ */
+ protected void refresh(boolean adjustHeight)
+ {
+ ap.validateAnnotationDimensions(adjustHeight);
ap.addNotify();
- ap.repaint();
- //validate();
- //ap.paintAlignment(true);
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ ap.paintAlignment(true);
+ }
+ else
+ {
+ // lightweight repaint
+ ap.repaint();
+ }
}
/**
*/
boolean editLabelDescription(AlignmentAnnotation annotation)
{
+ // TODO i18n
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Name ",
"Annotation Description ", "Edit Annotation Name/Description",
return true;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void mousePressed(MouseEvent evt)
{
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
oldY = evt.getY();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
- {
- int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
- int end = selectedRow;
-
- if (start != end)
- {
- // Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment
- .getAlignmentAnnotation()[start];
- if (end == -1)
- {
- end = ap.av.alignment.getAlignmentAnnotation().length - 1;
- }
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
-
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
- }
-
- resizePanel = false;
- dragEvent = null;
- repaint();
- ap.annotationPanel.repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
- {
- if (evt.getY() < 10)
- {
- resizePanel = true;
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
- {
- if (dragEvent == null)
- {
- resizePanel = false;
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
- {
- dragEvent = evt;
-
- if (resizePanel)
- {
- Dimension d = ap.annotationScroller.getPreferredSize();
- int dif = evt.getY() - oldY;
-
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
-
- if ((d.height - dif) > 20)
- {
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
- d = ap.annotationSpaceFillerHolder.getPreferredSize();
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- d.width, d.height - dif));
- ap.paintAlignment(true);
- }
-
- ap.addNotify();
- }
- else
- {
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
- {
- resizePanel = evt.getY() < 10;
-
- getSelectedRow(evt.getY() - scrollOffset);
-
- if (selectedRow > -1
- && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ if (evt.isPopupTrigger())
{
- AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
- StringBuffer desc = new StringBuffer();
- if (aa.description != null
- && !aa.description.equals("New description"))
- {
- // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips
- desc.append(aa.getDescription(true).trim());
- // check to see if the description is an html fragment.
- if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("<html>")<0))
- {
- // clean the description ready for embedding in html
- desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<"));
- desc.insert(0, "<html>");
- } else {
- // remove terminating html if any
- int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("</html>");
- if (i>-1) {
- desc.setLength(desc.length()-7+i);
- }
- }
- if (aa.hasScore())
- {
- desc.append("<br/>");
- }
-
-
- } else {
- // begin the tooltip's html fragment
- desc.append("<html>");
- }
- if (aa.hasScore())
- {
- // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value).
- desc.append(" Score: " + aa.score);
- }
-
- if (desc.length() > 6)
- {
- desc.append("</html>");
- this.setToolTipText(desc.toString());
- }
- else
- this.setToolTipText(null);
+ showPopupMenu(evt);
}
-
}
/**
- * DOCUMENT ME!
+ * Build and show the Pop-up menu at the right-click mouse position
*
* @param evt
- * DOCUMENT ME!
*/
- public void mouseClicked(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- if (SwingUtilities.isLeftMouseButton(evt))
- {
- if (selectedRow > -1 && selectedRow < aa.length)
- {
- if (aa[selectedRow].groupRef != null)
- {
- if (evt.getClickCount() >= 2)
- {
- // 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.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- ap.av.sendSelection();
- }
- else
- {
- 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);
- }
- else if (evt.getClickCount() >= 2)
- {
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
- ap.av.setSelectionGroup(sg);
- ap.av.sendSelection();
- ap.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- }
+ evt.consume();
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
- }
- }
- }
- if (!SwingUtilities.isRightMouseButton(evt))
- {
- return;
- }
-
- JPopupMenu pop = new JPopupMenu("Annotations");
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(HIDE);
item.addActionListener(this);
pop.add(item);
+ // JAL-1264 hide all sequence-specific annotations of this type
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ final String label = aa[selectedRow].label;
+ JMenuItem hideType = new JMenuItem();
+ String text = MessageManager.getString("label.hide_all") + " "
+ + label;
+ hideType.setText(text);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ // for (AlignmentAnnotation ann : ap.av.getAlignment()
+ // .getAlignmentAnnotation())
+ // {
+ // if (ann.sequenceRef != null && ann.label != null
+ // && ann.label.equals(label))
+ // {
+ // ann.visible = false;
+ // }
+ // }
+ refresh(true);
+ }
+ });
+ pop.add(hideType);
+ }
+ }
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
// property methods
if (selectedRow < aa.length)
{
+ final String label = aa[selectedRow].label;
if (!aa[selectedRow].autoCalculated)
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
pop.add(item);
}
}
- else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ else if (label.indexOf("Consensus") > -1)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- "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.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (aaa.groupRef != null)
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ ap.getAnnotationPanel().paint(
+ ap.getAnnotationPanel().getGraphics());
}
else
{
ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
+ ap.alignmentChanged();
}
});
pop.add(cbmi);
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- "Show Group Histogram",
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
});
pop.add(chist);
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- "Show Group Logo",
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
});
pop.add(cprofl);
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- "Normalise Group Logo",
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
-
+
// TODO: pass on reference
// to ap
// so the
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- "Show Logo", av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- "Normalise Logo", av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
}
/**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
+ int start = selectedRow;
+ getSelectedRow(evt.getY() - getScrollOffset());
+ int end = selectedRow;
+
+ if (start != end)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
+
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+ }
+
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.getAnnotationPanel().repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationScroller.getPreferredSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
+
+ if ((d.height - dif) > 20)
+ {
+ ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+ d.height - dif));
+ d = ap.annotationSpaceFillerHolder.getPreferredSize();
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ d.width, d.height - dif));
+ ap.paintAlignment(true);
+ }
+
+ ap.addNotify();
+ }
+ else
+ {
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
+
+ getSelectedRow(evt.getY() - getScrollOffset());
+
+ if (selectedRow > -1
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ {
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .getAlignmentAnnotation()[selectedRow];
+
+ StringBuffer desc = new StringBuffer();
+ if (aa.description != null
+ && !aa.description.equals("New description"))
+ {
+ // TODO: we could refactor and merge this code with the code in
+ // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+ // tooltips
+ desc.append(aa.getDescription(true).trim());
+ // check to see if the description is an html fragment.
+ if (desc.length() < 6
+ || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
+ {
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
+ .replaceAll("<"));
+ desc.insert(0, "<html>");
+ }
+ else
+ {
+ // remove terminating html if any
+ int i = desc.substring(desc.length() - 7).toLowerCase()
+ .lastIndexOf("</html>");
+ if (i > -1)
+ {
+ desc.setLength(desc.length() - 7 + i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("<br/>");
+ }
+ // if (aa.hasProperties())
+ // {
+ // desc.append("<table>");
+ // for (String prop : aa.getProperties())
+ // {
+ // desc.append("<tr><td>" + prop + "</td><td>"
+ // + aa.getProperty(prop) + "</td><tr>");
+ // }
+ // desc.append("</table>");
+ // }
+ }
+ else
+ {
+ // begin the tooltip's html fragment
+ desc.append("<html>");
+ if (aa.hasScore())
+ {
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ desc.append(" Score: " + aa.score);
+ }
+ }
+ if (desc.length() > 6)
+ {
+ desc.append("</html>");
+ this.setToolTipText(desc.toString());
+ }
+ else
+ {
+ this.setToolTipText(null);
+ }
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt))
+ {
+ if (selectedRow > -1 && selectedRow < aa.length)
+ {
+ if (aa[selectedRow].groupRef != null)
+ {
+ if (evt.getClickCount() >= 2)
+ {
+ // todo: make the ap scroll to the selection - not necessary, first
+ // click highlights/scrolls, second selects
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ // 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);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+ else
+ {
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
+ }
+ return;
+ }
+ else if (aa[selectedRow].sequenceRef != null)
+ {
+ if (evt.getClickCount() == 1)
+ {
+ ap.getSeqPanel().ap
+ .getIdPanel()
+ .highlightSearchResults(
+ Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ }
+ else if (evt.getClickCount() >= 2)
+ {
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ 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);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+
+ }
+ }
+ return;
+ }
+ }
+
+ /**
* do a single sequence copy to jalview and the system clipboard
*
* @param sq
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
- SequenceI[] seqs = new SequenceI[]
- { sq };
+ SequenceI[] seqs = new SequenceI[] { sq };
String[] omitHidden = null;
- SequenceI[] dseqs = new SequenceI[]
- { sq.getDatasetSequence() };
+ SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
if (dseqs[0] == null)
{
dseqs[0] = new Sequence(sq);
sq.setDatasetSequence(dseqs[0]);
}
Alignment ds = new Alignment(dseqs);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
sq.getLength(), seqs);
}
+ int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
+ List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
+ if (hiddenCols != null)
+ {
+ alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
+ hiddenCols);
+ }
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, alignmentStartEnd);
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
- Vector hiddenColumns = null;
- if (av.hasHiddenColumns)
+ ArrayList<int[]> hiddenColumns = null;
+ if (av.hasHiddenColumns())
{
- hiddenColumns = new Vector();
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ hiddenColumns = new ArrayList<int[]>();
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(i);
-
- hiddenColumns.addElement(new int[]
- { region[0], region[1] });
+ hiddenColumns.add(new int[] { region[0], region[1] });
}
}
- Desktop.jalviewClipboard = new Object[]
- { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+ Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
+ // of a consensus
+ // sequence ? need to
+ // flag
// sequence as special.
hiddenColumns };
}
* @param g1
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
RenderingHints.VALUE_ANTIALIAS_ON);
}
- drawComponent(g2, width);
+ drawComponent(g2, true, width);
}
/**
- * DOCUMENT ME!
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
*
* @param g
- * DOCUMENT ME!
+ * Graphics2D instance (needed for font scaling)
+ * @param width
+ * Width for scaling labels
+ *
*/
public void drawComponent(Graphics g, int width)
{
+ drawComponent(g, false, width);
+ }
+
+ private final boolean debugRedraw = false;
+
+ /**
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
+ */
+ public void drawComponent(Graphics g, boolean clip, int width)
+ {
if (av.getFont().getSize() < 10)
{
g.setFont(font);
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
- g.translate(0, scrollOffset);
+ g.translate(0, getScrollOffset());
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
int y = 0;
int x = 0;
int graphExtras = 0;
int offset = 0;
-
+ Font baseFont = g.getFont();
+ FontMetrics baseMetrics = fm;
+ int ofontH = fontHeight;
+ int sOffset = 0;
+ int visHeight = 0;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+ .getAnnotationPanel().getVisibleVRange() : null;
+ if (clip && visr != null)
+ {
+ sOffset = visr[0];
+ visHeight = visr[1];
+ }
+ boolean visible = true, before = false, after = false;
if (aa != null)
{
hasHiddenRows = false;
+ int olY = 0;
for (int i = 0; i < aa.length; i++)
{
- g.setColor(Color.black);
-
+ visible = true;
if (!aa[i].visible)
{
hasHiddenRows = true;
continue;
}
-
+ olY = y;
y += aa[i].height;
+ if (clip)
+ {
+ if (y < sOffset)
+ {
+ if (!before)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("before vis: " + i);
+ }
+ before = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ if (olY > visHeight)
+ {
+
+ if (!after)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("Scroll offset: " + sOffset
+ + " after vis: " + i);
+ }
+ after = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ }
+ g.setColor(Color.black);
offset = -aa[i].height / 2;
offset -= fm.getDescent();
}
else
+ {
offset += fm.getDescent();
+ }
x = width - fm.stringWidth(aa[i].label) - 3;
if (aa[i].graphGroup > -1)
{
int groupSize = 0;
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
groupSize++;
}
}
-
if (groupSize * (fontHeight + 8) < aa[i].height)
{
graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
}
-
- for (int gg = 0; gg < aa.length; gg++)
+ else
{
- if (aa[gg].graphGroup == aa[i].graphGroup)
+ // scale font to fit
+ float h = aa[i].height / (float) groupSize, s;
+ if (h < 9)
+ {
+ visible = false;
+ }
+ else
+ {
+ fontHeight = -8 + (int) h;
+ s = ((float) fontHeight) / (float) ofontH;
+ Font f = baseFont.deriveFont(AffineTransform
+ .getScaleInstance(s, s));
+ g.setFont(f);
+ fm = g.getFontMetrics();
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ }
+ }
+ if (visible)
+ {
+ for (int gg = 0; gg < aa.length; gg++)
{
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, y - graphExtras);
- if (aa[gg].annotations[0] != null)
+ if (aa[gg].graphGroup == aa[i].graphGroup)
{
- g.setColor(aa[gg].annotations[0].colour);
- }
+ x = width - fm.stringWidth(aa[gg].label) - 3;
+ g.drawString(aa[gg].label, x, y - graphExtras);
- g.drawLine(x, y - graphExtras - 3,
- x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+ if (aa[gg]._linecolour != null)
+ {
- g.setColor(Color.black);
- graphExtras += fontHeight + 8;
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras
+ + 3);
+ }
+
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
}
}
+ g.setFont(baseFont);
+ fm = baseMetrics;
+ fontHeight = ofontH;
}
else
{
if (resizePanel)
{
- g.drawImage(image, 2, 0 - scrollOffset, this);
+ g.drawImage(image, 2, 0 - getScrollOffset(), this);
}
else if (dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
- dragEvent.getY() - scrollOffset);
+ dragEvent.getY() - getScrollOffset());
}
- if ((aa == null) || (aa.length < 1))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
- 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);
}
}
+
+ public int getScrollOffset()
+ {
+ return scrollOffset;
+ }
}
git://source.jalview.org / jalview.git / blobdiff