/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*/
package jalview.gui;
+import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.Color;
+import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.List;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * The panel that holds the labels for alignment annotations, providing
+ * tooltips, context menus, drag to reorder rows, and drag to adjust panel
+ * height
*/
-public class AnnotationLabels extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel
+ implements MouseListener, MouseMotionListener, ActionListener
{
+ // width in pixels within which height adjuster arrows are shown and active
+ private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
- String TOGGLE_LABELSCALE = MessageManager
+ private static final Font font = new Font("Arial", Font.PLAIN, 11);
+
+ private static final String TOGGLE_LABELSCALE = MessageManager
.getString("label.scale_label_to_column");
- String ADDNEW = MessageManager.getString("label.add_new_row");
+ private static final String ADDNEW = MessageManager
+ .getString("label.add_new_row");
- String EDITNAME = MessageManager
+ private static final String EDITNAME = MessageManager
.getString("label.edit_label_description");
- String HIDE = MessageManager.getString("label.hide_row");
+ private static final String HIDE = MessageManager
+ .getString("label.hide_row");
- String DELETE = MessageManager.getString("label.delete_row");
+ private static final String DELETE = MessageManager
+ .getString("label.delete_row");
- String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
+ private static final String SHOWALL = MessageManager
+ .getString("label.show_all_hidden_rows");
- String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+ private static final String OUTPUT_TEXT = MessageManager
+ .getString("label.export_annotation");
- String COPYCONS_SEQ = MessageManager
+ private static final String COPYCONS_SEQ = MessageManager
.getString("label.copy_consensus_sequence");
- boolean resizePanel = false;
+ private static Image adjusterImage;
+
+ private static int adjusterImageHeight;
- Image image;
+ private final boolean debugRedraw = false;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
AlignViewport av;
- boolean resizing = false;
-
- MouseEvent dragEvent;
+ private MouseEvent dragEvent;
- int oldY;
+ private int oldY;
- int selectedRow;
+ private int selectedRow;
private int scrollOffset = 0;
- Font font = new Font("Arial", Font.PLAIN, 11);
-
private boolean hasHiddenRows;
+ private boolean resizePanel = false;
+
/**
- * Creates a new AnnotationLabels object.
+ * Creates a new AnnotationLabels object
*
* @param ap
- * DOCUMENT ME!
*/
public AnnotationLabels(AlignmentPanel ap)
{
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
+ if (adjusterImage == null)
+ {
+ loadAdjusterImage();
+ }
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(ap.getAnnotationPanel());
+ }
+
+ public AnnotationLabels(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ /**
+ * Loads the gif for the panel height adjustment
+ */
+ protected void loadAdjusterImage()
+ {
java.net.URL url = getClass().getResource("/images/idwidth.gif");
Image temp = null;
if (url != null)
{
- temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+ temp = Toolkit.getDefaultToolkit().createImage(url);
}
try
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
- image = bi;
-
- addMouseListener(this);
- addMouseMotionListener(this);
- addMouseWheelListener(ap.getAnnotationPanel());
- }
-
- public AnnotationLabels(AlignViewport av)
- {
- this.av = av;
+ adjusterImage = bi;
+ adjusterImageHeight = bi.getHeight();
}
/**
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
+ boolean fullRepaint = false;
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
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.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] });
+ new AlignmentAnnotation[]
+ { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- refresh();
-
- }
+ ap.refresh(fullRepaint);
- /**
- * Redraw sensibly.
- */
- protected void refresh()
- {
- ap.validateAnnotationDimensions(false);
- ap.addNotify();
- 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;
}
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ getSelectedRow(evt.getY() - getScrollOffset());
+ oldY = evt.getY();
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ }
+ }
+
/**
- * DOCUMENT ME!
+ * Build and show the Pop-up menu at the right-click mouse position
*
* @param evt
- * DOCUMENT ME!
*/
- public void mousePressed(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt)
{
- getSelectedRow(evt.getY() - getScrollOffset());
- oldY = evt.getY();
+ evt.consume();
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ if (selectedRow < 0)
+ {
+ if (hasHiddenRows)
+ { // let the user make everything visible again
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ item = new JMenuItem(EDITNAME);
+ 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;
+ // }
+ // }
+ ap.refresh(true);
+ }
+ });
+ pop.add(hideType);
+ }
+ }
+ item = new JMenuItem(DELETE);
+ item.addActionListener(this);
+ pop.add(item);
+ if (hasHiddenRows)
+ {
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ item = new JMenuItem(OUTPUT_TEXT);
+ item.addActionListener(this);
+ pop.add(item);
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
+ if (selectedRow < aa.length)
+ {
+ final String label = aa[selectedRow].label;
+ if (!aa[selectedRow].autoCalculated)
+ {
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ // display formatting settings for this row.
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+ aa[selectedRow].scaleColLabel);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ }
+ else if (label.indexOf("Consensus") > -1)
+ {
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
+ : ap.av.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.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ 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
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
}
/**
- * DOCUMENT ME!
+ * Reorders annotation rows after a drag of a label
*
* @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 dragging to resize instead, start == end
+ */
if (start != end)
{
// Swap these annotations
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
- {
- if (evt.getY() < 10)
- {
- resizePanel = true;
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * Removes the height adjuster image on leaving the panel, unless currently
+ * dragging it
*/
+ @Override
public void mouseExited(MouseEvent evt)
{
- if (dragEvent == null)
+ if (resizePanel && dragEvent == null)
{
resizePanel = false;
repaint();
}
/**
- * DOCUMENT ME!
+ * A mouse drag may be either an adjustment of the panel height (if flag
+ * resizePanel is set on), or a reordering of the annotation rows. The former
+ * is dealt with by this method, the latter in mouseReleased.
*
* @param evt
- * DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
dragEvent = evt;
if ((d.height - dif) > 20)
{
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
+ 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.annotationSpaceFillerHolder
+ .setPreferredSize(new Dimension(d.width, d.height - dif));
+ ap.paintAlignment(true, false);
}
ap.addNotify();
}
/**
- * DOCUMENT ME!
+ * Updates the tooltip as the mouse moves over the labels
*
* @param evt
- * DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
- resizePanel = evt.getY() < 10;
+ showOrHideAdjuster(evt);
getSelectedRow(evt.getY() - getScrollOffset());
- if (selectedRow > -1
- && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ if (selectedRow > -1 && ap.av.getAlignment()
+ .getAlignmentAnnotation().length > selectedRow)
{
AlignmentAnnotation aa = ap.av.getAlignment()
.getAlignmentAnnotation()[selectedRow];
// 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))
+ 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)
{
// 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);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
- {
- final AlignmentAnnotation[] aa = ap.av.getAlignment()
- .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.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- 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 (!(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.av.sendSelection();
- ap.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- }
-
- }
- }
- }
- if (!SwingUtilities.isRightMouseButton(evt))
- {
- return;
- }
-
- JPopupMenu pop = new JPopupMenu(
- MessageManager.getString("label.annotations"));
- JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
- pop.add(item);
- if (selectedRow < 0)
- {
- if (hasHiddenRows)
- { // let the user make everything visible again
- item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
- pop.add(item);
- }
- pop.show(this, evt.getX(), evt.getY());
- return;
- }
- item = new JMenuItem(EDITNAME);
- 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();
- }
- });
- pop.add(hideType);
- }
- }
- item = new JMenuItem(DELETE);
- item.addActionListener(this);
- pop.add(item);
- if (hasHiddenRows)
- {
- item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
- pop.add(item);
- }
- item = new JMenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- pop.add(item);
- // TODO: annotation object should be typed for autocalculated/derived
- // property methods
- if (selectedRow < aa.length)
- {
- final String label = aa[selectedRow].label;
- if (!aa[selectedRow].autoCalculated)
- {
- if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ if (aa.hasScore())
{
- // display formatting settings for this row.
- pop.addSeparator();
- // av and sequencegroup need to implement same interface for
- item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
- aa[selectedRow].scaleColLabel);
- item.addActionListener(this);
- pop.add(item);
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ desc.append(" Score: " + aa.score);
}
}
- else if (label.indexOf("Consensus") > -1)
+ if (desc.length() > 6)
{
- pop.addSeparator();
- // av and sequencegroup need to implement same interface for
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .isIgnoreGapsConsensus());
- final AlignmentAnnotation aaa = aa[selectedRow];
- cbmi.addActionListener(new ActionListener()
+ desc.append("</html>");
+ this.setToolTipText(desc.toString());
+ }
+ else
+ {
+ this.setToolTipText(null);
+ }
+ }
+ }
+
+ /**
+ * Shows the height adjuster image if the mouse moves into the top left
+ * region, or hides it if the mouse leaves the regio
+ *
+ * @param evt
+ */
+ protected void showOrHideAdjuster(MouseEvent evt)
+ {
+ boolean was = resizePanel;
+ resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+
+ if (resizePanel != was)
+ {
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR
+ : Cursor.DEFAULT_CURSOR));
+ repaint();
+ }
+ }
+
+ @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)
{
- public void actionPerformed(ActionEvent e)
+ if (evt.getClickCount() >= 2)
{
- if (aaa.groupRef != null)
+ // 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
+ || !(Platform.isControlDown(evt) || evt.isShiftDown()))
{
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel().paint(
- ap.getAnnotationPanel().getGraphics());
+ if (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
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ // 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();
}
- });
- pop.add(cbmi);
- // av and sequencegroup need to implement same interface for
- if (aaa.groupRef != null)
- {
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
- aa[selectedRow].groupRef.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setShowConsensusHistogram(chist.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
- aa[selectedRow].groupRef.isShowSequenceLogo());
- cprofl.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setshowSequenceLogo(cprofl.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprofl);
- final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
- aa[selectedRow].groupRef.isNormaliseSequenceLogo());
- cproflnorm.addActionListener(new ActionListener()
+ else
{
- public void actionPerformed(ActionEvent e)
- {
-
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
- // automatically enable logo display if we're clicked
- aaa.groupRef.setshowSequenceLogo(true);
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cproflnorm);
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
+ }
+ return;
}
- else
+ else if (aa[selectedRow].sequenceRef != null)
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"),
- av.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
+ if (evt.getClickCount() == 1)
{
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"),
- av.isShowSequenceLogo());
- cprof.addActionListener(new ActionListener()
+ ap.getSeqPanel().ap.getIdPanel()
+ .highlightSearchResults(Arrays.asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
+ }
+ else if (evt.getClickCount() >= 2)
{
- public void actionPerformed(ActionEvent e)
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null)
{
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(cprof.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ // we make a copy rather than edit the current selection if no
+ // modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(Platform.isControlDown(evt) || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ else
+ {
+ if (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);
+ }
+ }
}
- });
- pop.add(cprof);
- final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"),
- av.isNormaliseSequenceLogo());
- cprofnorm.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
+ else
{
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(true);
- av.setNormaliseSequenceLogo(cprofnorm.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
}
- });
- pop.add(cprofnorm);
+ ap.av.setSelectionGroup(sg);
+ ap.paintAlignment(false, false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+
}
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
}
+ return;
}
- pop.show(this, evt.getX(), evt.getY());
}
/**
if (dseqs[0] == null)
{
dseqs[0] = new Sequence(sq);
- dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
+ dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars,
+ sq.getSequenceAsString()));
sq.setDatasetSequence(dseqs[0]);
}
Alignment ds = new Alignment(dseqs);
if (av.hasHiddenColumns())
{
- omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
- sq.getLength(), seqs);
+ omitHidden = av.getAlignment().getHiddenColumns()
+ .getVisibleSequenceStrings(0, sq.getLength(), seqs);
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
- List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
- if (hiddenCols != null)
+ if (av.hasHiddenColumns())
{
- alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd,
- hiddenCols);
+ alignmentStartEnd = av.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
}
- String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden, alignmentStartEnd);
+
+ String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+ seqs, omitHidden, alignmentStartEnd);
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
ArrayList<int[]> hiddenColumns = null;
+
if (av.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<int[]>();
- for (int[] region : av.getColumnSelection().getHiddenColumns())
- {
- hiddenColumns.add(new int[] { region[0], region[1] });
- }
+ hiddenColumns = av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
* @param g1
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
drawComponent(g, false, width);
}
- private final boolean debugRedraw = false;
-
/**
* Draw the full set of annotation Labels for the alignment at the given
* cursor
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
- int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
- .getAnnotationPanel().getVisibleVRange() : null;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null)
+ ? ap.getAnnotationPanel().getVisibleVRange()
+ : null;
if (clip && visr != null)
{
sOffset = visr[0];
{
if (debugRedraw)
{
- System.out.println("Scroll offset: " + sOffset
- + " after vis: " + i);
+ System.out.println(
+ "Scroll offset: " + sOffset + " after vis: " + i);
}
after = true;
}
}
if (groupSize * (fontHeight + 8) < aa[i].height)
{
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
else
{
{
fontHeight = -8 + (int) h;
s = ((float) fontHeight) / (float) ofontH;
- Font f = baseFont.deriveFont(AffineTransform
- .getScaleInstance(s, s));
+ Font f = baseFont
+ .deriveFont(AffineTransform.getScaleInstance(s, s));
g.setFont(f);
fm = g.getFontMetrics();
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
}
if (visible)
g.setColor(aa[gg]._linecolour);
g.drawLine(x, y - graphExtras + 3,
- x + fm.stringWidth(aa[gg].label), y - graphExtras
- + 3);
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras + 3);
}
g.setColor(Color.black);
}
}
- if (resizePanel)
- {
- g.drawImage(image, 2, 0 - getScrollOffset(), this);
- }
- else if (dragEvent != null && aa != null)
+ if (!resizePanel && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
{
return scrollOffset;
}
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff