/*
- * 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.
*
*/
package jalview.gui;
+import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
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.Vector;
+import java.util.Collections;
+import java.util.List;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
- String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+ .compile("<");
+
+ String TOGGLE_LABELSCALE = MessageManager
+ .getString("label.scale_label_to_column");
String ADDNEW = MessageManager.getString("label.add_new_row");
- String EDITNAME = MessageManager.getString("label.edit_label_description");
+ String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
String HIDE = MessageManager.getString("label.hide_row");
String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
- String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+ 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);
addMouseListener(this);
addMouseMotionListener(this);
- addMouseWheelListener(ap.annotationPanel);
+ addMouseWheelListener(ap.getAnnotationPanel());
}
public AnnotationLabels(AlignViewport av)
* @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] }, null, null);
+ new AlignmentAnnotation[] { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- refresh();
+ refresh(fullRepaint);
}
/**
* Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
*/
- protected void refresh()
+ protected void refresh(boolean adjustHeight)
{
- ap.validateAnnotationDimensions(false);
+ ap.validateAnnotationDimensions(adjustHeight);
ap.addNotify();
- ap.repaint();
+ 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.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.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.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ if (evt.isPopupTrigger())
{
- 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(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/>");
- }
- // 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);
- }
+ 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)
{
+ evt.consume();
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.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)
- {
- if (evt.getClickCount() == 1)
- {
- 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 = 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"));
item.addActionListener(this);
pop.add(item);
// JAL-1264 hide all sequence-specific annotations of this type
- final String label = aa[selectedRow].label;
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;
+ String text = MessageManager.getString("label.hide_all") + " "
+ + label;
hideType.setText(text);
hideType.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- for (AlignmentAnnotation ann : ap.av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ann.sequenceRef != null && ann.label != null
- && ann.label.equals(label))
- {
- ann.visible = false;
- }
- }
- refresh();
+ 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);
// property methods
if (selectedRow < aa.length)
{
+ final String label = aa[selectedRow].label;
if (!aa[selectedRow].autoCalculated)
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_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(
- MessageManager.getString("label.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(
- MessageManager.getString("label.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(
- MessageManager.getString("label.normalise_group_logo"),
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.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(
- MessageManager.getString("label.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(
- MessageManager.getString("label.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
}
/**
- * do a single sequence copy to jalview and the system clipboard
+ * DOCUMENT ME!
*
- * @param sq
- * sequence to be copied to clipboard
+ * @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
+ * sequence to be copied to clipboard
*/
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.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;
+ 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)
{
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.getAlignment().getAlignmentAnnotation();
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
- int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
- .getVisibleVRange() : null;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+ .getAnnotationPanel().getVisibleVRange() : null;
if (clip && visr != null)
{
sOffset = visr[0];
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 (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
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