/*
- * 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 2.9)
+ * Copyright (C) 2015 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.Vector;
+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;
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)
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))
{
*/
public void mousePressed(MouseEvent evt)
{
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
oldY = evt.getY();
}
public void mouseReleased(MouseEvent evt)
{
int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
int end = selectedRow;
if (start != end)
resizePanel = false;
dragEvent = null;
repaint();
- ap.annotationPanel.repaint();
+ ap.getAnnotationPanel().repaint();
}
/**
Dimension d = ap.annotationScroller.getPreferredSize();
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)
{
{
resizePanel = evt.getY() < 10;
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
if (selectedRow > -1
&& ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
|| (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
{
// clean the description ready for embedding in html
- desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
.replaceAll("<"));
desc.insert(0, "<html>");
}
{
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 (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);
+ }
}
-
}
/**
{
// todo: make the ap scroll to the selection - not necessary, first
// click highlights/scrolls, second selects
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
ap.av.setSelectionGroup(// new SequenceGroup(
aa[selectedRow].groupRef); // );
ap.paintAlignment(false);
}
else
{
- ap.seqPanel.ap.idPanel
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
}
return;
}
{
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
- .asList(new SequenceI[]
- { aa[selectedRow].sequenceRef }));
+ ap.getSeqPanel().ap
+ .getIdPanel()
+ .highlightSearchResults(
+ Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- // we make a copy rather than edit the current selection if no modifiers pressed
+ // 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 {
+ }
+ else
+ {
if (evt.isControlDown())
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
- } else {
- // notionally, we should also add intermediate sequences from last added sequence ?
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
sg.addSequence(aa[selectedRow].sequenceRef, true);
}
}
- } else {
+ }
+ else
+ {
sg = new SequenceGroup();
sg.setStartRes(0);
- sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
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;
- }
- }
+ 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();
}
});
// 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(
- "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()
{
{
// 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
{
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()
{
});
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()
{
});
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()
{
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- "Show Logo", av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- "Normalise Logo", av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
*/
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 = AlignFrame.getStartEnd(alignmentStartEnd,
+ 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 };
}
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];
offset -= fm.getDescent();
}
else
+ {
offset += fm.getDescent();
+ }
x = width - fm.stringWidth(aa[i].label) - 3;
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