/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 java.util.regex.Pattern;
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.event.*;
+import java.awt.geom.AffineTransform;
import java.awt.image.*;
import javax.swing.*;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
+ static String TOGGLE_LABELSCALE = "Scale Label to Column";
+
static String ADDNEW = "Add New Row";
static String EDITNAME = "Edit Label/Description";
Font font = new Font("Arial", Font.PLAIN, 11);
+ private boolean hasHiddenRows;
+
/**
* Creates a new AnnotationLabels object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AnnotationLabels(AlignmentPanel ap)
{
{
}
- BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
- .getWidth(this), BufferedImage.TYPE_INT_RGB);
+ BufferedImage bi = new BufferedImage(temp.getHeight(this),
+ temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
addMouseListener(this);
addMouseMotionListener(this);
+ addMouseWheelListener(ap.annotationPanel);
}
public AnnotationLabels(AlignViewport av)
* DOCUMENT ME!
*
* @param y
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScrollOffset(int y)
{
repaint();
}
+ /**
+ * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+ * y
+ *
+ * @param y
+ * coordinate position to search for a row
+ */
void getSelectedRow(int y)
{
int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ selectedRow = -2;
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
+ selectedRow = -1;
if (!aa[i].visible)
{
continue;
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
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);
}
else if (evt.getActionCommand().equals(EDITNAME))
{
else if (evt.getActionCommand().equals(HIDE))
{
aa[selectedRow].visible = false;
-
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.quality = null;
- }
}
else if (evt.getActionCommand().equals(DELETE))
{
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
}
else if (evt.getActionCommand().equals(SHOWALL))
{
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- SequenceI cons = av.getConsensusSeq();
+ SequenceI cons = null;
+ if (aa[selectedRow].groupRef != null)
+ {
+ cons = aa[selectedRow].groupRef.getConsensusSeq();
+ }
+ else
+ {
+ cons = av.getConsensusSeq();
+ }
if (cons != null)
{
copy_annotseqtoclipboard(cons);
}
}
+ else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+ {
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
+ }
- ap.annotationPanel.adjustPanelHeight();
- ap.annotationScroller.validate();
- ap.paintAlignment(true);
+ ap.validateAnnotationDimensions(false);
+ ap.addNotify();
+ ap.repaint();
+ // validate();
+ // ap.paintAlignment(true);
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
boolean editLabelDescription(AlignmentAnnotation annotation)
{
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Name ",
- "Annotation Description ", "Edit Annotation Name/Description");
+ "Annotation Description ", "Edit Annotation Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
if (start != end)
{
// Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment
+ AlignmentAnnotation startAA = ap.av.getAlignment()
.getAlignmentAnnotation()[start];
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
}
resizePanel = false;
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
getSelectedRow(evt.getY() - scrollOffset);
if (selectedRow > -1
- && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
{
- AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
- StringBuffer desc = new StringBuffer("<html>");
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .getAlignmentAnnotation()[selectedRow];
+ StringBuffer desc = new StringBuffer();
if (aa.description != null
&& !aa.description.equals("New description"))
{
- desc.append(aa.getDescription(true));
- if (aa.hasScore)
- desc.append("<br>");
+ // 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())
{
- desc.append("Score: " + aa.score);
+ // 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)
+ if (desc.length() > 6)
{
desc.append("</html>");
this.setToolTipText(desc.toString());
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
+ 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)
+ {
+ 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());
+ }
+
+ }
+ }
+ }
if (!SwingUtilities.isRightMouseButton(evt))
{
return;
}
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- JPopupMenu pop = new JPopupMenu("Annotations");
+ JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
-
- if ((aa == null) || (aa.length == 0))
+ pop.add(item);
+ if (selectedRow < 0)
{
- item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
- pop.add(item);
+ 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;
}
-
- pop.add(item);
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(SHOWALL);
- 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);
- // annotation object should be typed
- if (selectedRow < aa.length && aa[selectedRow] == ap.av.consensus)
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
+ if (selectedRow < aa.length)
{
- pop.addSeparator();
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
- cbmi.addActionListener(new ActionListener()
+ if (!aa[selectedRow].autoCalculated)
{
- public void actionPerformed(ActionEvent e)
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ // 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);
}
- });
- pop.add(cbmi);
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
- }
+ }
+ else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ "Ignore Gaps In Consensus",
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .getIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addActionListener(new ActionListener()
+ {
+ 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());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "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(
+ "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(
+ "Normalise Group Logo",
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ 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(
+ "Show Histogram", av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ 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(
+ "Show Logo", av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ 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(
+ "Normalise Logo", av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ 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());
}
* do a single sequence copy to jalview and the system clipboard
*
* @param sq
- * sequence to be copied to clipboard
+ * sequence to be copied to clipboard
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
sq.setDatasetSequence(dseqs[0]);
}
Alignment ds = new Alignment(dseqs);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
sq.getLength(), seqs);
String output = new FormatAdapter().formatSequences("Fasta", seqs,
omitHidden);
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
- new StringSelection(output), Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
Vector hiddenColumns = null;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
hiddenColumns = new Vector();
for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
Desktop.jalviewClipboard = new Object[]
{ seqs, ds, // what is the dataset of a consensus sequence ? need to flag
- // sequence as special.
+ // sequence as special.
hiddenColumns };
}
* DOCUMENT ME!
*
* @param g1
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
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!
+ * @param g 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.translate(0, scrollOffset);
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.annotationPanel!=null) ? ap.annotationPanel.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;
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)
{
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, y - graphExtras);
- if (aa[gg].annotations[0] != null)
+ 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++)
+ {
+ 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
{
else if (dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
- .getY()
- - scrollOffset);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY() - scrollOffset);
}
- if ((aa == null) || (aa.length < 1))
+ if (!av.wrapAlignment && ((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);
}
}
}
git://source.jalview.org / jalview.git / blobdiff