/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
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!
addMouseListener(this);
addMouseMotionListener(this);
+ addMouseWheelListener(ap.annotationPanel);
}
public AnnotationLabels(AlignViewport av)
void getSelectedRow(int y)
{
int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
selectedRow = -2;
if (aa != null)
{
*/
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(DELETE))
{
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
}
else if (evt.getActionCommand().equals(SHOWALL))
{
ap.validateAnnotationDimensions(false);
ap.addNotify();
ap.repaint();
- //validate();
- //ap.paintAlignment(true);
+ // validate();
+ // ap.paintAlignment(true);
}
/**
if (start != end)
{
// Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment
+ AlignmentAnnotation startAA = ap.av.getAlignment()
.getAlignmentAnnotation()[start];
if (end == -1)
{
- end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
}
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+ 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;
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];
-
+ 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
+ // 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))
+ 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 = 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);
- }
+ }
+ 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 {
+
+ }
+ 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).
+ // TODO: limit precision of score to avoid noise from imprecise doubles
+ // (64.7 becomes 64.7+/some tiny value).
desc.append(" Score: " + aa.score);
}
*/
public void mouseClicked(MouseEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
if (selectedRow > -1 && selectedRow < aa.length)
{
if (evt.getClickCount() >= 2)
{
- // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
+ // 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); // );
return;
}
- JPopupMenu pop = new JPopupMenu("Annotations");
+ JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
{
public void actionPerformed(ActionEvent e)
{
-
+
// TODO: pass on reference
// to ap
// so the
sq.setDatasetSequence(dseqs[0]);
}
Alignment ds = new Alignment(dseqs);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
sq.getLength(), seqs);
.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++)
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);
+
+ if (aa[gg]._linecolour != null)
+ {
- g.drawLine(x, y - graphExtras - 3,
- x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+ 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.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
}
}
+ g.setFont(baseFont);
+ fm = baseMetrics;
+ fontHeight = ofontH;
}
else
{
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