/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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.image.*;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
import java.util.List;
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class IdCanvas extends JPanel
+public class IdCanvas extends JPanel implements ViewportListenerI
{
protected AlignViewport av;
AnnotationPanel ap;
- Font idfont;
+ private Font idfont;
/**
* Creates a new IdCanvas object.
setLayout(new BorderLayout());
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
+ av.getRanges().addPropertyChangeListener(this);
}
/**
*
* @param gg
* DOCUMENT ME!
+ * @param hiddenRows
+ * true - check and display hidden row marker if need be
* @param s
* DOCUMENT ME!
* @param i
* @param ypos
* DOCUMENT ME!
*/
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
- int ypos)
+ public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+ int i, int starty, int ypos)
{
int xPos = 0;
int panelWidth = getWidth();
- int charHeight = av.charHeight;
+ int charHeight = av.getCharHeight();
if ((searchResults != null) && searchResults.contains(s))
{
gg.setColor(Color.black);
}
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth
- fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
*/
public void fastPaint(int vertical)
{
- if (gg == null)
+ /*
+ * for now, not attempting fast paint of wrapped ids...
+ */
+ if (gg == null || av.getWrapAlignment())
{
repaint();
return;
}
- gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+ ViewportRanges ranges = av.getRanges();
+
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+ -vertical * av.getCharHeight());
- int ss = av.startSeq;
- int es = av.endSeq;
+ int ss = ranges.getStartSeq();
+ int es = ranges.getEndSeq();
int transY = 0;
if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq)
+ if (ss < ranges.getStartSeq())
{ // ie scrolling too fast, more than a page at a time
- ss = av.startSeq;
+ ss = ranges.getStartSeq();
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - ((vertical + 1) * av.getCharHeight());
}
}
- else if (vertical < 0)
+ else if (vertical < 0) // scroll up
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
g.setColor(Color.white);
int oldHeight = imgHeight;
imgHeight = getHeight();
- imgHeight -= (imgHeight % av.charHeight);
+ imgHeight -= (imgHeight % av.getCharHeight());
if (imgHeight < 1)
{
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
- drawIds(av.getStartSeq(), av.endSeq);
+ drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
g.drawImage(image, 0, 0, this);
}
*/
void drawIds(int starty, int endy)
{
- if (av.seqNameItalics)
+ if (av.isSeqNameItalics())
{
- idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
- .getSize());
+ setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize()));
}
else
{
- idfont = av.getFont();
+ setIdfont(av.getFont());
}
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
fm = gg.getFontMetrics();
if (av.antiAlias)
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ boolean hasHiddenRows = av.hasHiddenRows();
+
if (av.getWrapAlignment())
{
- int maxwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight();
+ drawIdsWrapped(starty, hasHiddenRows);
+ return;
+ }
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
+ // No need to hang on to labels if we're not wrapped
+ labels = null;
- int annotationHeight = 0;
+ // Now draw the id strings
+ int panelWidth = getWidth();
+ int xPos = 0;
+
+ SequenceI sequence;
+ // Now draw the id strings
+ for (int i = starty; i <= endy; i++)
+ {
+ sequence = av.getAlignment().getSequenceAt(i);
- if (av.showAnnotation)
+ if (sequence == null)
{
- if (ap == null)
- {
- ap = new AnnotationPanel(av);
- }
+ continue;
+ }
- annotationHeight = ap.adjustPanelHeight();
- if (labels == null)
- {
- labels = new AnnotationLabels(av);
- }
+ if (hasHiddenRows || av.isDisplayReferenceSeq())
+ {
+ setHiddenFont(sequence);
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ // Selected sequence colours
+ if ((searchResults != null) && searchResults.contains(sequence))
+ {
+ currentColor = Color.black;
+ currentTextColor = Color.white;
+ }
+ else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
+ .getSequences(null).contains(sequence))
+ {
+ currentColor = Color.lightGray;
+ currentTextColor = Color.black;
+ }
+ else
{
- hgap += av.charHeight;
+ currentColor = av.getSequenceColour(sequence);
+ currentTextColor = Color.black;
}
- int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+ gg.setColor(currentColor);
- int rowSize = av.getEndRes() - av.getStartRes();
+ gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+ av.getCharHeight());
- // Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
- && (row < maxwidth); ypos += cHeight, row += rowSize)
+ gg.setColor(currentTextColor);
+
+ String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+ if (av.isRightAlignIds())
{
- for (int i = starty; i < alheight; i++)
- {
- SequenceI s = av.getAlignment().getSequenceAt(i);
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
- {
- setHiddenFont(s);
- }
- else
- {
- gg.setFont(idfont);
- }
-
- drawIdString(gg, s, i, 0, ypos);
- }
+ xPos = panelWidth - fm.stringWidth(string) - 4;
+ }
- if (labels != null && av.showAnnotation)
- {
- gg.translate(0, ypos + (alheight * av.charHeight));
- labels.drawComponent(gg, getWidth());
- gg.translate(0, -ypos - (alheight * av.charHeight));
- }
+ gg.drawString(string, xPos,
+ (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
+
+ if (hasHiddenRows)
+ {
+ drawMarker(i, starty, 0);
}
}
- else
- {
- // No need to hang on to labels if we're not wrapped
- labels = null;
+ }
- // Now draw the id strings
- int panelWidth = getWidth();
- int xPos = 0;
+ /**
+ * Draws sequence ids in wrapped mode
+ *
+ * @param starty
+ * @param hasHiddenRows
+ */
+ protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- SequenceI sequence;
- // Now draw the id strings
- for (int i = starty; i < endy; i++)
- {
- sequence = av.getAlignment().getSequenceAt(i);
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
+ }
- if (sequence == null)
- {
- continue;
- }
+ int annotationHeight = 0;
- if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
- {
- setHiddenFont(sequence);
- }
+ if (av.isShowAnnotation())
+ {
+ if (ap == null)
+ {
+ ap = new AnnotationPanel(av);
+ }
- // Selected sequence colours
- if ((searchResults != null) && searchResults.contains(sequence))
- {
- currentColor = Color.black;
- currentTextColor = Color.white;
- }
- else if ((av.getSelectionGroup() != null)
- && av.getSelectionGroup().getSequences(null)
- .contains(sequence))
- {
- currentColor = Color.lightGray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.getSequenceColour(sequence);
- currentTextColor = Color.black;
- }
+ annotationHeight = ap.adjustPanelHeight();
+ if (labels == null)
+ {
+ labels = new AnnotationLabels(av);
+ }
+ }
- gg.setColor(currentColor);
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
- gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
- av.charHeight);
+ int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
- gg.setColor(currentTextColor);
+ ViewportRanges ranges = av.getRanges();
- String string = sequence.getDisplayId(av.getShowJVSuffix());
+ int rowSize = ranges.getViewportWidth();
- if (av.rightAlignIds)
+ /*
+ * draw repeating sequence ids until out of sequence data or
+ * out of visible space, whichever comes first
+ */
+ int ypos = hgap;
+ int row = ranges.getStartRes();
+ while ((ypos <= getHeight()) && (row < maxwidth))
+ {
+ for (int i = starty; i < alheight; i++)
+ {
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ if (hasHiddenRows || av.isDisplayReferenceSeq())
{
- xPos = panelWidth - fm.stringWidth(string) - 4;
+ setHiddenFont(s);
}
-
- gg.drawString(string, xPos,
- (((i - starty) * av.charHeight) + av.charHeight)
- - (av.charHeight / 5));
-
- if (av.hasHiddenRows() && av.showHiddenMarkers)
+ else
{
- drawMarker(i, starty, 0);
+ gg.setFont(getIdfont());
}
+ drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
+ }
+
+ if (labels != null && av.isShowAnnotation())
+ {
+ gg.translate(0, ypos + (alheight * av.getCharHeight()));
+ labels.drawComponent(gg, getWidth());
+ gg.translate(0, -ypos - (alheight * av.getCharHeight()));
}
+ ypos += cHeight;
+ row += rowSize;
}
}
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment()
+ .getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
{
gg.fillPolygon(
new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
- getWidth() }, new int[]
- {
- (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight
- / 4, (i - starty) * av.charHeight + yoffset }, 3);
+ { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[]
+ { (i - starty) * av.getCharHeight() + yoffset,
+ (i - starty) * av.getCharHeight() + yoffset
+ + av.getCharHeight() / 4,
+ (i - starty) * av.getCharHeight() + yoffset },
+ 3);
}
if (above)
{
gg.fillPolygon(
new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
- getWidth() }, new int[]
- {
- (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset
- - av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset }, 3);
+ { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(), getWidth() },
+ new int[]
+ { (i - starty + 1) * av.getCharHeight() + yoffset,
+ (i - starty + 1) * av.getCharHeight() + yoffset
+ - av.getCharHeight() / 4,
+ (i - starty + 1) * av.getCharHeight() + yoffset },
+ 3);
}
}
void setHiddenFont(SequenceI seq)
{
- Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
- .getSize());
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,
+ av.getFont().getSize());
- if (av.isHiddenRepSequence(seq))
+ if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
{
gg.setFont(bold);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
}
searchResults = list;
repaint();
}
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
+
+ /**
+ * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
+ * scrolling and resizing change viewport ranges. Scrolling changes both start
+ * and end points, but resize only changes end values. Here we only want to
+ * fastpaint on a scroll, with resize using a normal paint, so scroll events
+ * are identified as changes to the horizontal or vertical start value.
+ * <p>
+ * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
+ * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
+ * provided, but it generates a change of "startres" which does require an
+ * update here.
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String propertyName = evt.getPropertyName();
+ if (propertyName.equals(ViewportRanges.STARTSEQ)
+ || (av.getWrapAlignment()
+ && propertyName.equals(ViewportRanges.STARTRES)))
+ {
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ fastPaint(((int[]) evt.getNewValue())[1]
+ - ((int[]) evt.getOldValue())[1]);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff