X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=318d74d7a2900f329ec73351ae07c7cdebbf1a70;hb=60ee9fb76ea07566ece5c3455a1abedfff467354;hp=cd7c23179992b82e5f30ea7bc6acedd71f9566b0;hpb=39e39119e514275f48786e592cc24c251d212c66;p=jalview.git
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index cd7c231..318d74d 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,66 +1,95 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * 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.
- *
- * 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 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
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.util.List;
+
+import javax.swing.JComponent;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class SeqCanvas
- extends JComponent
+public class SeqCanvas extends JComponent implements ViewportListenerI
{
final FeatureRenderer fr;
+
final SequenceRenderer sr;
+
BufferedImage img;
+
Graphics2D gg;
- int imgWidth;
- int imgHeight;
+
AlignViewport av;
- SearchResults searchResults = null;
+
boolean fastPaint = false;
+
int LABEL_WEST;
+
int LABEL_EAST;
int cursorX = 0;
+
int cursorY = 0;
/**
* Creates a new SeqCanvas object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
*/
public SeqCanvas(AlignmentPanel ap)
{
this.av = ap.av;
+ updateViewport();
fr = new FeatureRenderer(ap);
sr = new SequenceRenderer(av);
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
+
+ av.getRanges().addPropertyChangeListener(this);
}
public SequenceRenderer getSequenceRenderer()
@@ -73,69 +102,88 @@ public class SeqCanvas
return fr;
}
+ int charHeight = 0, charWidth = 0;
+
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param endx DOCUMENT ME!
- * @param ypos DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
*/
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
- int scalestartx = startx - (startx % 10) + 10;
-
- g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
+ updateViewport();
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
{
- int value = i;
- if (av.hasHiddenColumns)
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
{
- value = av.getColumnSelection().adjustForHiddenColumns(value);
+ continue;
}
+ String mstring = mark.text;
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
-
- g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
- 2);
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+ }
+ g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
+ - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
+ ypos - 2);
+ }
}
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param endx DOCUMENT ME!
- * @param ypos DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
*/
void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
+ ypos += charHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ startx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- SequenceI seq = av.alignment.getSequenceAt(i);
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
int index = startx;
int value = -1;
@@ -148,43 +196,48 @@ public class SeqCanvas
continue;
}
- value = av.alignment.getSequenceAt(i).findPosition(index);
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
if (value != -1)
{
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
- av.charWidth / 2;
- g.drawString(value + "", x,
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+ - charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startx DOCUMENT ME!
- * @param endx DOCUMENT ME!
- * @param ypos DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
*/
void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
- ypos += av.charHeight;
+ ypos += charHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
SequenceI seq;
// EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- seq = av.alignment.getSequenceAt(i);
+ seq = av.getAlignment().getSequenceAt(i);
int index = endx;
int value = -1;
@@ -204,184 +257,235 @@ public class SeqCanvas
if (value != -1)
{
- g.drawString(String.valueOf(value), 0,
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+ g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
- boolean fastpainting=false;
+
+ boolean fastpainting = false;
+
/**
- * need to make this thread safe
- * move alignment rendering in response to slider adjustment
- * @param horizontal shift along
- * @param vertical shift up or down in repaint
+ * need to make this thread safe move alignment rendering in response to
+ * slider adjustment
+ *
+ * @param horizontal
+ * shift along
+ * @param vertical
+ * shift up or down in repaint
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting)
+ if (fastpainting || gg == null)
{
return;
}
- fastpainting=true;
- if (gg == null)
- {
- return;
- }
-
+ fastpainting = true;
fastPaint = true;
+ updateViewport();
- gg.copyArea(horizontal * av.charWidth,
- vertical * av.charHeight,
- imgWidth,
- imgHeight,
- -horizontal * av.charWidth,
- -vertical * av.charHeight);
-
- int sr = av.startRes;
- int er = av.endRes;
- int ss = av.startSeq;
- int es = av.endSeq;
+ ViewportRanges ranges = av.getRanges();
+ int sr = ranges.getStartRes();
+ int er = ranges.getEndRes();
+ int ss = ranges.getStartSeq();
+ int es = ranges.getEndSeq();
int transX = 0;
int transY = 0;
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
+
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- er++;
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * charWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
{
- er = sr - horizontal - 1;
+ er = sr - horizontal;
}
else 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 = img.getHeight() - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
gg.translate(transX, transY);
drawPanel(gg, sr, er, ss, es, 0);
- gg.translate( -transX, -transY);
+ gg.translate(-transX, -transY);
repaint();
- fastpainting=false;
+ fastpainting = false;
}
/**
- * Definitions of startx and endx (hopefully):
- * SMJS This is what I'm working towards!
- * startx is the first residue (starting at 0) to display.
- * endx is the last residue to display (starting at 0).
- * starty is the first sequence to display (starting at 0).
- * endy is the last sequence to display (starting at 0).
- * NOTE 1: The av limits are set in setFont in this class and
- * in the adjustment listener in SeqPanel when the scrollbars move.
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+ * towards! startx is the first residue (starting at 0) to display. endx is
+ * the last residue to display (starting at 0). starty is the first sequence
+ * to display (starting at 0). endy is the last sequence to display (starting
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+ * adjustment listener in SeqPanel when the scrollbars move.
*/
// Set this to false to force a full panel paint
+ @Override
public void paintComponent(Graphics g)
{
- BufferedImage lcimg = img; // take reference since other threads may null img and call later.
super.paintComponent(g);
- if (lcimg != null && (fastPaint
- || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().height)))
+ updateViewport();
+
+ // img is a cached version of the last view we drew
+ // selectImage will hold any selection we have
+ // lcimg is a local *copy* of img which we'll draw selectImage on top of
+
+ ViewportRanges ranges = av.getRanges();
+ BufferedImage selectImage = drawSelectionGroup(
+ av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
+
+ if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height))
{
+ BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
+
fastPaint = false;
return;
}
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
+ int width = getWidth();
+ int height = getHeight();
- imgWidth -= (imgWidth % av.charWidth);
- imgHeight -= (imgHeight % av.charHeight);
+ width -= (width % charWidth);
+ height -= (height % charHeight);
- if ( (imgWidth < 1) || (imgHeight < 1))
+ if ((width < 1) || (height < 1))
{
return;
}
- if (lcimg == null || imgWidth != lcimg.getWidth() || imgHeight != lcimg.getHeight())
+ if (img == null || width != img.getWidth() || height != img.getHeight())
{
- try
- {
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
- gg = (Graphics2D) img.getGraphics();
- gg.setFont(av.getFont());
- }
- catch (OutOfMemoryError er)
- {
- System.gc();
- System.out.println(er + " making image, SeqCanvas");
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.
- desktop,
- "Out of memory creating alignment image!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
- return;
- }
+ img = setupImage();
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ }
+ if (img == null)
+ {
+ return;
}
+
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
-
+
gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
-
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
+
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
+ BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
+ }
+
+ /*
+ * Make a local image by combining the cached image img
+ * with any selection
+ */
+ private BufferedImage buildLocalImage(BufferedImage selectImage)
+ {
+ // clone the cached image
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+ Graphics2D g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
+ {
+ g2d.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2d.drawImage(selectImage, 0, 0, this);
+ }
+ g2d.dispose();
+ return lcimg;
+ }
+ private void paintSeqGroup()
+ {
+ fastPaint = true;
+ repaint();
+ }
+
+ private BufferedImage setupImage()
+ {
+ BufferedImage lcimg = null;
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ if ((width < 1) || (height < 1))
+ {
+ return null;
+ }
+
+ try
+ {
+ lcimg = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ } catch (OutOfMemoryError er)
+ {
+ System.gc();
+ System.err.println(
+ "Selection Group image OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
+
+ return null;
+ }
+
+ return lcimg;
}
/**
* DOCUMENT ME!
- *
- * @param cwidth DOCUMENT ME!
- *
+ *
+ * @param cwidth
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public int getWrappedCanvasWidth(int cwidth)
@@ -391,21 +495,22 @@ public class SeqCanvas
LABEL_EAST = 0;
LABEL_WEST = 0;
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
}
/**
* Generates a string of zeroes.
+ *
* @return String
*/
String getMask()
@@ -413,9 +518,9 @@ public class SeqCanvas
String mask = "00";
int maxWidth = 0;
int tmp;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- tmp = av.alignment.getSequenceAt(i).getEnd();
+ tmp = av.getAlignment().getSequenceAt(i).getEnd();
if (tmp > maxWidth)
{
maxWidth = tmp;
@@ -431,52 +536,61 @@ public class SeqCanvas
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param canvasWidth DOCUMENT ME!
- * @param canvasHeight DOCUMENT ME!
- * @param startRes DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param canvasWidth
+ * DOCUMENT ME!
+ * @param canvasHeight
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
*/
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
- int startRes)
+ public void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
{
+ updateViewport();
AlignmentI al = av.getAlignment();
FontMetrics fm = getFontMetrics(av.getFont());
- if (av.scaleRightWrapped)
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += charHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
int endx;
int ypos = hgap;
- int maxwidth = av.alignment.getWidth() - 1;
+ int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
}
- while ( (ypos <= canvasHeight) && (startRes < maxwidth))
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
@@ -488,50 +602,46 @@ public class SeqCanvas
g.setFont(av.getFont());
g.setColor(Color.black);
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
- g.translate( - (canvasWidth - LABEL_EAST), 0);
+ g.translate(-(canvasWidth - LABEL_EAST), 0);
}
g.translate(LABEL_WEST, 0);
- if (av.scaleAboveWrapped)
+ if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
g.setColor(Color.blue);
int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
- i++)
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
{
- res = av.getColumnSelection().findHiddenRegionPosition(i) -
- startRes;
+ res = pos - startRes;
if (res < 0 || res > endx - startRes)
{
continue;
}
- gg.fillPolygon(new int[]
- {res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4,
- res * av.charWidth},
- new int[]
- {
- ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2) + 8
- }, 3);
+ gg.fillPolygon(
+ new int[] { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[] { ypos - (charHeight / 2),
+ ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ 3);
}
}
@@ -542,17 +652,17 @@ public class SeqCanvas
if (clip == null)
{
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
}
else
{
- g.setClip(0, (int) clip.getBounds().getY(),
- cWidth * av.charWidth, (int) clip.getBounds().getHeight());
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
+ (int) clip.getBounds().getHeight());
}
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 3);
if (annotations == null)
@@ -560,11 +670,12 @@ public class SeqCanvas
annotations = new AnnotationPanel(av);
}
- annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);
+ annotations.renderer.drawComponent(annotations, av, g, -1,
+ startRes, endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
g.setClip(clip);
- g.translate( -LABEL_WEST, 0);
+ g.translate(-LABEL_WEST, 0);
ypos += cHeight + getAnnotationHeight() + hgap;
@@ -573,9 +684,10 @@ public class SeqCanvas
}
AnnotationPanel annotations;
+
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
@@ -590,32 +702,37 @@ public class SeqCanvas
/**
* DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
- * @param startSeq DOCUMENT ME!
- * @param endSeq DOCUMENT ME!
- * @param offset DOCUMENT ME!
+ *
+ * @param g1
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ * @param startSeq
+ * DOCUMENT ME!
+ * @param endSeq
+ * DOCUMENT ME!
+ * @param offset
+ * DOCUMENT ME!
*/
- void drawPanel(Graphics g1, int startRes, int endRes,
- int startSeq, int endSeq, int offset)
+ public void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
- if (!av.hasHiddenColumns)
+ updateViewport();
+ if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
}
else
{
- java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
-
int screenY = 0;
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; i < regions.size(); i++)
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
{
- int[] region = (int[]) regions.elementAt(i);
int hideStart = region[0];
int hideEnd = region[1];
@@ -627,7 +744,7 @@ public class SeqCanvas
blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
@@ -635,112 +752,119 @@ public class SeqCanvas
{
g1.setColor(Color.blue);
- g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
- 0 + offset,
- (blockEnd - blockStart + 1) * av.charWidth - 1,
- (endSeq - startSeq) * av.charHeight + offset);
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq + 1) * charHeight + offset);
}
- g1.translate( -screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ return;
+ }
}
if (screenY <= (endRes - startRes))
{
+ // remaining visible region to render
blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate( -screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
}
}
}
- //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
// int x1, int x2, int y1, int y2, int startx, int starty,
- void draw(Graphics g,
- int startRes, int endRes,
- int startSeq, int endSeq,
- int offset)
+ private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
+ sr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
- /// First draw the sequences
- /////////////////////////////
- for (int i = startSeq; i < endSeq; i++)
+ // / First draw the sequences
+ // ///////////////////////////
+ for (int i = startSeq; i <= endSeq; i++)
{
- nextSeq = av.alignment.getSequenceAt(i);
-
- sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
- startRes, endRes,
- offset + ( (i - startSeq) * av.charHeight));
+ nextSeq = av.getAlignment().getSequenceAt(i);
+ if (nextSeq == null)
+ {
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
+ continue;
+ }
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
- fr.drawSequence(g, nextSeq, startRes, endRes,
- offset + ( (i - startSeq) * av.charHeight));
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset
+ + ((i - startSeq) * charHeight), false);
}
- /// Highlight search Results once all sequences have been drawn
- //////////////////////////////////////////////////////////
- if (searchResults != null)
+ // / Highlight search Results once all sequences have been drawn
+ // ////////////////////////////////////////////////////////
+ if (av.hasSearchResults())
{
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,
- endRes);
+ int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+ startRes, endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1],
- (visibleResults[r] - startRes) *
- av.charWidth,
- offset + ( (i - startSeq) * av.charHeight));
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
- if (av.cursorMode && cursorY == i
- && cursorX >= startRes && cursorX <= endRes)
+ if (av.cursorMode && cursorY == i && cursorX >= startRes
+ && cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
- offset + ( (i - startSeq) * av.charHeight));
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
- if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
}
- void drawGroupsBoundaries(Graphics g1,
- int startRes, int endRes,
- int startSeq, int endSeq,
- int offset)
+ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
Graphics2D g = (Graphics2D) g1;
//
- /////////////////////////////////////
+ // ///////////////////////////////////
// Now outline any areas if necessary
- /////////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
+ // ///////////////////////////////////
+
+ SequenceGroup group = null;
int sx = -1;
int sy = -1;
int ex = -1;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * av.charWidth;
+ int visWidth = (endRes - startRes + 1) * charWidth;
- if ( (group == null) && (av.alignment.getGroups().size() > 0))
+ if (av.getAlignment().getGroups().size() > 0)
{
- group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
@@ -754,35 +878,35 @@ public class SeqCanvas
int top = -1;
int bottom = -1;
- for (i = startSeq; i < endSeq; i++)
+ for (i = startSeq; i <= endSeq; i++)
{
- sx = (group.getStartRes() - startRes) * av.charWidth;
- sy = offset + ( (i - startSeq) * av.charHeight);
- ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
- av.charWidth) -
- 1;
+ // position of start residue of group relative to startRes, in pixels
+ sx = (group.getStartRes() - startRes) * charWidth;
+ sy = offset + ((i - startSeq) * charHeight);
+ // width of group in pixels
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
if (sx + ex < 0 || sx > visWidth)
{
continue;
}
- if ( (sx <= (endRes - startRes) * av.charWidth) &&
- group.getSequences(null).
- contains(av.alignment.getSequenceAt(i)))
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i)))
{
- if ( (bottom == -1) &&
- !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i + 1)))
+ if ((bottom == -1)
+ && !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i + 1)))
{
- bottom = sy + av.charHeight;
+ bottom = sy + charHeight;
}
if (!inGroup)
{
- if ( ( (top == -1) && (i == 0)) ||
- !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i - 1)))
+ if (((top == -1) && (i == 0))
+ || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
@@ -790,31 +914,23 @@ public class SeqCanvas
oldY = sy;
inGroup = true;
- if (group == av.getSelectionGroup())
- {
- g.setStroke(new BasicStroke(1,
- BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
- g.setColor(Color.RED);
- }
- else
- {
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
}
}
else
{
if (inGroup)
{
+ // if start position is visible, draw vertical line to left of
+ // group
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
}
+ // if end position is visible, draw vertical line to right of
+ // group
if (sx + ex < visWidth)
{
g.drawLine(sx + ex, oldY, sx + ex, sy);
@@ -831,17 +947,19 @@ public class SeqCanvas
ex = visWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * charWidth;
}
+ // draw horizontal line at top of group
if (top != -1)
{
g.drawLine(sx, top, sx + ex, top);
top = -1;
}
+ // draw horizontal line at bottom of group
if (bottom != -1)
{
g.drawLine(sx, bottom, sx + ex, bottom);
@@ -855,7 +973,7 @@ public class SeqCanvas
if (inGroup)
{
- sy = offset + ( (i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * charHeight);
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
@@ -876,9 +994,9 @@ public class SeqCanvas
{
ex = visWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * charWidth;
}
if (top != -1)
@@ -900,31 +1018,326 @@ public class SeqCanvas
g.setStroke(new BasicStroke());
- if (groupIndex >= av.alignment.getGroups().size())
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups().get(groupIndex);
+
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ // get a new image of the correct size
+ BufferedImage selectionImage = setupImage();
+
+ if (selectionImage == null)
+ {
+ return null;
+ }
+
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ // nothing to draw
+ return null;
+ }
+
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+ g.translate(LABEL_WEST, 0);
+ // set background to transparent
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+ g.setComposite(AlphaComposite.Src);
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
+
+ if (!av.hasHiddenColumns())
+ {
+ drawSelectionGroupPart(g, group, startRes, endRes, startSeq, endSeq);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ // Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+ // Graphics g1 = selectionImage.getGraphics();
+
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
{
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g.translate(screenY * charWidth, 0);
+
+ drawSelectionGroupPart(g, group,
+ blockStart, blockEnd, startSeq, endSeq);
+
+ g.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
break;
}
+ }
- group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g.translate(screenY * charWidth, 0);
+ drawSelectionGroupPart(g, group,
+ blockStart, blockEnd, startSeq, endSeq);
+ g.translate(-screenY * charWidth, 0);
}
- while (groupIndex < av.alignment.getGroups().size());
+ }
+ g.translate(-LABEL_WEST, 0);
+ return selectionImage;
+ }
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawSelectionGroupPart(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq)
+ {
+ // set up values in case the alignment is wrapped
+ int verticalOffset = 0;
+ int horizontalOffset = 0;
+ if (av.getWrapAlignment())
+ {
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ // get the start res of the group and work out the offsets for it in the wrapped alignment
+ int groupstart = group.getStartRes();
+ int cWidth = (getWidth() - LABEL_EAST - LABEL_WEST) / charWidth;
+
+ // group is in which slice of alignment? res position / width in residues
+ int slice = groupstart / cWidth;
+ // vertical offset is increased by slice number * number of sequences * height of each sequence
+ verticalOffset = slice * (av.getAlignment().getHeight() * charHeight
+ + getAnnotationHeight() + hgap) + hgap;
+
+ // horizontal offset is number of residues to subtract from group residue
+ // position
+ horizontalOffset = (slice * cWidth);
}
+ int visWidth = av.getRanges().getViewportWidth() * charWidth;
+
+ // set x start and end positions of group
+ int startx = (group.getStartRes() - startRes - horizontalOffset)
+ * charWidth;
+ int endx = (group.getEndRes() - startRes + 1 - horizontalOffset)
+ * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ // get sequences to determine y positions of group
+ for (i = startSeq; i <= endSeq; ++i)
+ {
+ int sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1) && !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
+
+ oldY = sy;
+ inGroup = true;
+ }
+ }
+ else
+ {
+ if (inGroup)
+ {
+ // if start position is visible, draw vertical line to left of
+ // group
+ if (startx >= 0 && startx < visWidth * charWidth)
+ {
+ g.drawLine(startx, oldY, startx, sy);
+ }
+
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (endx <= visWidth * charWidth)
+ {
+ g.drawLine(endx, oldY, endx, sy);
+ }
+
+ if (endx > visWidth * charWidth)
+ {
+ endx = visWidth * charWidth;
+ }
+
+ // draw horizontal line at top of group
+ if (top != -1)
+ {
+ g.drawLine(startx, top, endx, top);
+ top = -1;
+ }
+
+ // draw horizontal line at bottom of group
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom, endx, bottom);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+ }
+ if (inGroup)
+ {
+ int sy = verticalOffset + (i - startSeq) * charHeight;
+ if (startx >= 0 && startx < visWidth)
+ {
+ g.drawLine(startx, oldY, startx, sy);
+ }
+
+ if (endx < visWidth)
+ {
+ g.drawLine(endx, oldY, endx, sy);
+ }
+
+ if (endx > visWidth)
+ {
+ endx = visWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(startx, top, endx, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom - 1, endx, bottom - 1);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
}
/**
* DOCUMENT ME!
- *
- * @param results DOCUMENT ME!
+ *
+ * @param results
+ * DOCUMENT ME!
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
img = null;
- searchResults = results;
+ av.setSearchResults(results);
repaint();
}
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ paintSeqGroup();
+ }
+ else if (av.getWrapAlignment())
+ {
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ repaint();
+ }
+ }
+ else
+ {
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ ViewportRanges vpRanges = av.getRanges();
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
+ {
+ scrollX = range;
+ }
+ else if (scrollX < -range)
+ {
+ scrollX = -range;
+ }
+ }
+
+ // 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.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // scroll - startres and endres both change
+ fastPaint(scrollX, 0);
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ }
+ }
}