/*
- * 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 <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 javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+
+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.util.List;
+
+import javax.swing.JComponent;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class SeqCanvas
- extends JComponent
+public class SeqCanvas extends JComponent
{
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());
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);
}
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().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;
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);
}
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;
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;
+
/**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
- * @param vertical DOCUMENT ME!
+ * 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 (gg == null)
+ if (fastpainting || gg == null)
{
return;
}
-
+ fastpainting = true;
fastPaint = true;
-
- gg.copyArea(horizontal * av.charWidth,
- vertical * av.charHeight,
- imgWidth,
- imgHeight,
- -horizontal * av.charWidth,
- -vertical * av.charHeight);
+ updateViewport();
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
int sr = av.startRes;
int er = av.endRes;
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)
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - (vertical * charHeight);
}
}
else if (vertical < 0)
gg.translate(transX, transY);
drawPanel(gg, sr, er, ss, es, 0);
- gg.translate( -transX, -transY);
+ gg.translate(-transX, -transY);
repaint();
+ 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.
+ updateViewport();
+ 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)))
+ if (lcimg != null
+ && (fastPaint
+ || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
+ .getClipBounds().height)))
{
g.drawImage(lcimg, 0, 0, this);
fastPaint = false;
imgWidth = getWidth();
imgHeight = getHeight();
- imgWidth -= (imgWidth % av.charWidth);
- imgHeight -= (imgHeight % av.charHeight);
+ imgWidth -= (imgWidth % charWidth);
+ imgHeight -= (imgHeight % charHeight);
- if ( (imgWidth < 1) || (imgHeight < 1))
+ if ((imgWidth < 1) || (imgHeight < 1))
{
return;
}
- if (lcimg == null || imgWidth != lcimg.getWidth() || imgHeight != lcimg.getHeight())
+ if (lcimg == null || imgWidth != lcimg.getWidth()
+ || imgHeight != lcimg.getHeight())
{
try
{
lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ BufferedImage.TYPE_INT_RGB);
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
- }
- catch (OutOfMemoryError er)
+ } 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);
- }
- });
+ System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
return;
}
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
gg.setColor(Color.white);
g.drawImage(lcimg, 0, 0, this);
-
}
/**
* DOCUMENT ME!
- *
- * @param cwidth DOCUMENT ME!
- *
+ *
+ * @param cwidth
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public int getWrappedCanvasWidth(int cwidth)
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()
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;
/**
* 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)
+ 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);
int endx;
int ypos = hgap;
- int maxwidth = av.alignment.getWidth() - 1;
+ int maxwidth = av.getAlignment().getWidth() - 1;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- while ( (ypos <= canvasHeight) && (startRes < maxwidth))
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
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++)
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+ .size(); i++)
{
- res = av.getColumnSelection().findHiddenRegionPosition(i) -
- startRes;
+ res = av.getColumnSelection().findHiddenRegionPosition(i)
+ - 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);
}
}
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);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 3);
if (annotations == null)
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;
}
AnnotationPanel annotations;
+
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
/**
* 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();
+ List<int[]> regions = av.getColumnSelection().getHiddenColumns();
int screenY = 0;
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; i < regions.size(); i++)
+ for (int[] region : regions)
{
- int[] region = (int[]) regions.elementAt(i);
int hideStart = region[0];
int hideEnd = region[1];
blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
{
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) * 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
- /////////////////////////////
+ // / 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));
}
- /// Highlight search Results once all sequences have been drawn
- //////////////////////////////////////////////////////////
+ // / Highlight search Results once all sequences have been drawn
+ // ////////////////////////////////////////////////////////
if (searchResults != null)
{
int[] visibleResults = searchResults.getResults(nextSeq, startRes,
- endRes);
+ 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();
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 ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
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;
+ sx = (group.getStartRes() - startRes) * charWidth;
+ sy = offset + ((i - startSeq) * charHeight);
+ 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;
}
if (group == av.getSelectionGroup())
{
- g.setStroke(new BasicStroke(1,
- BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+ 0f));
g.setColor(Color.RED);
}
else
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)
if (inGroup)
{
- sy = offset + ( (i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * charHeight);
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
{
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)
g.setStroke(new BasicStroke());
- if (groupIndex >= av.alignment.getGroups().size())
+ if (groupIndex >= av.getAlignment().getGroups().size())
{
break;
}
- group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
- }
- while (groupIndex < av.alignment.getGroups().size());
+ } while (groupIndex < av.getAlignment().getGroups().size());
}
/**
* DOCUMENT ME!
- *
- * @param results DOCUMENT ME!
+ *
+ * @param results
+ * DOCUMENT ME!
*/
public void highlightSearchResults(SearchResults results)
{
git://source.jalview.org / jalview.git / blobdiff