/*
- * 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 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.util.Comparison;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+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
{
+ private static String ZEROS = "0000000000";
+
final FeatureRenderer fr;
final SequenceRenderer sr;
AlignViewport av;
- SearchResults searchResults = null;
-
boolean fastPaint = false;
- int LABEL_WEST;
+ boolean fastpainting = false;
+
+ int labelWidthWest;
- int LABEL_EAST;
+ int labelWidthEast;
int cursorX = 0;
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()
return fr;
}
- /**
- * 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)
- {
- int scalestartx = startx - (startx % 10) + 10;
-
- g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
- {
- int value = i;
- if (av.hasHiddenColumns())
- {
- value = av.getColumnSelection().adjustForHiddenColumns(value);
- }
-
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
+ int charHeight = 0, charWidth = 0;
- 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);
- }
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
}
/**
* @param ypos
* DOCUMENT ME!
*/
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
- FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
-
- if (av.hasHiddenColumns())
- {
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
- }
-
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
+ updateViewport();
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
-
- // WEST SCALE
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
- {
- SequenceI seq = av.getAlignment().getSequenceAt(i);
- int index = startx;
- int value = -1;
-
- while (index < endx)
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
{
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index++;
-
- continue;
- }
-
- value = av.getAlignment().getSequenceAt(i).findPosition(index);
-
- break;
+ continue;
}
+ String mstring = mark.text;
- if (value != -1)
+ if (mark.major)
{
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- - av.charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ 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!
+ * Draw the scale to the left or right of a wrapped alignment
*
* @param g
- * DOCUMENT ME!
* @param startx
- * DOCUMENT ME!
+ * first column of wrapped width (0.. excluding any hidden columns)
* @param endx
- * DOCUMENT ME!
+ * last column of wrapped width (0.. excluding any hidden columns)
* @param ypos
- * DOCUMENT ME!
+ * vertical offset at which to begin the scale
+ * @param left
+ * if true, scale is left of residues, if false, scale is right
*/
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ void drawVerticalScale(Graphics g, int startx, int endx, int ypos,
+ boolean left)
{
- ypos += av.charHeight;
+ ypos += charHeight;
if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
+ startx = hiddenColumns.adjustForHiddenColumns(startx);
+ endx = hiddenColumns.adjustForHiddenColumns(endx);
}
+ FontMetrics fm = getFontMetrics(av.getFont());
- SequenceI seq;
- // EAST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- seq = av.getAlignment().getSequenceAt(i);
- int index = endx;
- int value = -1;
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
- while (index > startx)
+ /*
+ * find sequence position of first non-gapped position -
+ * to the right if scale left, to the left if scale right
+ */
+ int index = left ? startx : endx;
+ int value = -1;
+ while (index >= startx && index <= endx)
{
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ if (!Comparison.isGap(seq.getCharAt(index)))
+ {
+ value = seq.findPosition(index);
+ break;
+ }
+ if (left)
+ {
+ index++;
+ }
+ else
{
index--;
-
- continue;
}
-
- value = seq.findPosition(index);
-
- break;
}
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ /*
+ * draw scale value, justified, with half a character width
+ * separation from the sequence data
+ */
+ int justify = fm.stringWidth(String.valueOf(value)) + charWidth;
+ int xpos = left ? labelWidthWest - justify + charWidth / 2
+ : getWidth() - justify - charWidth / 2;
+
+ g.drawString(String.valueOf(value), xpos, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
- boolean fastpainting = false;
-
/**
* need to make this thread safe move alignment rendering in response to
* slider adjustment
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting)
+ if (fastpainting || gg == null)
{
return;
}
fastpainting = true;
- if (gg == null)
- {
- return;
- }
-
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 startRes = ranges.getStartRes();
+ int endRes = ranges.getEndRes();
+ int startSeq = ranges.getStartSeq();
+ int endSeq = ranges.getEndSeq();
int transX = 0;
int transY = 0;
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- er++;
- transX = (er - sr - horizontal) * av.charWidth;
- sr = er - horizontal;
+ transX = (endRes - startRes - horizontal) * charWidth;
+ startRes = endRes - horizontal;
}
else if (horizontal < 0)
{
- er = sr - horizontal - 1;
+ endRes = startRes - horizontal;
}
else if (vertical > 0) // scroll down
{
- ss = es - vertical;
+ startSeq = endSeq - vertical;
- if (ss < av.startSeq)
+ if (startSeq < ranges.getStartSeq())
{ // ie scrolling too fast, more than a page at a time
- ss = av.startSeq;
+ startSeq = ranges.getStartSeq();
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
{
- es = ss - vertical;
+ endSeq = startSeq - vertical;
- if (es > av.endSeq)
+ if (endSeq > ranges.getEndSeq())
{
- es = av.endSeq;
+ endSeq = ranges.getEndSeq();
}
}
gg.translate(transX, transY);
- drawPanel(gg, sr, er, ss, es, 0);
+ drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
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.
- */
-
- // Set this to false to force a full panel paint
+ @Override
public void paintComponent(Graphics g)
{
+ updateViewport();
BufferedImage lcimg = img; // take reference since other threads may null
// img and call later.
super.paintComponent(g);
imgWidth = getWidth();
imgHeight = getHeight();
- imgWidth -= (imgWidth % av.charWidth);
- imgHeight -= (imgHeight % av.charHeight);
+ imgWidth -= (imgWidth % charWidth);
+ imgHeight -= (imgHeight % charHeight);
if ((imgWidth < 1) || (imgHeight < 1))
{
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, imgHeight);
+ ViewportRanges ranges = av.getRanges();
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);
}
g.drawImage(lcimg, 0, 0, this);
}
/**
- * DOCUMENT ME!
+ * Returns the visible width of the canvas in residues, after allowing for
+ * East or West scales (if shown)
*
- * @param cwidth
- * DOCUMENT ME!
+ * @param canvasWidth
+ * the width in pixels (possibly including scales)
*
- * @return DOCUMENT ME!
+ * @return
*/
- public int getWrappedCanvasWidth(int cwidth)
+ public int getWrappedCanvasWidth(int canvasWidth)
{
FontMetrics fm = getFontMetrics(av.getFont());
- LABEL_EAST = 0;
- LABEL_WEST = 0;
+ labelWidthEast = 0;
+ labelWidthWest = 0;
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
- LABEL_EAST = fm.stringWidth(getMask());
+ labelWidthEast = getLabelWidth(fm);
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
- LABEL_WEST = fm.stringWidth(getMask());
+ labelWidthWest = labelWidthEast > 0 ? labelWidthEast
+ : getLabelWidth(fm);
}
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
/**
- * Generates a string of zeroes.
+ * Returns a pixel width suitable for showing the largest sequence coordinate
+ * (end position) in the alignment. Returns 2 plus the number of decimal
+ * digits to be shown (3 for 1-10, 4 for 11-99 etc).
*
- * @return String
+ * @param fm
+ * @return
*/
- String getMask()
+ protected int getLabelWidth(FontMetrics fm)
{
- String mask = "00";
+ /*
+ * find the biggest sequence end position we need to show
+ * (note this is not necessarily the sequence length)
+ */
int maxWidth = 0;
- int tmp;
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- tmp = av.getAlignment().getSequenceAt(i).getEnd();
- if (tmp > maxWidth)
- {
- maxWidth = tmp;
- }
+ maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
}
+ int length = 2;
for (int i = maxWidth; i > 0; i /= 10)
{
- mask += "0";
+ length++;
}
- return mask;
+
+ return fm.stringWidth(ZEROS.substring(0, length));
}
/**
public void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
- AlignmentI al = av.getAlignment();
-
- FontMetrics fm = getFontMetrics(av.getFont());
-
- if (av.scaleRightWrapped)
+ updateViewport();
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
- LABEL_EAST = fm.stringWidth(getMask());
+ FontMetrics fm = getFontMetrics(av.getFont());
+ labelWidth = getLabelWidth(fm);
}
- if (av.scaleLeftWrapped)
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
- 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 - labelWidthEast - labelWidthWest) / charWidth;
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
- int endx;
int ypos = hgap;
- int maxwidth = av.getAlignment().getWidth() - 1;
+ int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
}
+ int annotationHeight = getAnnotationHeight();
+ int sequencesHeight = av.getAlignment().getHeight() * charHeight;
+
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
- endx = startRes + cWidth - 1;
+ drawWrappedWidth(g, startRes, canvasHeight, cWidth, maxwidth, ypos);
- if (endx > maxwidth)
- {
- endx = maxwidth;
- }
+ ypos += sequencesHeight + annotationHeight + hgap;
- g.setFont(av.getFont());
- g.setColor(Color.black);
+ startRes += cWidth;
+ }
+ }
- if (av.scaleLeftWrapped)
- {
- drawWestScale(g, startRes, endx, ypos);
- }
+ /**
+ * @param g
+ * @param startRes
+ * @param canvasHeight
+ * @param canvasWidth
+ * @param maxWidth
+ * @param ypos
+ */
+ protected void drawWrappedWidth(Graphics g, int startRes,
+ int canvasHeight, int canvasWidth, int maxWidth, int ypos)
+ {
+ int endx;
+ endx = startRes + canvasWidth - 1;
- if (av.scaleRightWrapped)
- {
- g.translate(canvasWidth - LABEL_EAST, 0);
- drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - LABEL_EAST), 0);
- }
+ if (endx > maxWidth)
+ {
+ endx = maxWidth;
+ }
- g.translate(LABEL_WEST, 0);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
- if (av.scaleAboveWrapped)
- {
- drawNorthScale(g, startRes, endx, ypos);
- }
+ if (av.getScaleLeftWrapped())
+ {
+ drawVerticalScale(g, startRes, endx, ypos, true);
+ }
- if (av.hasHiddenColumns() && av.showHiddenMarkers)
- {
- g.setColor(Color.blue);
- int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
- {
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startRes;
+ if (av.getScaleRightWrapped())
+ {
+ drawVerticalScale(g, startRes, endx, ypos, false);
+ }
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
+ g.translate(labelWidthWest, 0);
- 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);
+ if (av.getScaleAboveWrapped())
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
+ {
+ g.setColor(Color.blue);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
+ {
+ int res = pos - startRes;
+
+ if (res < 0 || res > endx - startRes)
+ {
+ continue;
}
- }
- // When printing we have an extra clipped region,
- // the Printable page which we need to account for here
- Shape clip = g.getClip();
+ 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);
- }
- else
- {
- g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth,
- (int) clip.getBounds().getHeight());
}
+ }
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ // When printing we have an extra clipped region,
+ // the Printable page which we need to account for here
+ Shape clip = g.getClip();
- if (av.showAnnotation)
- {
- g.translate(0, cHeight + ypos + 3);
- if (annotations == null)
- {
- annotations = new AnnotationPanel(av);
- }
+ if (clip == null)
+ {
+ g.setClip(0, 0, canvasWidth * charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), canvasWidth * charWidth,
+ (int) clip.getBounds().getHeight());
+ }
- annotations.renderer.drawComponent(annotations, av, (Graphics2D) g,
- -1, startRes, endx + 1);
- g.translate(0, -cHeight - ypos - 3);
- }
- g.setClip(clip);
- g.translate(-LABEL_WEST, 0);
+ drawPanel(g, startRes, endx, 0, av.getAlignment().getHeight() - 1, ypos);
- ypos += cHeight + getAnnotationHeight() + hgap;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
- startRes += cWidth;
+ if (av.isShowAnnotation())
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+ endx + 1);
+ g.translate(0, -cHeight - ypos - 3);
}
+ g.setClip(clip);
+ g.translate(-labelWidthWest, 0);
}
AnnotationPanel annotations;
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
}
/**
- * DOCUMENT ME!
+ * Draws the visible region of the alignment on the graphics context. If there
+ * are hidden column markers in the visible region, then each sub-region
+ * between the markers is drawn separately, followed by the hidden column
+ * marker.
*
* @param g1
- * DOCUMENT ME!
* @param startRes
- * DOCUMENT ME!
+ * offset of the first column in the visible region (0..)
* @param endRes
- * DOCUMENT ME!
+ * offset of the last column in the visible region (0..)
* @param startSeq
- * DOCUMENT ME!
+ * offset of the first sequence in the visible region (0..)
* @param endSeq
- * DOCUMENT ME!
- * @param offset
- * DOCUMENT ME!
+ * offset of the last sequence in the visible region (0..)
+ * @param yOffset
+ * vertical offset at which to draw (for wrapped alignments)
*/
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
+ public void drawPanel(Graphics g1, final int startRes, final int endRes,
+ final int startSeq, final int endSeq, final int yOffset)
{
+ updateViewport();
if (!av.hasHiddenColumns())
{
- draw(g1, startRes, endRes, startSeq, endSeq, offset);
+ draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
}
else
{
- java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
-
int screenY = 0;
+ final int screenYMax = endRes - startRes;
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; regions != null && 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];
continue;
}
- blockEnd = hideStart - 1;
+ /*
+ * draw up to just before the next hidden region, or the end of
+ * the visible region, whichever comes first
+ */
+ blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
+ - screenY);
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
- if (av.getShowHiddenMarkers())
+ /*
+ * draw the downline of the hidden column marker (ScalePanel draws the
+ * triangle on top) if we reached it
+ */
+ if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
{
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 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq + 1) * charHeight + yOffset);
}
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
blockStart = hideEnd + 1;
+
+ if (screenY > screenYMax)
+ {
+ // already rendered last block
+ return;
+ }
}
- if (screenY <= (endRes - startRes))
+ if (screenY <= screenYMax)
{
- blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ // remaining visible region to render
+ blockEnd = blockStart + screenYMax - screenY;
+ g1.translate(screenY * charWidth, 0);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
}
}
}
- // 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)
+ /**
+ * Draws a region of the visible alignment
+ *
+ * @param g1
+ * @param startRes
+ * offset of the first column in the visible region (0..)
+ * @param endRes
+ * offset of the last column in the visible region (0..)
+ * @param startSeq
+ * offset of the first sequence in the visible region (0..)
+ * @param endSeq
+ * offset of the last sequence in the visible region (0..)
+ * @param yOffset
+ * vertical offset at which to draw (for wrapped alignments)
+ */
+ 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++)
+ for (int i = startSeq; i <= endSeq; i++)
{
nextSeq = av.getAlignment().getSequenceAt(i);
if (nextSeq == null)
continue;
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ + ((i - startSeq) * charHeight), false);
}
- // / Highlight search Results once all sequences have been drawn
- // ////////////////////////////////////////////////////////
- if (searchResults != null)
+ /*
+ * highlight search Results once sequence has been drawn
+ */
+ if (av.hasSearchResults())
{
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,
- endRes);
+ SearchResultsI searchResults = av.getSearchResults();
+ int[] visibleResults = searchResults.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));
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
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));
}
}
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.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
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;
+ 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)
+ if ((sx <= (endRes - startRes) * charWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
&& !group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i + 1)))
{
- bottom = sy + av.charHeight;
+ bottom = sy + charHeight;
}
if (!inGroup)
if (group == av.getSelectionGroup())
{
g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ 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)
break;
}
- group = (SequenceGroup) av.getAlignment().getGroups()
- .get(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}
/**
- * DOCUMENT ME!
+ * Highlights search results in the visible region by rendering as white text
+ * on a black background. Any previous highlighting is removed. Answers true
+ * if any highlight was left on the visible alignment (so status bar should be
+ * set to match), else false.
+ * <p>
+ * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
+ * alignment had to be scrolled to show the highlighted region, then it should
+ * be fully redrawn, otherwise a fast paint can be performed. This argument
+ * could be removed if fast paint of scrolled wrapped alignment is coded in
+ * future (JAL-2609).
*
* @param results
- * DOCUMENT ME!
+ * @param noFastPaint
+ * @return
+ */
+ public boolean highlightSearchResults(SearchResultsI results,
+ boolean noFastPaint)
+ {
+ if (fastpainting)
+ {
+ return false;
+ }
+ boolean wrapped = av.getWrapAlignment();
+
+ try
+ {
+ fastPaint = !noFastPaint;
+ fastpainting = fastPaint;
+
+ updateViewport();
+
+ /*
+ * to avoid redrawing the whole visible region, we instead
+ * redraw just the minimal regions to remove previous highlights
+ * and add new ones
+ */
+ SearchResultsI previous = av.getSearchResults();
+ av.setSearchResults(results);
+ boolean redrawn = false;
+ boolean drawn = false;
+ if (wrapped)
+ {
+ redrawn = drawMappedPositionsWrapped(previous);
+ drawn = drawMappedPositionsWrapped(results);
+ redrawn |= drawn;
+ }
+ else
+ {
+ redrawn = drawMappedPositions(previous);
+ drawn = drawMappedPositions(results);
+ redrawn |= drawn;
+ }
+
+ /*
+ * if highlights were either removed or added, repaint
+ */
+ if (redrawn)
+ {
+ repaint();
+ }
+
+ /*
+ * return true only if highlights were added
+ */
+ return drawn;
+
+ } finally
+ {
+ fastpainting = false;
+ }
+ }
+
+ /**
+ * Redraws the minimal rectangle in the visible region (if any) that includes
+ * mapped positions of the given search results. Whether or not positions are
+ * highlighted depends on the SearchResults set on the Viewport. This allows
+ * this method to be called to either clear or set highlighting. Answers true
+ * if any positions were drawn (in which case a repaint is still required),
+ * else false.
+ *
+ * @param results
+ * @return
*/
- public void highlightSearchResults(SearchResults results)
+ protected boolean drawMappedPositions(SearchResultsI results)
{
- img = null;
+ if (results == null)
+ {
+ return false;
+ }
- searchResults = results;
+ /*
+ * calculate the minimal rectangle to redraw that
+ * includes both new and existing search results
+ */
+ int firstSeq = Integer.MAX_VALUE;
+ int lastSeq = -1;
+ int firstCol = Integer.MAX_VALUE;
+ int lastCol = -1;
+ boolean matchFound = false;
+
+ ViewportRanges ranges = av.getRanges();
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getEndRes();
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region -
+ * remember the first and last sequence matched, and the first
+ * and last visible columns in the matched positions
+ */
+ matchFound = true;
+ firstSeq = Math.min(firstSeq, seqNo);
+ lastSeq = Math.max(lastSeq, seqNo);
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+ firstCol = Math.min(firstCol, firstMatchedColumn);
+ lastCol = Math.max(lastCol, lastMatchedColumn);
+ }
+ }
+ }
+ }
+
+ if (matchFound)
+ {
+ if (av.hasHiddenColumns())
+ {
+ firstCol = alignment.getHiddenColumns()
+ .findColumnPosition(firstCol);
+ lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+ }
+ int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
+ int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
+ gg.translate(transX, transY);
+ drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
+ gg.translate(-transX, -transY);
+ }
+
+ return matchFound;
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (true/*!av.getWrapAlignment()*/)
+ {
+ 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
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
+ }
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ }
+ }
+
+ /**
+ * Does a minimal update of the image for a scroll movement. This method
+ * handles scroll movements of up to one width of the wrapped alignment (one
+ * click in the vertical scrollbar). Larger movements (for example after a
+ * scroll to highlight a mapped position) trigger a full redraw instead.
+ *
+ * @param scrollX
+ * number of positions scrolled (right if positive, left if negative)
+ */
+ protected void fastPaintWrapped(int scrollX)
+ {
+ if (Math.abs(scrollX) > 0 /*av.getRanges().getViewportWidth()*/)
+ {
+ /*
+ * shift of more than one view width is too much
+ * to handle in this method
+ */
+ fastPaint = false;
+ repaint();
+ return;
+ }
+
+ fastPaint = true;
+ shiftWrappedAlignment(-scrollX);
+
+ // add new columns (scale above, sequence, annotation)
+ // at top left if scrollX < 0 or bottom right if scrollX > 0
repaint();
}
+
+ /**
+ * Shifts the visible alignment by the specified number of columns - left if
+ * negative, right if positive. Includes scale above, left or right and
+ * annotations (if shown). Does not draw newly visible columns.
+ *
+ * @param positions
+ */
+ protected void shiftWrappedAlignment(int positions)
+ {
+ if (positions == 0)
+ {
+ return;
+ }
+
+ int repeatHeight = getRepeatHeightWrapped();
+ ViewportRanges ranges = av.getRanges();
+ int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
+ * charWidth;
+ int visibleWidths = getHeight() / repeatHeight;
+ if (getHeight() % repeatHeight > 0)
+ {
+ visibleWidths++;
+ }
+ int viewportWidth = ranges.getViewportWidth();
+
+ if (positions > 0)
+ {
+ /*
+ * shift right (after scroll left)
+ * for each wrapped width (starting with the last), copy (width-positions)
+ * columns from the left margin to the right margin, and copy positions
+ * columns from the right margin of the row above (if any) to the
+ * left margin of the current row
+ */
+ int xpos = ranges.getStartRes() + (visibleWidths - 1) * viewportWidth;
+
+ /*
+ * get y-offset of last wrapped width
+ */
+ int y = getHeight() / repeatHeight * repeatHeight;
+ int copyFromLeftStart = labelWidthWest;
+ int copyFromRightStart = copyFromLeftStart + widthToCopy;
+
+ while (y >= 0)
+ {
+ // todo limit repeatHeight for a last part height width
+ gg.copyArea(copyFromLeftStart, y, widthToCopy, repeatHeight,
+ positions * charWidth, 0);
+ if (y > 0)
+ {
+ gg.copyArea(copyFromRightStart, y - repeatHeight, positions
+ * charWidth, repeatHeight, -widthToCopy, repeatHeight);
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, true);
+ }
+ if (av.getScaleRightWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, false);
+ }
+
+ y -= repeatHeight;
+ xpos -= viewportWidth;
+ }
+ }
+ else
+ {
+ /*
+ * shift left (after scroll right)
+ * for each wrapped width (starting with the first), copy (width-positions)
+ * columns from the right margin to the left margin, and copy positions
+ * columns from the left margin of the row below (if any) to the
+ * right margin of the current row
+ */
+ int xpos = ranges.getStartRes();
+ int y = 0;
+ int copyFromRightStart = labelWidthWest - positions * charWidth;
+
+ while (y < getHeight())
+ {
+ // todo limit repeatHeight for a last part height width
+ gg.copyArea(copyFromRightStart, y, widthToCopy, repeatHeight,
+ positions * charWidth, 0);
+ if (y + repeatHeight < getHeight())
+ {
+ gg.copyArea(labelWidthWest, y + repeatHeight, -positions
+ * charWidth, repeatHeight, widthToCopy, -repeatHeight);
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, true);
+ }
+ if (av.getScaleRightWrapped())
+ {
+ // drawVerticalScale(gg, xpos, xpos + viewportWidth, y, false);
+ }
+
+ y += repeatHeight;
+ xpos += ranges.getViewportWidth();
+ }
+ }
+ }
+
+ /**
+ * Redraws any positions in the search results in the visible region of a
+ * wrapped alignment. Any highlights are drawn depending on the search results
+ * set on the Viewport, not the <code>results</code> argument. This allows
+ * this method to be called either to clear highlights (passing the previous
+ * search results), or to draw new highlights.
+ *
+ * @param results
+ * @return
+ */
+ protected boolean drawMappedPositionsWrapped(SearchResultsI results)
+ {
+ if (results == null)
+ {
+ return false;
+ }
+
+ boolean matchFound = false;
+
+ int wrappedWidth = av.getWrappedWidth();
+ int wrappedHeight = getRepeatHeightWrapped();
+
+ ViewportRanges ranges = av.getRanges();
+ int canvasHeight = getHeight();
+ int repeats = canvasHeight / wrappedHeight;
+ if (canvasHeight / wrappedHeight > 0)
+ {
+ repeats++;
+ }
+
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getStartRes() + repeats
+ * ranges.getViewportWidth() - 1;
+
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region
+ */
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+
+ /*
+ * draw each mapped position separately (as contiguous positions may
+ * wrap across lines)
+ */
+ for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
+ {
+ int displayColumn = mappedPos;
+ if (av.hasHiddenColumns())
+ {
+ displayColumn = alignment.getHiddenColumns()
+ .findColumnPosition(displayColumn);
+ }
+
+ /*
+ * transX: offset from left edge of canvas to residue position
+ */
+ int transX = labelWidthWest
+ + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
+ * av.getCharWidth();
+
+ /*
+ * transY: offset from top edge of canvas to residue position
+ */
+ int transY = gapHeight;
+ transY += (displayColumn - ranges.getStartRes())
+ / wrappedWidth * wrappedHeight;
+ transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
+
+ /*
+ * yOffset is from graphics origin to start of visible region
+ */
+ int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
+ if (transY < getHeight())
+ {
+ matchFound = true;
+ gg.translate(transX, transY);
+ drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
+ yOffset);
+ gg.translate(-transX, -transY);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return matchFound;
+ }
+
+ /**
+ * Answers the height in pixels of a repeating section of the wrapped
+ * alignment, including space above, scale above if shown, sequences, and
+ * annotation panel if shown
+ *
+ * @return
+ */
+ protected int getRepeatHeightWrapped()
+ {
+ // gap (and maybe scale) above
+ int repeatHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ // add sequences
+ repeatHeight += av.getRanges().getViewportHeight() * charHeight;
+
+ // add annotations panel height if shown
+ repeatHeight += getAnnotationHeight();
+
+ return repeatHeight;
+ }
}
git://source.jalview.org / jalview.git / blobdiff