package jalview.appletgui;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.awt.FontMetrics;
AlignViewport av;
- SearchResults searchResults = null;
-
boolean fastPaint = false;
int cursorX = 0;
fr = new FeatureRenderer(av);
sr = new SequenceRenderer(av);
PaintRefresher.Register(this, av.getSequenceSetId());
+ updateViewport();
+ }
+
+ int avcharHeight = 0, avcharWidth = 0;
+
+ private void updateViewport()
+ {
+ avcharHeight = av.getCharHeight();
+ avcharWidth = av.getCharWidth();
}
- public AlignViewport getViewport()
+ public AlignmentViewport getViewport()
{
return av;
}
return sr;
}
- 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;
-
+ updateViewport();
g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
+ 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 * avcharWidth, ypos
+ - (avcharHeight / 2));
+ }
+ g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
+ - (avcharHeight / 2), (mpos * avcharWidth)
+ + (avcharWidth / 2), ypos - 2);
+ }
}
}
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ private void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
+ ypos += avcharHeight;
if (av.hasHiddenColumns())
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
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));
+ - avcharWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * avcharHeight))
+ - (avcharHeight / 5));
}
}
}
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ private void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
- ypos += av.charHeight;
+ ypos += avcharHeight;
if (av.hasHiddenColumns())
{
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
+ - (avcharHeight / 5));
}
}
}
return;
}
+ updateViewport();
+
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
- if (lastsr + horizontal != av.startRes)
+ if (lastsr + horizontal != av.getStartRes())
{
- horizontal = av.startRes - lastsr;
+ horizontal = av.getStartRes() - lastsr;
}
- lastsr = av.startRes;
+ lastsr = av.getStartRes();
fastPaint = true;
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
- imgWidth - horizontal * av.charWidth, imgHeight - vertical
- * av.charHeight, -horizontal * av.charWidth, -vertical
- * av.charHeight);
+ gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
+ - horizontal * avcharWidth,
+ imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
+ -vertical * avcharHeight);
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+ int sr = av.getStartRes(), er = av.getEndRes(), ss = av.getStartSeq(), es = av
+ .getEndSeq(), transX = 0, transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * avcharWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
else if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+ // time
{
- ss = av.startSeq;
+ ss = av.getStartSeq();
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - ((vertical + 1) * avcharHeight);
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > av.getEndSeq())
{
- es = av.endSeq;
+ es = av.getEndSeq();
}
}
* 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.
*/
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
return;
}
+ updateViewport();
// this draws the whole of the alignment
imgWidth = this.getSize().width;
imgHeight = this.getSize().height;
- imgWidth -= imgWidth % av.charWidth;
- imgHeight -= imgHeight % av.charHeight;
+ imgWidth -= imgWidth % avcharWidth;
+ imgHeight -= imgHeight % avcharHeight;
if (imgWidth < 1 || imgHeight < 1)
{
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.getStartRes());
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
+ av.getEndSeq(), 0);
}
g.drawImage(img, 0, 0, this);
public int getWrappedCanvasWidth(int cwidth)
{
- cwidth -= cwidth % av.charWidth;
+ cwidth -= cwidth % av.getCharWidth();
FontMetrics fm = getFontMetrics(av.getFont());
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) / av.getCharWidth();
}
/**
return mask;
}
- public void drawWrappedPanel(Graphics g, int canvasWidth,
+ private void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
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 = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += avcharHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
+ int cHeight = av.getAlignment().getHeight() * avcharHeight;
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.setEndRes(av.getStartRes() + cWidth);
int endx;
int ypos = hgap;
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(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;
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 * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4, res * avcharWidth },
+ new int[] { ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2) + 8 }, 3);
}
}
if (g.getClip() == null)
{
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
g.setClip(null);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
if (annotations == null)
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
return annotations.adjustPanelHeight();
}
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
+ private void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
-
if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
if (av.getShowHiddenMarkers())
{
g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
- - 1, (endSeq - startSeq) * av.charHeight
+ g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
+ - 1, (endSeq - startSeq) * avcharHeight
+ offset);
}
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * avcharWidth, 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 * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * avcharWidth, 0);
}
}
int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
-
+ sr.prepare(g, av.isRenderGaps());
+ updateViewport();
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);
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ startRes, endRes, offset + ((i - startSeq) * avcharHeight));
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ + ((i - startSeq) * avcharHeight));
}
// / Highlight search Results once all sequences have been drawn
// ////////////////////////////////////////////////////////
- if (searchResults != null)
+ if (av.hasSearchResults())
{
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+ startRes,
endRes);
if (visibleResults != null)
{
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ * avcharWidth, offset
+ + ((i - startSeq) * avcharHeight));
}
}
}
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) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
}
- void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+ private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
//
int bottom = -1;
int alHeight = av.getAlignment().getHeight() - 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) * avcharWidth;
+ sy = offset + ((i - startSeq) * avcharHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
if (sx + ex < 0 || sx > imgWidth)
{
continue;
}
- if ((sx <= (endRes - startRes) * av.charWidth)
+ if ((sx <= (endRes - startRes) * avcharWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
.contains(
av.getAlignment().getSequenceAt(i + 1))))
{
- bottom = sy + av.charHeight;
+ bottom = sy + avcharHeight;
}
if (!inGroup)
ex = imgWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * avcharWidth;
}
if (top != -1)
if (inGroup)
{
- sy = offset + ((i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * avcharHeight);
if (sx >= 0 && sx < imgWidth)
{
g.drawLine(sx, oldY, sx, sy);
{
ex = imgWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * avcharWidth;
}
if (top != -1)
break;
}
- group = av.getAlignment().getGroups()
- .get(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}
}
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
- searchResults = results;
-
+ av.setSearchResults(results);
repaint();
}
git://source.jalview.org / jalview.git / blobdiff