X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=2d8eb7df45a173da3c892bb02cd020a21dfd1b70;hb=aad3640b07f836362df7ea025fa09127a0a06145;hp=2a9c7048e29652f25df69b056a1af880ecf798a1;hpb=c2ec295699b0e198ae1981bd3807394060f5c6d6;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 2a9c704..2d8eb7d 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.VisibleContigsIterator; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.util.Comparison; @@ -42,6 +43,7 @@ import java.awt.RenderingHints; import java.awt.Shape; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; +import java.util.Iterator; import java.util.List; import javax.swing.JComponent; @@ -198,8 +200,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startX = hiddenColumns.adjustForHiddenColumns(startx); - endX = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -295,48 +297,52 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int endSeq = ranges.getEndSeq(); int transX = 0; int transY = 0; + + gg.copyArea(horizontal * charWidth, vertical * charHeight, + img.getWidth(), img.getHeight(), -horizontal * charWidth, + -vertical * charHeight); - gg.copyArea(horizontal * charWidth, vertical * charHeight, - img.getWidth(), img.getHeight(), -horizontal * charWidth, - -vertical * charHeight); - - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (endRes - startRes - horizontal) * charWidth; - startRes = endRes - horizontal; - } - else if (horizontal < 0) - { - endRes = startRes - horizontal; - } - else if (vertical > 0) // scroll down - { - startSeq = endSeq - vertical; - - if (startSeq < ranges.getStartSeq()) - { // ie scrolling too fast, more than a page at a time - startSeq = ranges.getStartSeq(); + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (endRes - startRes - horizontal) * charWidth; + startRes = endRes - horizontal; } - else + else if (horizontal < 0) { - transY = img.getHeight() - ((vertical + 1) * charHeight); + endRes = startRes - horizontal; } - } - else if (vertical < 0) - { - endSeq = startSeq - vertical; - if (endSeq > ranges.getEndSeq()) + if (vertical > 0) // scroll down { - endSeq = ranges.getEndSeq(); + startSeq = endSeq - vertical; + + if (startSeq < ranges.getStartSeq()) + { // ie scrolling too fast, more than a page at a time + startSeq = ranges.getStartSeq(); + } + else + { + transY = img.getHeight() - ((vertical + 1) * charHeight); + } + } + else if (vertical < 0) + { + endSeq = startSeq - vertical; + + if (endSeq > ranges.getEndSeq()) + { + endSeq = ranges.getEndSeq(); + } } - } - gg.translate(transX, transY); - drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); - gg.translate(-transX, -transY); + gg.translate(transX, transY); + drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); + gg.translate(-transX, -transY); - repaint(); + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the + // overview window and others may be adversely affected. + av.getAlignPanel().repaint(); } finally { fastpainting = false; @@ -350,20 +356,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); - + ViewportRanges ranges = av.getRanges(); - + int width = getWidth(); int height = getHeight(); - + width -= (width % charWidth); height -= (height % charHeight); - + // selectImage is the selection group outline image BufferedImage selectImage = drawSelectionGroup( ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); - + if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) @@ -387,16 +393,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); } - + if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } - + gg.setColor(Color.white); gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - + if (av.getWrapAlignment()) { drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); @@ -406,10 +412,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq(), 0); } - + // lcimg is a local *copy* of img which we'll draw selectImage on top of BufferedImage lcimg = buildLocalImage(selectImage); g.drawImage(lcimg, 0, 0, this); + + } + + if (av.cursorMode) + { + drawCursor(g, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq()); } } @@ -496,8 +509,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private BufferedImage buildLocalImage(BufferedImage selectImage) { // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); + BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + img.getType()); + + // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + // img.getType()); Graphics2D g2d = lcimg.createGraphics(); g2d.drawImage(img, 0, 0, null); @@ -508,6 +524,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); g2d.drawImage(selectImage, 0, 0, this); } + g2d.dispose(); return lcimg; @@ -536,8 +553,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + lcimg = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works } catch (OutOfMemoryError er) { System.gc(); @@ -771,8 +788,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * white fill the region to be drawn (so incremental fast paint doesn't * scribble over an existing image) */ - gg.setColor(Color.white); - gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth, + g.setColor(Color.white); + g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth, wrappedRepeatHeightPx); drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1, @@ -881,11 +898,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int charWidth = av.getCharWidth(); g.setColor(Color.blue); + int res; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + + Iterator it = hidden.getStartRegionIterator(startColumn, + endColumn); + while (it.hasNext()) { - int res = pos - startColumn; + res = it.next() - startColumn; if (res < 0 || res > endColumn - startColumn + 1) { @@ -912,9 +932,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int canvasWidth, int canvasHeight, int startRes) { - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + // height gap above each panel int hgap = charHeight; if (av.getScaleAboveWrapped()) @@ -934,7 +954,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); + .absoluteToVisibleColumn(maxwidth); } // chop the wrapped alignment extent up into panel-sized blocks and treat @@ -1012,29 +1032,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI else { int screenY = 0; - final int screenYMax = endRes - startRes; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) - { - int hideStart = region[0]; - int hideEnd = region[1]; + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + while (regions.hasNext()) + { + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; /* * 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 * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); @@ -1043,7 +1057,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * draw the downline of the hidden column marker (ScalePanel draws the * triangle on top) if we reached it */ - if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1) + if (av.getShowHiddenMarkers() + && (regions.hasNext() || regions.endsAtHidden())) { g1.setColor(Color.blue); @@ -1054,23 +1069,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > screenYMax) - { - // already rendered last block - return; - } - } - - if (screenY <= screenYMax) - { - // remaining visible region to render - blockEnd = blockStart + screenYMax - screenY; - g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); - - g1.translate(-screenY * charWidth, 0); } } @@ -1128,26 +1126,19 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasSearchResults()) { SearchResultsI searchResults = av.getSearchResults(); - int[] visibleResults = searchResults.getResults(nextSeq, - startRes, endRes); + int[] visibleResults = searchResults.getResults(nextSeq, startRes, + endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { seqRdr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * charWidth, offset - + ((i - startSeq) * charHeight)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); } } } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, - offset + ((i - startSeq) * charHeight)); - } } if (av.getSelectionGroup() != null @@ -1245,6 +1236,94 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return selectionImage; } + /** + * Draw the cursor as a separate image and overlay + * + * @param startRes + * start residue of area to draw cursor in + * @param endRes + * end residue of area to draw cursor in + * @param startSeq + * start sequence of area to draw cursor in + * @param endSeq + * end sequence of are to draw cursor in + * @return a transparent image of the same size as the sequence canvas, with + * the cursor drawn on it, if any + */ + private void drawCursor(Graphics g, int startRes, int endRes, + int startSeq, + int endSeq) + { + // convert the cursorY into a position on the visible alignment + int cursor_ypos = cursorY; + + // don't do work unless we have to + if (cursor_ypos >= startSeq && cursor_ypos <= endSeq) + { + int yoffset = 0; + int xoffset = 0; + int startx = startRes; + int endx = endRes; + + // convert the cursorX into a position on the visible alignment + int cursor_xpos = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(cursorX); + + if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) + { + + if (av.getWrapAlignment()) + { + // work out the correct offsets for the cursor + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); + int canvasWidth = getWidth(); + int canvasHeight = getHeight(); + + // height gap above each panel + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) + / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; + + endx = startx + cWidth - 1; + int ypos = hgap; // vertical offset + + // iterate down the wrapped panels + while ((ypos <= canvasHeight) && (endx < cursor_xpos)) + { + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; + + // update horizontal offset + startx += cWidth; + endx = startx + cWidth - 1; + } + yoffset = ypos; + xoffset = labelWidthWest; + } + + // now check if cursor is within range for x values + if (cursor_xpos >= startx && cursor_xpos <= endx) + { + // get the character the cursor is drawn at + SequenceI seq = av.getAlignment().getSequenceAt(cursorY); + char s = seq.getCharAt(cursorX); + + seqRdr.drawCursor(g, s, + xoffset + (cursor_xpos - startx) * av.getCharWidth(), + yoffset + (cursor_ypos - startSeq) * av.getCharHeight()); + } + } + } + } + + /* * Set up graphics for selection group */ @@ -1276,8 +1355,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, int startRes, int endRes, int startSeq, int endSeq, int offset) { - int charWidth = av.getCharWidth(); - + int charWidth = av.getCharWidth(); + if (!av.hasHiddenColumns()) { drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, @@ -1287,22 +1366,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { // package into blocks of visible columns int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; g.translate(screenY * charWidth, 0); drawPartialGroupOutline(g, group, @@ -1310,24 +1384,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI g.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > (endRes - startRes)) - { - // already rendered last block - break; - } - } - - if (screenY <= (endRes - startRes)) - { - // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; - g.translate(screenY * charWidth, 0); - drawPartialGroupOutline(g, group, - blockStart, blockEnd, startSeq, endSeq, offset); - - g.translate(-screenY * charWidth, 0); } } } @@ -1339,9 +1395,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int startRes, int endRes, int startSeq, int endSeq, int verticalOffset) { - int charHeight = av.getCharHeight(); - int charWidth = av.getCharWidth(); - + int charHeight = av.getCharHeight(); + int charWidth = av.getCharWidth(); int visWidth = (endRes - startRes + 1) * charWidth; int oldY = -1; @@ -1349,140 +1404,141 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean inGroup = false; int top = -1; int bottom = -1; - - int sx = -1; int sy = -1; - int xwidth = -1; - for (i = startSeq; i <= endSeq; i++) - { - // position of start residue of group relative to startRes, in pixels - sx = (group.getStartRes() - startRes) * charWidth; + List seqs = group.getSequences(null); - // width of group in pixels - xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - - 1; + // position of start residue of group relative to startRes, in pixels + int sx = (group.getStartRes() - startRes) * charWidth; - sy = verticalOffset + (i - startSeq) * charHeight; + // width of group in pixels + int xwidth = (((group.getEndRes() + 1) - group.getStartRes()) + * charWidth) - 1; - if (sx + xwidth < 0 || sx > visWidth) - { - continue; - } - - if ((sx <= (endRes - startRes) * charWidth) - && group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i))) + if (!(sx + xwidth < 0 || sx > visWidth)) + { + for (i = startSeq; i <= endSeq; 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; - } + sy = verticalOffset + (i - startSeq) * charHeight; - oldY = sy; - inGroup = true; - } - } - else - { - if (inGroup) + if ((sx <= (endRes - startRes) * charWidth) + && seqs.contains(av.getAlignment().getSequenceAt(i))) { - // 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 + xwidth < visWidth) - { - g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); - } - - if (sx < 0) + if ((bottom == -1) + && !seqs.contains(av.getAlignment().getSequenceAt(i + 1))) { - xwidth += sx; - sx = 0; + bottom = sy + charHeight; } - // don't let width extend beyond current block, or group extent - // fixes JAL-2672 - if (sx + xwidth >= (endRes - startRes + 1) * charWidth) - { - xwidth = (endRes - startRes + 1) * charWidth - sx; - } - - // draw horizontal line at top of group - if (top != -1) + if (!inGroup) { - g.drawLine(sx, top, sx + xwidth, top); - top = -1; - } + if (((top == -1) && (i == 0)) || !seqs + .contains(av.getAlignment().getSequenceAt(i - 1))) + { + top = sy; + } - // draw horizontal line at bottom of group - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + xwidth, bottom); - bottom = -1; + oldY = sy; + inGroup = true; } + } + else if (inGroup) + { + drawVerticals(g, sx, xwidth, visWidth, oldY, sy); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom); + // reset top and bottom + top = -1; + bottom = -1; inGroup = false; } } - } - - if (inGroup) - { - sy = verticalOffset + ((i - startSeq) * charHeight); - if (sx >= 0 && sx < visWidth) + if (inGroup) { - g.drawLine(sx, oldY, sx, sy); + sy = verticalOffset + ((i - startSeq) * charHeight); + drawVerticals(g, sx, xwidth, visWidth, oldY, sy); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom); } + } + } - if (sx + xwidth < visWidth) - { - g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); - } + /** + * Draw horizontal selection group boundaries at top and bottom positions + * + * @param g + * graphics object to draw on + * @param sx + * start x position + * @param xwidth + * width of gap + * @param visWidth + * visWidth maximum available width + * @param top + * position to draw top of group at + * @param bottom + * position to draw bottom of group at + */ + private void drawHorizontals(Graphics2D g, int sx, int xwidth, + int visWidth, int top, int bottom) + { + int width = xwidth; + int startx = sx; + if (startx < 0) + { + width += startx; + startx = 0; + } - if (sx < 0) - { - xwidth += sx; - sx = 0; - } + // don't let width extend beyond current block, or group extent + // fixes JAL-2672 + if (startx + width >= visWidth) + { + width = visWidth - startx; + } - if (sx + xwidth > visWidth) - { - xwidth = visWidth; - } - else if (sx + xwidth >= (endRes - startRes + 1) * charWidth) - { - xwidth = (endRes - startRes + 1) * charWidth; - } + if (top != -1) + { + g.drawLine(startx, top, startx + width, top); + } - if (top != -1) - { - g.drawLine(sx, top, sx + xwidth, top); - top = -1; - } + if (bottom != -1) + { + g.drawLine(startx, bottom - 1, startx + width, bottom - 1); + } + } - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1); - bottom = -1; - } + /** + * Draw vertical lines at sx and sx+xwidth providing they lie within + * [0,visWidth) + * + * @param g + * graphics object to draw on + * @param sx + * start x position + * @param xwidth + * width of gap + * @param visWidth + * visWidth maximum available width + * @param oldY + * top y value + * @param sy + * bottom y value + */ + private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth, + int oldY, int sy) + { + // if start position is visible, draw vertical line to left of + // group + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } - inGroup = false; + // if end position is visible, draw vertical line to right of + // group + if (sx + xwidth < visWidth) + { + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); } } @@ -1569,7 +1625,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositions(SearchResultsI results) { - if (results == null) + if ((results == null) || (gg == null)) // JAL-2784 check gg is not null { return false; } @@ -1591,9 +1647,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } for (int seqNo = ranges.getStartSeq(); seqNo <= ranges @@ -1636,8 +1692,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstCol = alignment.getHiddenColumns() - .findColumnPosition(firstCol); - lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol); + .absoluteToVisibleColumn(firstCol); + lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol); } int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth(); int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight(); @@ -1660,15 +1716,31 @@ public class SeqCanvas extends JComponent implements ViewportListenerI repaint(); return; } + else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) + { + fastPaint = false; + repaint(); + return; + } int scrollX = 0; - if (eventName.equals(ViewportRanges.STARTRES)) + if (eventName.equals(ViewportRanges.STARTRES) + || eventName.equals(ViewportRanges.STARTRESANDSEQ)) { // Make sure we're not trying to draw a panel // larger than the visible window + if (eventName.equals(ViewportRanges.STARTRES)) + { + scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + } + else + { + scrollX = ((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]; + } ViewportRanges vpRanges = av.getRanges(); - scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); - int range = vpRanges.getViewportWidth(); + + int range = vpRanges.getEndRes() - vpRanges.getStartRes(); if (scrollX > range) { scrollX = range; @@ -1678,30 +1750,50 @@ public class SeqCanvas extends JComponent implements ViewportListenerI 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. - - // scroll - startres and endres both change - if (eventName.equals(ViewportRanges.STARTRES)) - { - if (av.getWrapAlignment()) + // 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)) { - fastPaintWrapped(scrollX); + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } } - else + else if (eventName.equals(ViewportRanges.STARTSEQ)) { - fastPaint(scrollX, 0); + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } } else if (eventName.equals(ViewportRanges.STARTSEQ)) { // scroll fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + } } /** @@ -1967,7 +2059,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositionsWrapped(SearchResultsI results) { - if (results == null) + if ((results == null) || (gg == null)) // JAL-2784 check gg is not null { return false; } @@ -1995,9 +2087,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); @@ -2036,7 +2128,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /*