X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=8d429c70c6b37b1bdbb0849807c6b6e3eea49c17;hb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;hp=9de545261cec93715152ed7c8e92860e1fa6e585;hpb=171bb10b5fdc06925e47025829e6cede32b85b63;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 9de5452..8d429c7 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -37,7 +37,7 @@ import java.awt.Graphics; import java.awt.Image; import java.awt.Panel; import java.beans.PropertyChangeEvent; -import java.util.List; +import java.util.Iterator; public class SeqCanvas extends Panel implements ViewportListenerI { @@ -113,12 +113,12 @@ public class SeqCanvas extends Panel implements ViewportListenerI { if (mstring != null) { - g.drawString(mstring, mpos * avcharWidth, ypos - - (avcharHeight / 2)); + g.drawString(mstring, mpos * avcharWidth, + ypos - (avcharHeight / 2)); } - g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2) - - (avcharHeight / 2), (mpos * avcharWidth) - + (avcharWidth / 2), ypos - 2); + g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), + (ypos + 2) - (avcharHeight / 2), + (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2); } } } @@ -167,8 +167,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI { int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) - avcharWidth / 2; - g.drawString(value + "", x, (ypos + (i * avcharHeight)) - - (avcharHeight / 5)); + g.drawString(value + "", x, + (ypos + (i * avcharHeight)) - (avcharHeight / 5)); } } } @@ -207,8 +207,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight)) - - (avcharHeight / 5)); + g.drawString(String.valueOf(value), 0, + (ypos + (i * avcharHeight)) - (avcharHeight / 5)); } } } @@ -237,14 +237,14 @@ public class SeqCanvas extends Panel implements ViewportListenerI lastsr = ranges.getStartRes(); fastPaint = true; - gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth - - horizontal * avcharWidth, + gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, + imgWidth - horizontal * avcharWidth, imgHeight - vertical * avcharHeight, -horizontal * avcharWidth, -vertical * avcharHeight); - int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges - .getStartSeq(), es = ranges - .getEndSeq(), transX = 0, transY = 0; + int sr = ranges.getStartRes(), er = ranges.getEndRes(), + ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0, + transY = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { @@ -261,7 +261,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI ss = es - vertical; if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page // at a - // time + // time { ss = ranges.getStartSeq(); } @@ -307,8 +307,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI { if (img != null - && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g - .getClipBounds().height))) + && (fastPaint || (getSize().width != g.getClipBounds().width) + || (getSize().height != g.getClipBounds().height))) { g.drawImage(img, 0, 0, this); fastPaint = false; @@ -417,71 +417,71 @@ public class SeqCanvas extends Panel implements ViewportListenerI int canvasHeight, int startRes) { AlignmentI al = av.getAlignment(); - + FontMetrics fm = getFontMetrics(av.getFont()); - + LABEL_EAST = 0; LABEL_WEST = 0; - + if (av.getScaleRightWrapped()) { LABEL_EAST = fm.stringWidth(getMask()); } - + if (av.getScaleLeftWrapped()) { LABEL_WEST = fm.stringWidth(getMask()); } - + int hgap = avcharHeight; if (av.getScaleAboveWrapped()) { hgap += avcharHeight; } - + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth; int cHeight = av.getAlignment().getHeight() * avcharHeight; - + av.setWrappedWidth(cWidth); - + av.getRanges().setViewportStartAndWidth(startRes, cWidth); - + int endx; int ypos = hgap; - + int maxwidth = av.getAlignment().getWidth(); - + if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() .findColumnPosition(maxwidth); } - + while ((ypos <= canvasHeight) && (startRes < maxwidth)) { endx = startRes + cWidth - 1; - + if (endx > maxwidth) { endx = maxwidth; } - + g.setColor(Color.black); - + if (av.getScaleLeftWrapped()) { drawWestScale(g, startRes, endx, ypos); } - + if (av.getScaleRightWrapped()) { g.translate(canvasWidth - LABEL_EAST, 0); drawEastScale(g, startRes, endx, ypos); g.translate(-(canvasWidth - LABEL_EAST), 0); } - + g.translate(LABEL_WEST, 0); - + if (av.getScaleAboveWrapped()) { drawNorthScale(g, startRes, endx, ypos); @@ -491,33 +491,27 @@ public class SeqCanvas extends Panel implements ViewportListenerI HiddenColumns hidden = av.getAlignment().getHiddenColumns(); g.setColor(Color.blue); int res; - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + Iterator it = hidden.getBoundedStartIterator(startRes, + endx + 1, true); + while (it.hasNext()) { - res = pos - startRes; - - if (res < 0 || res > endx - startRes) - { - continue; - } - - 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); - + res = it.next() - startRes; + 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 * avcharWidth, canvasHeight); } - + drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); g.setClip(null); - + if (av.isShowAnnotation()) { g.translate(0, cHeight + ypos + 4); @@ -525,17 +519,17 @@ public class SeqCanvas extends Panel implements ViewportListenerI { annotations = new AnnotationPanel(av); } - + annotations.drawComponent(g, startRes, endx + 1); g.translate(0, -cHeight - ypos - 4); } g.translate(-LABEL_WEST, 0); - + ypos += cHeight + getAnnotationHeight() + hgap; - + startRes += cWidth; } - + } AnnotationPanel annotations; @@ -555,8 +549,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI return annotations.adjustPanelHeight(); } - private void drawPanel(Graphics g1, int startRes, int endRes, - int startSeq, int endSeq, int offset) + private void drawPanel(Graphics g1, final int startRes, final int endRes, + final int startSeq, final int endSeq, final int offset) { if (!av.hasHiddenColumns()) @@ -565,52 +559,52 @@ public class SeqCanvas extends Panel implements ViewportListenerI } else { - int screenY = 0; + final int screenYMax = endRes - startRes; int blockStart = startRes; int blockEnd = endRes; - if (av.hasHiddenColumns()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + Iterator regions = hidden.getBoundedVisRegionIterator(startRes, + endRes); + while (regions.hasNext()) { - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - for (int[] region : hidden.getHiddenColumnsCopy()) - { - int hideStart = region[0]; - int hideEnd = region[1]; + int[] region = regions.next(); - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + blockStart = region[0]; - 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(region[1], blockStart + screenYMax - screenY); - g1.translate(screenY * avcharWidth, 0); + g1.translate(screenY * avcharWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - if (av.getShowHiddenMarkers()) - { - g1.setColor(Color.blue); - g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - - 1, (endSeq - startSeq + 1) * avcharHeight - + offset); - } + /* + * draw the downline of the hidden column marker (ScalePanel draws the + * triangle on top) if we reached it + */ + if (av.getShowHiddenMarkers() && blockEnd == region[1]) + { + g1.setColor(Color.blue); + g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1, + 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1, + (endSeq - startSeq + 1) * avcharHeight + offset); + } - g1.translate(-screenY * avcharWidth, 0); - screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; + g1.translate(-screenY * avcharWidth, 0); + screenY += blockEnd - blockStart + 1; - if (screenY > (endRes - startRes)) - { - // already rendered last block - return; - } + if (screenY > screenYMax) + { + // already rendered last block + return; } } - if (screenY <= (endRes - startRes)) + if (screenY <= screenYMax) { // remaining visible region to render blockEnd = blockStart + (endRes - startRes) - screenY; @@ -649,8 +643,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI if (av.isShowSequenceFeatures()) { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * avcharHeight), false); + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * avcharHeight), false); } // / Highlight search Results once all sequences have been drawn @@ -658,16 +652,15 @@ public class SeqCanvas extends Panel implements ViewportListenerI if (av.hasSearchResults()) { int[] visibleResults = av.getSearchResults().getResults(nextSeq, - startRes, - endRes); + 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) - * avcharWidth, offset - + ((i - startSeq) * avcharHeight)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * avcharWidth, + offset + ((i - startSeq) * avcharHeight)); } } } @@ -723,7 +716,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI { sx = (group.getStartRes() - startRes) * avcharWidth; sy = offset + ((i - startSeq) * avcharHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1; + ex = (((group.getEndRes() + 1) - group.getStartRes()) + * avcharWidth) - 1; if (sx + ex < 0 || sx > imgWidth) { @@ -731,22 +725,20 @@ public class SeqCanvas extends Panel implements ViewportListenerI } if ((sx <= (endRes - startRes) * avcharWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) + && group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i))) { if ((bottom == -1) - && (i >= alHeight || !group.getSequences(null) - .contains( - av.getAlignment().getSequenceAt(i + 1)))) + && (i >= alHeight || !group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i + 1)))) { bottom = sy + avcharHeight; } if (!inGroup) { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) + if (((top == -1) && (i == 0)) || !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i - 1))) { top = sy; }