X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=7216bfe9f2235f2edba53dd060379a8b7eb6ecfd;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4b3cd1cff4debe925b07f5f802e424e966deab6c;hpb=6ff627c729ffdea1bbf658a463e3e993aad493bb;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 4b3cd1c..7216bfe 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -24,6 +24,9 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.renderer.ScaleRenderer; +import jalview.renderer.ScaleRenderer.ScaleMark; +import jalview.viewmodel.AlignmentViewport; import java.awt.Color; import java.awt.FontMetrics; @@ -61,9 +64,18 @@ public class SeqCanvas extends Panel fr = new FeatureRenderer(av); sr = new SequenceRenderer(av); PaintRefresher.Register(this, av.getSequenceSetId()); + updateViewport(); } - public AlignViewport getViewport() + int avcharHeight = 0, avcharWidth = 0; + + private void updateViewport() + { + avcharHeight = av.getCharHeight(); + avcharWidth = av.getCharWidth(); + } + + public AlignmentViewport getViewport() { return av; } @@ -78,35 +90,38 @@ public class SeqCanvas extends Panel 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); @@ -143,16 +158,16 @@ public class SeqCanvas extends Panel 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()) { @@ -183,8 +198,8 @@ public class SeqCanvas extends Panel 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)); } } } @@ -198,6 +213,8 @@ public class SeqCanvas extends Panel 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 @@ -209,16 +226,16 @@ public class SeqCanvas extends Panel lastsr = av.startRes; 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; 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) @@ -235,7 +252,7 @@ public class SeqCanvas extends Panel } else { - transY = imgHeight - vertical * av.charHeight; + transY = imgHeight - vertical * avcharHeight; } } else if (vertical < 0) @@ -264,11 +281,13 @@ public class SeqCanvas extends Panel * 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) { @@ -288,12 +307,13 @@ public class SeqCanvas extends Panel 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) { @@ -328,24 +348,24 @@ public class SeqCanvas extends Panel 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(); } /** @@ -375,31 +395,31 @@ public class SeqCanvas extends Panel 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); @@ -426,12 +446,12 @@ public class SeqCanvas extends Panel 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); @@ -440,11 +460,11 @@ public class SeqCanvas extends Panel 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; @@ -459,25 +479,24 @@ public class SeqCanvas extends Panel 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) @@ -501,7 +520,7 @@ public class SeqCanvas extends Panel int getAnnotationHeight() { - if (!av.showAnnotation) + if (!av.isShowAnnotation()) { return 0; } @@ -514,11 +533,10 @@ public class SeqCanvas extends Panel 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); @@ -526,56 +544,57 @@ public class SeqCanvas extends Panel else { - - int screenY = 0; int blockStart = startRes; int blockEnd = endRes; - if (av.getColumnSelection() != null - && av.getColumnSelection().getHiddenColumns() != null) + if (av.hasHiddenColumns()) { - java.util.Vector regions = av.getColumnSelection() - .getHiddenColumns(); + for (int[] region : av.getColumnSelection().getHiddenColumns()) + { + int hideStart = region[0]; + int hideEnd = region[1]; - for (int i = 0; i < regions.size(); i++) - { - int[] region = (int[]) regions.elementAt(i); - int hideStart = region[0]; - int hideEnd = region[1]; + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + blockEnd = hideStart - 1; - blockEnd = hideStart - 1; + g1.translate(screenY * avcharWidth, 0); - g1.translate(screenY * av.charWidth, 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) * avcharHeight + + 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 + offset); - } + g1.translate(-screenY * avcharWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; - g1.translate(-screenY * av.charWidth, 0); - screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - } + if (screenY > (endRes - startRes)) + { + // already rendered last block + return; + } + } } if (screenY <= (endRes - startRes)) { + // remaining visible region to render blockEnd = blockStart + (endRes - startRes) - screenY; - g1.translate(screenY * av.charWidth, 0); + g1.translate(screenY * avcharWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - g1.translate(-screenY * av.charWidth, 0); + g1.translate(-screenY * avcharWidth, 0); } } @@ -587,8 +606,8 @@ public class SeqCanvas extends Panel int offset) { g.setFont(av.getFont()); - sr.prepare(g, av.renderGaps); - + sr.prepare(g, av.isRenderGaps()); + updateViewport(); SequenceI nextSeq; // / First draw the sequences @@ -603,12 +622,12 @@ public class SeqCanvas extends Panel } 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 @@ -623,8 +642,8 @@ public class SeqCanvas extends Panel { sr.drawHighlightedText(nextSeq, visibleResults[r], visibleResults[r + 1], (visibleResults[r] - startRes) - * av.charWidth, offset - + ((i - startSeq) * av.charHeight)); + * avcharWidth, offset + + ((i - startSeq) * avcharHeight)); } } } @@ -632,9 +651,8 @@ public class SeqCanvas extends Panel 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)); } } @@ -646,7 +664,7 @@ public class SeqCanvas extends Panel } - void drawGroupsBoundaries(Graphics g, int startRes, int endRes, + private void drawGroupsBoundaries(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) { // @@ -679,16 +697,16 @@ public class SeqCanvas extends Panel 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))) { @@ -697,7 +715,7 @@ public class SeqCanvas extends Panel .contains( av.getAlignment().getSequenceAt(i + 1)))) { - bottom = sy + av.charHeight; + bottom = sy + avcharHeight; } if (!inGroup) @@ -747,9 +765,9 @@ public class SeqCanvas extends Panel 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) @@ -771,7 +789,7 @@ public class SeqCanvas extends Panel if (inGroup) { - sy = offset + ((i - startSeq) * av.charHeight); + sy = offset + ((i - startSeq) * avcharHeight); if (sx >= 0 && sx < imgWidth) { g.drawLine(sx, oldY, sx, sy); @@ -792,9 +810,9 @@ public class SeqCanvas extends Panel { 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) @@ -819,8 +837,7 @@ public class SeqCanvas extends Panel break; } - group = av.getAlignment().getGroups() - .get(groupIndex); + group = av.getAlignment().getGroups().get(groupIndex); } while (groupIndex < av.getAlignment().getGroups().size()); }