X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7d953989280b719458107acbddd20ed0802e899d;hb=refs%2Fheads%2Ffeatures%2FJAL-653_JAL-1766_htslib_refseqsupport;hp=03231c535e75f32cd518baa0ce265e8d7ded5398;hpb=648f0d7f48b5865bd43b5edbe71f5e483f0cc455;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 03231c5..7d95398 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/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. * @@ -20,11 +20,26 @@ */ package jalview.gui; -import java.awt.*; -import java.awt.image.*; -import javax.swing.*; - -import jalview.datamodel.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.renderer.ScaleRenderer; +import jalview.renderer.ScaleRenderer.ScaleMark; +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.util.List; + +import javax.swing.JComponent; /** * DOCUMENT ME! @@ -48,8 +63,6 @@ public class SeqCanvas extends JComponent AlignViewport av; - SearchResults searchResults = null; - boolean fastPaint = false; int LABEL_WEST; @@ -69,6 +82,7 @@ public class SeqCanvas extends JComponent public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; + updateViewport(); fr = new FeatureRenderer(ap); sr = new SequenceRenderer(av); setLayout(new BorderLayout()); @@ -86,6 +100,14 @@ public class SeqCanvas extends JComponent return fr; } + int charHeight = 0, charWidth = 0; + + private void updateViewport() + { + charHeight = av.getCharHeight(); + charWidth = av.getCharWidth(); + } + /** * DOCUMENT ME! * @@ -98,28 +120,29 @@ public class SeqCanvas extends JComponent * @param ypos * DOCUMENT ME! */ - 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; - - g.setColor(Color.black); - - // NORTH SCALE - for (int i = scalestartx; i < endx; i += 10) + updateViewport(); + 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 * charWidth, ypos - (charHeight / 2)); + } + g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2) + - (charHeight / 2), (mpos * charWidth) + (charWidth / 2), + ypos - 2); + } } } @@ -138,7 +161,7 @@ public class SeqCanvas extends JComponent void drawWestScale(Graphics g, int startx, int endx, int ypos) { FontMetrics fm = getFontMetrics(av.getFont()); - ypos += av.charHeight; + ypos += charHeight; if (av.hasHiddenColumns()) { @@ -176,9 +199,9 @@ public class SeqCanvas extends JComponent 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)); + - charWidth / 2; + g.drawString(value + "", x, (ypos + (i * charHeight)) + - (charHeight / 5)); } } } @@ -197,7 +220,7 @@ public class SeqCanvas extends JComponent */ void drawEastScale(Graphics g, int startx, int endx, int ypos) { - ypos += av.charHeight; + ypos += charHeight; if (av.hasHiddenColumns()) { @@ -228,8 +251,8 @@ public class SeqCanvas extends JComponent if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight)) - - (av.charHeight / 5)); + g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight)) + - (charHeight / 5)); } } } @@ -247,33 +270,28 @@ public class SeqCanvas extends JComponent */ public void fastPaint(int horizontal, int vertical) { - if (fastpainting) + if (fastpainting || gg == null) { return; } fastpainting = true; - if (gg == null) - { - return; - } - fastPaint = true; - - 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; + updateViewport(); + gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, + imgHeight, -horizontal * charWidth, -vertical * charHeight); + + ViewportRanges ranges = av.getRanges(); + int sr = ranges.getStartRes(); + int er = ranges.getEndRes(); + int ss = ranges.getStartSeq(); + int es = ranges.getEndSeq(); int transX = 0; int transY = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { er++; - transX = (er - sr - horizontal) * av.charWidth; + transX = (er - sr - horizontal) * charWidth; sr = er - horizontal; } else if (horizontal < 0) @@ -284,22 +302,22 @@ public class SeqCanvas extends JComponent { ss = es - vertical; - if (ss < av.startSeq) + if (ss < ranges.getStartSeq()) { // ie scrolling too fast, more than a page at a time - ss = av.startSeq; + ss = ranges.getStartSeq(); } else { - transY = imgHeight - (vertical * av.charHeight); + transY = imgHeight - ((vertical + 1) * charHeight); } } else if (vertical < 0) { es = ss - vertical; - if (es > av.endSeq) + if (es > ranges.getEndSeq()) { - es = av.endSeq; + es = ranges.getEndSeq(); } } @@ -321,8 +339,10 @@ public class SeqCanvas extends JComponent */ // 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); @@ -341,8 +361,8 @@ public class SeqCanvas extends JComponent imgWidth = getWidth(); imgHeight = getHeight(); - imgWidth -= (imgWidth % av.charWidth); - imgHeight -= (imgHeight % av.charHeight); + imgWidth -= (imgWidth % charWidth); + imgHeight -= (imgHeight % charHeight); if ((imgWidth < 1) || (imgHeight < 1)) { @@ -377,13 +397,15 @@ public class SeqCanvas extends JComponent 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); @@ -405,17 +427,17 @@ public class SeqCanvas extends JComponent 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) / charWidth; } /** @@ -459,32 +481,33 @@ public class SeqCanvas extends JComponent public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) { + updateViewport(); 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 = 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 - LABEL_EAST - LABEL_WEST) / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; av.setWrappedWidth(cWidth); - av.endRes = av.startRes + cWidth; + av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth); int endx; int ypos = hgap; @@ -507,12 +530,12 @@ public class SeqCanvas extends JComponent g.setFont(av.getFont()); 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); @@ -521,12 +544,12 @@ public class SeqCanvas extends JComponent 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; @@ -541,12 +564,12 @@ public class SeqCanvas extends JComponent 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 * charWidth - charHeight / 4, + res * charWidth + charHeight / 4, res * charWidth }, + new int[] { ypos - (charHeight / 2), + ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 }, + 3); } } @@ -557,17 +580,17 @@ public class SeqCanvas extends JComponent if (clip == null) { - g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); + g.setClip(0, 0, cWidth * charWidth, canvasHeight); } else { - g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth, + g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth, (int) clip.getBounds().getHeight()); } drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); - if (av.showAnnotation) + if (av.isShowAnnotation()) { g.translate(0, cHeight + ypos + 3); if (annotations == null) @@ -575,8 +598,8 @@ public class SeqCanvas extends JComponent annotations = new AnnotationPanel(av); } - annotations.renderer.drawComponent(annotations, av, (Graphics2D) g, - -1, startRes, endx + 1); + annotations.renderer.drawComponent(annotations, av, g, -1, + startRes, endx + 1); g.translate(0, -cHeight - ypos - 3); } g.setClip(clip); @@ -592,7 +615,7 @@ public class SeqCanvas extends JComponent int getAnnotationHeight() { - if (!av.showAnnotation) + if (!av.isShowAnnotation()) { return 0; } @@ -621,24 +644,24 @@ public class SeqCanvas extends JComponent * @param offset * DOCUMENT ME! */ - void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, - int endSeq, int offset) + public void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) { + updateViewport(); if (!av.hasHiddenColumns()) { draw(g1, startRes, endRes, startSeq, endSeq, offset); } else { - java.util.Vector regions = av.getColumnSelection().getHiddenColumns(); + List regions = av.getColumnSelection().getHiddenColumns(); int screenY = 0; int blockStart = startRes; int blockEnd = endRes; - for (int i = 0; regions != null && i < regions.size(); i++) + for (int[] region : regions) { - int[] region = (int[]) regions.elementAt(i); int hideStart = region[0]; int hideEnd = region[1]; @@ -650,7 +673,7 @@ public class SeqCanvas extends JComponent blockEnd = hideStart - 1; - g1.translate(screenY * av.charWidth, 0); + g1.translate(screenY * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); @@ -658,23 +681,30 @@ public class SeqCanvas extends JComponent { 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 + offset, (blockEnd - blockStart + 1) * charWidth - 1, + (endSeq - startSeq) * charHeight + offset); } - g1.translate(-screenY * av.charWidth, 0); + g1.translate(-screenY * 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 * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - g1.translate(-screenY * av.charWidth, 0); + g1.translate(-screenY * charWidth, 0); } } @@ -682,17 +712,17 @@ public class SeqCanvas extends JComponent // 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) + 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) @@ -702,28 +732,29 @@ public class SeqCanvas extends JComponent continue; } sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), - startRes, endRes, offset + ((i - startSeq) * av.charHeight)); + startRes, endRes, offset + ((i - startSeq) * charHeight)); if (av.isShowSequenceFeatures()) { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * av.charHeight)); + fr.drawSequence(g, nextSeq, startRes, + endRes, offset + + ((i - startSeq) * charHeight)); } // / Highlight search Results once all sequences have been drawn // //////////////////////////////////////////////////////// - if (searchResults != null) + if (av.hasSearchResults()) { - int[] visibleResults = searchResults.getResults(nextSeq, startRes, - endRes); + int[] visibleResults = av.getSearchResults().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)); } } } @@ -731,9 +762,8 @@ public class SeqCanvas extends JComponent 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)); } } @@ -759,11 +789,11 @@ public class SeqCanvas extends JComponent 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; } @@ -777,18 +807,18 @@ public class SeqCanvas extends JComponent 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))) { @@ -796,7 +826,7 @@ public class SeqCanvas extends JComponent && !group.getSequences(null).contains( av.getAlignment().getSequenceAt(i + 1))) { - bottom = sy + av.charHeight; + bottom = sy + charHeight; } if (!inGroup) @@ -814,8 +844,8 @@ public class SeqCanvas extends JComponent 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 @@ -850,9 +880,9 @@ public class SeqCanvas extends JComponent 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) @@ -874,7 +904,7 @@ public class SeqCanvas extends JComponent if (inGroup) { - sy = offset + ((i - startSeq) * av.charHeight); + sy = offset + ((i - startSeq) * charHeight); if (sx >= 0 && sx < visWidth) { g.drawLine(sx, oldY, sx, sy); @@ -895,9 +925,9 @@ public class SeqCanvas extends JComponent { 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) @@ -924,8 +954,7 @@ public class SeqCanvas extends JComponent break; } - group = (SequenceGroup) av.getAlignment().getGroups() - .get(groupIndex); + group = av.getAlignment().getGroups().get(groupIndex); } while (groupIndex < av.getAlignment().getGroups().size()); @@ -939,11 +968,11 @@ public class SeqCanvas extends JComponent * @param results * DOCUMENT ME! */ - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { img = null; - searchResults = results; + av.setSearchResults(results); repaint(); }