X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FOverviewCanvas.java;h=de55996b1bf7f0249f647ab9b799c8db8e247448;hb=be7bf233b7e6af4f824613b1dbd3d5338498b4c8;hp=6a7e56cc7c304352057a791b35f363500fa12079;hpb=299d350019dc2701cd2d9812e8ce1285146bc045;p=jalview.git diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index 6a7e56c..de55996 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -1,9 +1,30 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.gui; import jalview.api.AlignViewportI; -import jalview.datamodel.SequenceI; -import jalview.renderer.AnnotationRenderer; -import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.renderer.OverviewRenderer; +import jalview.renderer.OverviewResColourFinder; import jalview.viewmodel.OverviewDimensions; import java.awt.Color; @@ -11,21 +32,22 @@ import java.awt.Dimension; import java.awt.Graphics; import java.awt.image.BufferedImage; -import javax.swing.JComponent; +import javax.swing.JPanel; -public class OverviewCanvas extends JComponent +@SuppressWarnings("serial") +public class OverviewCanvas extends JPanel { private static final Color TRANS_GREY = new Color(100, 100, 100, 25); - private BufferedImage miniMe; + // This is set true if the alignment view changes whilst + // the overview is being calculated + private volatile boolean restart = false; - private BufferedImage lastMiniMe = null; + private volatile boolean updaterunning = false; - public boolean updating = false; + private boolean disposed = false; - // This is set true if the user resizes whilst - // the overview is being calculated - public volatile boolean updateAgain = false; + BufferedImage lastMiniMe = null; // Can set different properties in this seqCanvas than // main visible SeqCanvas @@ -33,201 +55,268 @@ public class OverviewCanvas extends JComponent private jalview.renderer.seqfeatures.FeatureRenderer fr; - private final AnnotationRenderer renderer = new AnnotationRenderer(); + private OverviewDimensions od; + + private OverviewRenderer or = null; + + private AlignViewportI av; + + private OverviewResColourFinder cf; - OverviewDimensions od; + private ProgressPanel progressPanel; - OverviewPanel op; + private boolean showSequenceFeatures; - AlignViewport av; + private boolean showAnnotation; - AlignmentPanel ap; + private jalview.api.FeatureRenderer featureRenderer; - public OverviewCanvas(OverviewDimensions overviewDims, - AlignViewportI alignvp, AlignmentPanel alignp, OverviewPanel overp) + private OverviewPanel panel; + + private boolean showProgress; + + public OverviewCanvas(OverviewPanel panel, + OverviewDimensions overviewDims, + AlignViewportI alignvp, ProgressPanel pp) { + this.panel = panel; od = overviewDims; - av = alignp.av; - ap = alignp; - op = overp; - + lastMiniMe = null; + av = alignvp; + progressPanel = pp; + showProgress = (pp != null); sr = new SequenceRenderer(av); sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(ap); + fr = new jalview.renderer.seqfeatures.FeatureRenderer(av); + + boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false); + Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol); + + setSize(od.getWidth(), od.getHeight()); + setPreferredSize(getSize()); // BH 2019.07.29 added } - public void draw(boolean showSequenceFeatures, boolean showAnnotation) + /** + * Update the overview dimensions object used by the canvas (e.g. if we change + * from showing hidden columns to hiding them or vice versa) + * + * @param overviewDims + */ + public void resetOviewDims(OverviewDimensions overviewDims) { - miniMe = null; + od = overviewDims; + lastMiniMe = null; + } - if (showSequenceFeatures) + /** + * Signals to drawing code that the associated alignment viewport has changed + * and a redraw will be required + */ + public boolean restartDraw() + { + synchronized (this) { - fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + if (updaterunning) + { + setRestart("restartDraw"); + } + else + { + updaterunning = true; + restart = false; + } + return restart; } + } - // why do we need to set preferred size again? was set in - // updateOverviewImage - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - - miniMe = new BufferedImage(od.getWidth(), od.getHeight(), - BufferedImage.TYPE_INT_RGB); - - Graphics mg = miniMe.getGraphics(); - mg.setColor(Color.orange); - mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight()); - - // calculate sampleCol and sampleRow - // alignment width is max number of residues/bases - // alignment height is number of sequences - int alwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getAbsoluteHeight(); - - // sampleCol or sampleRow is the width/height allocated to each residue - // in particular, sometimes we may need more than one row/col of the - // BufferedImage allocated - // sampleCol is how much of a residue to assign to each pixel - // sampleRow is how many sequences to assign to each pixel - float sampleCol = alwidth / (float) od.getWidth(); - float sampleRow = alheight / (float) od.getSequencesHeight(); - - buildImage(sampleRow, sampleCol); - - if (showAnnotation) + private void setRestart(String why) + { + // System.out.println("OC restart true " + why); + restart = true; + if (or != null) { - renderer.updateFromAlignViewport(av); - for (int col = 0; col < od.getWidth() && !updateAgain; col++) - { - mg.translate(col, od.getSequencesHeight()); - renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), - av.getAlignmentConservationAnnotation().annotations, - (int) (sampleCol) + 1, od.getGraphHeight(), - (int) (col * sampleCol), (int) (col * sampleCol) + 1); - mg.translate(-col, -od.getSequencesHeight()); + or.setRedraw(true); + } + } - } + /** + * Draw the overview sequences + * + * @param showSequenceFeatures + * true if sequence features are to be shown + * @param showAnnotation + * true if the annotation is to be shown + * @param featureRenderer + * the renderer to transfer feature colouring from + */ + public void draw(boolean showSequenceFeatures, boolean showAnnotation, + jalview.api.FeatureRenderer featureRenderer) + { + this.showSequenceFeatures = showSequenceFeatures; + this.showAnnotation = showAnnotation; + this.featureRenderer = featureRenderer; + if (showSequenceFeatures) + { + fr.transferSettings(featureRenderer); } - System.gc(); + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + AlignmentI al = av.getAlignment(); + or = new OverviewRenderer(panel.ap, fr, od, al, av.getResidueShading(), + cf, showProgress); + if (showProgress) + { + or.addPropertyChangeListener(progressPanel); + } + or.drawMiniMe(); + } - updating = false; + synchronized void finalizeDraw(BufferedImage miniMe) + { - if (updateAgain) + if (showProgress && or != null) { - updateAgain = false; - op.updateOverviewImage(); + or.removePropertyChangeListener(progressPanel); + } + if (restart) + { + or = null; + restart = false; + if (!disposed) + { + draw(showSequenceFeatures, showAnnotation, featureRenderer); + } } else { + if (showAnnotation && or != null) + { + or.drawGraph(av.getAlignmentConservationAnnotation()); + } + or = null; + updaterunning = false; lastMiniMe = miniMe; + repaint(); } } @Override public void paintComponent(Graphics g) { - if (updating || updateAgain) + + int w = getWidth(); + int h = getHeight(); + if (w == 0 || od.getBoxWidth() <= 0) + { + // BH 2019.07.27 removes two unnecessary paints, since boxwidth can be -1 + // or 0 during early-stage painting + return; + } + + boolean drawMe = (lastMiniMe != null); + if (restart) { - if (lastMiniMe == null) + if (drawMe) { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + g.drawImage(lastMiniMe, 0, 0, w, h, this); } else { - g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + g.setColor(Color.white); + g.fillRect(0, 0, w, h); } g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); + g.fillRect(0, 0, w, h); + drawMe = false; } - else if (lastMiniMe != null) + else if (drawMe) { - g.drawImage(lastMiniMe, 0, 0, this); - if (lastMiniMe != miniMe) + // is this a resize? + if (w != od.getWidth() || h != od.getHeight()) { - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); + + lastMiniMe = null; + return; + // // if there is annotation, scale the alignment and annotation + // // separately + // if (od.getGraphHeight() <= 0 && od.getSequencesHeight() <= 0) + // { + // od.setWidth(w); + // od.setHeight(h); + // return; + // } + // try + // { + // BufferedImage topImage = lastMiniMe.getSubimage(0, 0, + // od.getWidth(), od.getSequencesHeight()); + // + // BufferedImage bottomImage = lastMiniMe.getSubimage(0, + // od.getSequencesHeight(), od.getWidth(), + // od.getGraphHeight()); + // + // // must be done at this point as we rely on using old width/height + // // above, and new width/height below + // od.setWidth(w); + // od.setHeight(h); + // + // // stick the images back together so lastMiniMe is consistent in the + // // event of a repaint - BUT probably not thread safe + // + // // right -- this fails with fast user action. + // + // lastMiniMe = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB); + // Graphics lg = lastMiniMe.getGraphics(); + // lg.drawImage(topImage, 0, 0, w, od.getSequencesHeight(), null); + // lg.drawImage(bottomImage, 0, od.getSequencesHeight(), w, + // od.getGraphHeight(), this); + // lg.dispose(); + // + // } catch (RasterFormatException e) + // { + // System.out.println("OC Raster Exception " + lastMiniMe.getWidth() + // + "/" + w + "," + lastMiniMe.getHeight() + "/" + h + " " + // + od.getSequencesHeight() + " " + od.getGraphHeight()); + // } + // BH 2019: removed -- this is now taken care of using vpbox in + // OverviewDimension + // // make sure the box is in the right place + // od.setBoxPosition(av.getAlignment().getHiddenSequences(), + // av.getAlignment().getHiddenColumns()); } } + if (drawMe) + { + g.drawImage(lastMiniMe, 0, 0, w, h, this); + } + // draw the box g.setColor(Color.red); + // System.out.println("OC paintComponent nd=" + ndraw + " nr=" + nrepaint + // + " np=" + ++npaint); od.drawBox(g); } - /* - * Build the overview panel image - */ - private void buildImage(float sampleRow, float sampleCol) - { - int lastcol = -1; - int lastrow = -1; - int rgbcolor = Color.white.getRGB(); - - SequenceI seq = null; - FeatureColourFinder finder = new FeatureColourFinder(fr); - - final boolean hasHiddenCols = av.hasHiddenColumns(); - boolean hiddenRow = false; - // get hidden row and hidden column map once at beginning. - // clone featureRenderer settings to avoid race conditions... if state is - // updated just need to refresh again - for (int row = 0; row < od.getSequencesHeight() && !updateAgain; row++) - { - boolean doCopy = true; - int currentrow = (int) (row * sampleRow); - if (currentrow != lastrow) - { - doCopy = false; + // private int ndraw, npaint, nrepaint; - lastrow = currentrow; - - // get the sequence which would be at alignment index 'lastrow' if no - // rows were hidden, and determine whether it is hidden or not - hiddenRow = av.getAlignment().isHidden(lastrow); - seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow); - } - - for (int col = 0; col < od.getWidth() && !updateAgain; col++) - { - if (doCopy) - { - rgbcolor = miniMe.getRGB(col, row - 1); - } - else if ((int) (col * sampleCol) != lastcol - || (int) (row * sampleRow) != lastrow) - { - lastcol = (int) (col * sampleCol); - rgbcolor = getColumnColourFromSequence(seq, hiddenRow, - hasHiddenCols, lastcol, finder); - } - // else we just use the color we already have , so don't need to set it - - miniMe.setRGB(col, row, rgbcolor); - } - } - } + // @Override + // public void repaint() + // { + // System.out.println("OC repaint " + (++nrepaint)); + // super.repaint(); + // } - /* - * Find the colour of a sequence at a specified column position - */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol, - FeatureColourFinder finder) + public void dispose() { - Color color = Color.white; - - if ((seq != null) && (seq.getLength() > lastcol)) + disposed = true; + od = null; + lastMiniMe = null; + synchronized (this) { - color = sr.getResidueColour(seq, lastcol, finder); + setRestart("dispose"); } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection() - .isVisible(lastcol))) - { - color = color.darker().darker(); - } - - return color.getRGB(); } }