From 3b5d07562d8974f2fde820a1390c404d8734ebeb Mon Sep 17 00:00:00 2001 From: kiramt Date: Thu, 23 Mar 2017 13:46:36 +0000 Subject: [PATCH] JAL-2388 Factored out applet overview canvas, threading adjustments --- src/jalview/appletgui/OverviewCanvas.java | 256 +++++++++++++++++++++++++++++ src/jalview/appletgui/OverviewPanel.java | 220 +++---------------------- src/jalview/gui/OverviewCanvas.java | 18 +- src/jalview/gui/OverviewPanel.java | 8 +- 4 files changed, 293 insertions(+), 209 deletions(-) create mode 100644 src/jalview/appletgui/OverviewCanvas.java diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java new file mode 100644 index 0000000..dea8ddc --- /dev/null +++ b/src/jalview/appletgui/OverviewCanvas.java @@ -0,0 +1,256 @@ +/* + * 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.appletgui; + +import jalview.datamodel.SequenceI; +import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.viewmodel.OverviewDimensions; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Image; + +import javax.swing.JComponent; + +public class OverviewCanvas extends JComponent +{ + // This is set true if the alignment view changes whilst + // the overview is being calculated + private volatile boolean restart = false; + + private volatile boolean updaterunning = false; + + private OverviewDimensions od; + + private Image miniMe; + + private Image offscreen; + + private AlignViewport av; + + private AlignmentPanel ap; + + // Can set different properties in this seqCanvas than + // main visible SeqCanvas + private SequenceRenderer sr; + + private FeatureRenderer fr; + + private Frame nullFrame; + + public OverviewCanvas(OverviewDimensions overviewDims, + AlignViewport alignvp, AlignmentPanel alignp) + { + od = overviewDims; + av = alignp.av; + ap = alignp; + + nullFrame = new Frame(); + nullFrame.addNotify(); + + sr = new SequenceRenderer(av); + sr.graphics = nullFrame.getGraphics(); + sr.renderGaps = false; + sr.forOverview = true; + fr = new FeatureRenderer(av); + } + + /* + * Signals to drawing code that the associated alignment viewport + * has changed and a redraw will be required + */ + public boolean restartDraw() + { + synchronized (this) + { + if (updaterunning) + { + restart = true; + } + else + { + updaterunning = true; + } + return restart; + } + } + + public void draw(boolean showSequenceFeatures, boolean showAnnotation) + { + miniMe = null; + + if (av.isShowSequenceFeatures()) + { + fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); + } + + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + + miniMe = nullFrame.createImage(od.getWidth(), od.getHeight()); + offscreen = nullFrame.createImage(od.getWidth(), od.getHeight()); + + Graphics mg = miniMe.getGraphics(); + + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getAbsoluteHeight(); + float sampleCol = alwidth / (float) od.getWidth(); + float sampleRow = alheight / (float) od.getSequencesHeight(); + + buildImage(sampleRow, sampleCol, mg); + + // check for conservation annotation to make sure overview works for DNA too + if (showAnnotation) + { + for (int col = 0; col < od.getWidth() && !restart; col++) + { + mg.translate(col, od.getSequencesHeight()); + ap.annotationPanel.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()); + } + } + System.gc(); + + if (restart) + { + restart = false; + draw(showSequenceFeatures, showAnnotation); + } + else + { + updaterunning = false; + } + } + + /* + * Build the overview panel image + */ + private void buildImage(float sampleRow, float sampleCol, Graphics mg) + { + int lastcol = 0; + int lastrow = 0; + int xstart = 0; + int ystart = 0; + Color color = Color.yellow; + int sameRow = 0; + int sameCol = 0; + + SequenceI seq = null; + FeatureColourFinder finder = new FeatureColourFinder(fr); + + final boolean hasHiddenCols = av.hasHiddenColumns(); + boolean hiddenRow = false; + + for (int row = 0; row < od.getSequencesHeight() && !restart; row++) + { + if ((int) (row * sampleRow) == lastrow) + { + sameRow++; + } + else + { + // 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(); col++) + { + if ((int) (col * sampleCol) == lastcol + && (int) (row * sampleRow) == lastrow) + { + sameCol++; + } + else + { + lastcol = (int) (col * sampleCol); + + color = getColumnColourFromSequence(seq, hiddenRow, + hasHiddenCols, lastcol, finder); + + mg.setColor(color); + if (sameCol == 1 && sameRow == 1) + { + mg.drawLine(xstart, ystart, xstart, ystart); + } + else + { + mg.fillRect(xstart, ystart, sameCol, sameRow); + } + + xstart = col; + sameCol = 1; + } + } + lastrow = (int) (row * sampleRow); + ystart = row; + sameRow = 1; + } + } + } + + /* + * Find the colour of a sequence at a specified column position + */ + private Color getColumnColourFromSequence( + jalview.datamodel.SequenceI seq, boolean hiddenRow, + boolean hasHiddenCols, int lastcol, FeatureColourFinder finder) + { + Color color = Color.white; + if (seq.getLength() > lastcol) + { + color = sr.getResidueColour(seq, lastcol, finder); + } + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) + { + color = color.darker().darker(); + } + return color; + } + + @Override + public void update(Graphics g) + { + paint(g); + } + + @Override + public void paint(Graphics g) + { + Graphics og = offscreen.getGraphics(); + if (miniMe != null) + { + og.drawImage(miniMe, 0, 0, this); + og.setColor(Color.red); + od.drawBox(og); + g.drawImage(offscreen, 0, 0, this); + } + } + +} diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 3ef2936..8962bdc 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -20,15 +20,10 @@ */ package jalview.appletgui; -import jalview.datamodel.SequenceI; -import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.viewmodel.OverviewDimensions; -import java.awt.Color; +import java.awt.BorderLayout; import java.awt.Dimension; -import java.awt.Frame; -import java.awt.Graphics; -import java.awt.Image; import java.awt.Panel; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; @@ -41,45 +36,27 @@ public class OverviewPanel extends Panel implements Runnable, { private OverviewDimensions od; - private Image miniMe; - - private Image offscreen; + private OverviewCanvas oviewCanvas; private AlignViewport av; private AlignmentPanel ap; - private boolean resizing = false; - - // This is set true if the user resizes whilst - // the overview is being calculated - private boolean resizeAgain = false; - - // Can set different properties in this seqCanvas than - // main visible SeqCanvas - private SequenceRenderer sr; - - private FeatureRenderer fr; - - private Frame nullFrame; + private boolean updateRunning = false; public OverviewPanel(AlignmentPanel alPanel) { this.av = alPanel.av; this.ap = alPanel; setLayout(null); - nullFrame = new Frame(); - nullFrame.addNotify(); - - sr = new SequenceRenderer(av); - sr.graphics = nullFrame.getGraphics(); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(av); od = new OverviewDimensions(av.getRanges(), (av.isShowAnnotation() && av.getSequenceConsensusHash() != null)); + oviewCanvas = new OverviewCanvas(od, av, ap); + setLayout(new BorderLayout()); + add(oviewCanvas, BorderLayout.CENTER); + setSize(new Dimension(od.getWidth(), od.getHeight())); addComponentListener(new ComponentAdapter() { @@ -155,19 +132,6 @@ public class OverviewPanel extends Panel implements Runnable, */ public void updateOverviewImage() { - if (resizing) - { - resizeAgain = true; - return; - } - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.seqPanel.seqCanvas.fr); - } - - resizing = true; - if ((getSize().width > 0) && (getSize().height > 0)) { od.setWidth(getSize().width); @@ -175,156 +139,26 @@ public class OverviewPanel extends Panel implements Runnable, } setSize(new Dimension(od.getWidth(), od.getHeight())); + if (updateRunning) + { + oviewCanvas.restartDraw(); + return; + } + + updateRunning = true; Thread thread = new Thread(this); thread.start(); repaint(); + updateRunning = false; } @Override public void run() { - miniMe = null; - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); - } - - if (getSize().width > 0 && getSize().height > 0) - { - od.setWidth(getSize().width); - od.setHeight(getSize().height); - } - - setSize(new Dimension(od.getWidth(), od.getHeight())); - - miniMe = nullFrame.createImage(od.getWidth(), od.getHeight()); - offscreen = nullFrame.createImage(od.getWidth(), od.getHeight()); - - Graphics mg = miniMe.getGraphics(); - - int alwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getAbsoluteHeight(); - float sampleCol = alwidth / (float) od.getWidth(); - float sampleRow = alheight / (float) od.getSequencesHeight(); - - buildImage(sampleRow, sampleCol, mg); - - // check for conservation annotation to make sure overview works for DNA too - if (av.isShowAnnotation() - && (av.getAlignmentConservationAnnotation() != null)) - { - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - mg.translate(col, od.getSequencesHeight()); - ap.annotationPanel.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()); - } - } - System.gc(); - - resizing = false; - + oviewCanvas.draw(av.isShowSequenceFeatures(), + (av.isShowAnnotation() && av + .getAlignmentConservationAnnotation() != null)); setBoxPosition(); - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - } - - /* - * Build the overview panel image - */ - private void buildImage(float sampleRow, float sampleCol, Graphics mg) - { - int lastcol = 0; - int lastrow = 0; - int xstart = 0; - int ystart = 0; - Color color = Color.yellow; - int sameRow = 0; - int sameCol = 0; - - SequenceI seq = null; - FeatureColourFinder finder = new FeatureColourFinder(fr); - - final boolean hasHiddenCols = av.hasHiddenColumns(); - boolean hiddenRow = false; - - for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++) - { - if ((int) (row * sampleRow) == lastrow) - { - sameRow++; - } - else - { - // get the sequence which would be at alignment index 'lastrow' if no - // columns 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(); col++) - { - if ((int) (col * sampleCol) == lastcol - && (int) (row * sampleRow) == lastrow) - { - sameCol++; - } - else - { - lastcol = (int) (col * sampleCol); - - color = getColumnColourFromSequence(seq, hiddenRow, - hasHiddenCols, lastcol, finder); - - mg.setColor(color); - if (sameCol == 1 && sameRow == 1) - { - mg.drawLine(xstart, ystart, xstart, ystart); - } - else - { - mg.fillRect(xstart, ystart, sameCol, sameRow); - } - - xstart = col; - sameCol = 1; - } - } - lastrow = (int) (row * sampleRow); - ystart = row; - sameRow = 1; - } - } - } - - /* - * Find the colour of a sequence at a specified column position - */ - private Color getColumnColourFromSequence( - jalview.datamodel.SequenceI seq, boolean hiddenRow, - boolean hasHiddenCols, int lastcol, FeatureColourFinder finder) - { - Color color = Color.white; - if (seq.getLength() > lastcol) - { - color = sr.getResidueColour(seq, lastcol, finder); - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection() - .isVisible(lastcol))) - { - color = color.darker().darker(); - } - return color; } /** @@ -339,23 +173,7 @@ public class OverviewPanel extends Panel implements Runnable, repaint(); } - @Override - public void update(Graphics g) - { - paint(g); - } - @Override - public void paint(Graphics g) - { - Graphics og = offscreen.getGraphics(); - if (miniMe != null) - { - og.drawImage(miniMe, 0, 0, this); - og.setColor(Color.red); - od.drawBox(og); - g.drawImage(offscreen, 0, 0, this); - } - } + } diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index df831e1..8c02423 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -42,6 +42,8 @@ public class OverviewCanvas extends JComponent // the overview is being calculated private volatile boolean restart = false; + private volatile boolean updaterunning = false; + private BufferedImage miniMe; private BufferedImage lastMiniMe = null; @@ -79,9 +81,20 @@ public class OverviewCanvas extends JComponent * Signals to drawing code that the associated alignment viewport * has changed and a redraw will be required */ - public void restartDraw() + public boolean restartDraw() { - restart = true; + synchronized (this) + { + if (updaterunning) + { + restart = true; + } + else + { + updaterunning = true; + } + return restart; + } } public void draw(boolean showSequenceFeatures, boolean showAnnotation) @@ -143,6 +156,7 @@ public class OverviewCanvas extends JComponent } else { + updaterunning = false; lastMiniMe = miniMe; } } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index bc4a19f..faa94e9 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -49,8 +49,6 @@ public class OverviewPanel extends JPanel implements Runnable private AlignmentPanel ap; - boolean updateRunning = false; - /** * Creates a new OverviewPanel object. * @@ -129,17 +127,15 @@ public class OverviewPanel extends JPanel implements Runnable setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - if (updateRunning) + if (oviewCanvas.restartDraw()) { - oviewCanvas.restartDraw(); return; } - updateRunning = true; Thread thread = new Thread(this); thread.start(); repaint(); - updateRunning = false; + } @Override -- 1.7.10.2