From e5b6a315d9cffef8b66a8be031c4cdb542fb3a6e Mon Sep 17 00:00:00 2001 From: kiramt Date: Tue, 21 Mar 2017 15:38:01 +0000 Subject: [PATCH] JAL-2388 Unpleasant but operational refactor into OverviewCanvas --- src/jalview/gui/OverviewCanvas.java | 243 +++++++++++++++++++++++++++++++++++ src/jalview/gui/OverviewPanel.java | 226 ++------------------------------ 2 files changed, 253 insertions(+), 216 deletions(-) create mode 100644 src/jalview/gui/OverviewCanvas.java diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java new file mode 100644 index 0000000..ba5881e --- /dev/null +++ b/src/jalview/gui/OverviewCanvas.java @@ -0,0 +1,243 @@ +package jalview.gui; + +import jalview.api.AlignViewportI; +import jalview.datamodel.SequenceI; +import jalview.renderer.AnnotationRenderer; +import jalview.viewmodel.OverviewDimensions; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Graphics; +import java.awt.image.BufferedImage; + +import javax.swing.JComponent; + +public class OverviewCanvas extends JComponent +{ + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); + + private BufferedImage miniMe; + + private BufferedImage lastMiniMe = null; + + public boolean resizing = false; + + // This is set true if the user resizes whilst + // the overview is being calculated + public boolean resizeAgain = false; + + // Can set different properties in this seqCanvas than + // main visible SeqCanvas + private SequenceRenderer sr; + + private jalview.renderer.seqfeatures.FeatureRenderer fr; + + private final AnnotationRenderer renderer = new AnnotationRenderer(); + + OverviewDimensions od; + + OverviewPanel op; + + AlignViewport av; + + AlignmentPanel ap; + + public OverviewCanvas(OverviewDimensions overviewDims, + AlignViewportI alignvp, AlignmentPanel alignp, OverviewPanel overp) + { + od = overviewDims; + av = alignp.av; + ap = alignp; + op = overp; + + sr = new SequenceRenderer(av); + sr.renderGaps = false; + sr.forOverview = true; + fr = new FeatureRenderer(ap); + } + + public void draw(boolean showSequenceFeatures, boolean showAnnotation) + { + miniMe = null; + + if (showSequenceFeatures) + { + fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + } + + // 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) + { + renderer.updateFromAlignViewport(av); + for (int col = 0; col < od.getWidth() && !resizeAgain; 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()); + + } + } + System.gc(); + + resizing = false; + + if (resizeAgain) + { + resizeAgain = false; + op.updateOverviewImage(); + } + else + { + lastMiniMe = miniMe; + } + } + + @Override + public void paintComponent(Graphics g) + { + if (resizing || resizeAgain) + { + if (lastMiniMe == null) + { + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); + } + else + { + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + } + g.setColor(TRANS_GREY); + g.fillRect(0, 0, getWidth(), getHeight()); + } + else if (lastMiniMe != null) + { + g.drawImage(lastMiniMe, 0, 0, this); + if (lastMiniMe != miniMe) + { + g.setColor(TRANS_GREY); + g.fillRect(0, 0, getWidth(), getHeight()); + } + } + + g.setColor(Color.red); + od.drawBox(g); + } + + /* + * Build the overview panel image + */ + private void buildImage(float sampleRow, float sampleCol) + { + int lastcol = -1; + int lastrow = -1; + int color = Color.white.getRGB(); + + SequenceI seq = null; + + 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() && !resizeAgain; row++) + { + boolean doCopy = true; + int currentrow = (int) (row * sampleRow); + if (currentrow != lastrow) + { + doCopy = false; + + 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() && !resizeAgain; col++) + { + if (doCopy) + { + color = miniMe.getRGB(col, row - 1); + } + else if ((int) (col * sampleCol) != lastcol + || (int) (row * sampleRow) != lastrow) + { + lastcol = (int) (col * sampleCol); + color = getColumnColourFromSequence(seq, hiddenRow, + hasHiddenCols, lastcol); + } + // else we just use the color we already have , so don't need to set it + + miniMe.setRGB(col, row, color); + } + } + } + + /* + * Find the colour of a sequence at a specified column position + */ + private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, + boolean hiddenRow, boolean hasHiddenCols, int lastcol) + { + int color; + + if (seq == null) + { + color = Color.white.getRGB(); + } + else if (seq.getLength() > lastcol) + { + color = sr.getResidueBoxColour(seq, lastcol).getRGB(); + + if (av.isShowSequenceFeatures()) + { + color = fr.findFeatureColour(color, seq, lastcol); + } + } + else + { + color = Color.white.getRGB(); + } + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) + { + color = new Color(color).darker().darker().getRGB(); + } + + return color; + } + +} diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 67cdbc2..01ca978 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,19 +20,15 @@ */ package jalview.gui; -import jalview.datamodel.SequenceI; -import jalview.renderer.AnnotationRenderer; import jalview.viewmodel.OverviewDimensions; -import java.awt.Color; +import java.awt.BorderLayout; import java.awt.Dimension; -import java.awt.Graphics; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.MouseMotionAdapter; -import java.awt.image.BufferedImage; import javax.swing.JPanel; @@ -45,33 +41,14 @@ import javax.swing.JPanel; */ public class OverviewPanel extends JPanel implements Runnable { - private static final Color TRANS_GREY = new Color(100, 100, 100, 25); - - private final AnnotationRenderer renderer = new AnnotationRenderer(); - private OverviewDimensions od; - private BufferedImage miniMe; - - private BufferedImage lastMiniMe = null; + 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 jalview.renderer.seqfeatures.FeatureRenderer fr; - /** * Creates a new OverviewPanel object. * @@ -82,15 +59,13 @@ public class OverviewPanel extends JPanel implements Runnable { this.av = alPanel.av; this.ap = alPanel; - setLayout(null); - - sr = new SequenceRenderer(av); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(alPanel); od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation()); + oviewCanvas = new OverviewCanvas(od, av, ap, this); + setLayout(new BorderLayout()); + add(oviewCanvas, BorderLayout.CENTER); + addComponentListener(new ComponentAdapter() { @Override @@ -142,13 +117,13 @@ public class OverviewPanel extends JPanel implements Runnable */ public void updateOverviewImage() { - if (resizing) + if (oviewCanvas.resizing) { - resizeAgain = true; + oviewCanvas.resizeAgain = true; return; } - resizing = true; + oviewCanvas.resizing = true; if ((getWidth() > 0) && (getHeight() > 0)) { @@ -166,159 +141,10 @@ public class OverviewPanel extends JPanel implements Runnable @Override public void run() { - miniMe = null; - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); - } - - // 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 (av.isShowAnnotation()) - { - renderer.updateFromAlignViewport(av); - for (int col = 0; col < od.getWidth() && !resizeAgain; 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()); - - } - } - System.gc(); - - resizing = false; - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - else - { - lastMiniMe = miniMe; - } - + oviewCanvas.draw(av.isShowSequenceFeatures(), av.isShowAnnotation()); setBoxPosition(); } - /* - * Build the overview panel image - */ - private void buildImage(float sampleRow, float sampleCol) - { - int lastcol = -1; - int lastrow = -1; - int color = Color.white.getRGB(); - - SequenceI seq = null; - - 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() && !resizeAgain; row++) - { - boolean doCopy = true; - int currentrow = (int) (row * sampleRow); - if (currentrow != lastrow) - { - doCopy = false; - - 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() && !resizeAgain; col++) - { - if (doCopy) - { - color = miniMe.getRGB(col, row - 1); - } - else if ((int) (col * sampleCol) != lastcol - || (int) (row * sampleRow) != lastrow) - { - lastcol = (int) (col * sampleCol); - color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols, - lastcol); - } - // else we just use the color we already have , so don't need to set it - - miniMe.setRGB(col, row, color); - } - } - } - - /* - * Find the colour of a sequence at a specified column position - */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol) - { - int color; - - if (seq == null) - { - color = Color.white.getRGB(); - } - else if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = Color.white.getRGB(); - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection() - .isVisible(lastcol))) - { - color = new Color(color).darker().darker().getRGB(); - } - - return color; - } - /** * Update the overview panel box when the associated alignment panel is * changed @@ -330,36 +156,4 @@ public class OverviewPanel extends JPanel implements Runnable .getHiddenSequences(), av.getColumnSelection(), av.getRanges()); repaint(); } - - - @Override - public void paintComponent(Graphics g) - { - if (resizing || resizeAgain) - { - if (lastMiniMe == null) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - } - else - { - g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); - } - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); - } - else if (lastMiniMe != null) - { - g.drawImage(lastMiniMe, 0, 0, this); - if (lastMiniMe != miniMe) - { - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); - } - } - - g.setColor(Color.red); - od.drawBox(g); - } } -- 1.7.10.2