X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=1b5d5da4bb677d3f4ba3584ef1227f3a400958f4;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=48dcf3cdf96f89dacdb0bc024adcfed5e8d99cf9;hpb=4b05014f4458eccd740e8ce94be255323687c302;p=jalview.git diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java index 48dcf3c..1b5d5da 100644 --- a/src/jalview/renderer/OverviewRenderer.java +++ b/src/jalview/renderer/OverviewRenderer.java @@ -22,8 +22,11 @@ package jalview.renderer; import jalview.api.AlignmentColsCollectionI; import jalview.api.AlignmentRowsCollectionI; +import jalview.api.RendererListenerI; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.renderer.seqfeatures.FeatureRenderer; @@ -34,12 +37,21 @@ import java.awt.Color; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.image.BufferedImage; +import java.beans.PropertyChangeSupport; public class OverviewRenderer { - private FeatureColourFinder finder; + // transparency of hidden cols/seqs overlay + private final float TRANSPARENCY = 0.5f; + + public static final String UPDATE = "OverviewUpdate"; + + private static final int MAX_PROGRESS = 100; + + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); - private jalview.api.SequenceRenderer sr; + private FeatureColourFinder finder; // image to render on private BufferedImage miniMe; @@ -50,17 +62,32 @@ public class OverviewRenderer // raw number of pixels to allocate to each row private float pixelsPerSeq; + // height in pixels of graph + private int graphHeight; + // flag to indicate whether to halt drawing private volatile boolean redraw = false; - public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer, - FeatureRenderer fr, OverviewDimensions od) + // reference to alignment, needed to get sequence groups + private AlignmentI al; + + private ResidueShaderI shader; + + private OverviewResColourFinder resColFinder; + + public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od, + AlignmentI alignment, ResidueShaderI resshader, + OverviewResColourFinder colFinder) { - sr = seqRenderer; finder = new FeatureColourFinder(fr); + resColFinder = colFinder; + + al = alignment; + shader = resshader; pixelsPerCol = od.getPixelsPerCol(); pixelsPerSeq = od.getPixelsPerSeq(); + graphHeight = od.getGraphHeight(); miniMe = new BufferedImage(od.getWidth(), od.getHeight(), BufferedImage.TYPE_INT_RGB); } @@ -80,9 +107,12 @@ public class OverviewRenderer int rgbcolor = Color.white.getRGB(); int seqIndex = 0; int pixelRow = 0; + int alignmentHeight = miniMe.getHeight() - graphHeight; + int totalPixels = miniMe.getWidth() * alignmentHeight; - BufferedImage hiddenImage = buildHiddenImage(rows, cols, - miniMe.getWidth(), miniMe.getHeight()); + int lastRowUpdate = 0; + int lastUpdate = 0; + changeSupport.firePropertyChange(UPDATE, -1, 0); for (int alignmentRow : rows) { @@ -90,14 +120,17 @@ public class OverviewRenderer { break; } - + // get details of this alignment row SequenceI seq = rows.getSequence(alignmentRow); - + + // rate limiting step when rendering overview for lots of groups + SequenceGroup[] allGroups = al.findAllGroups(seq); + // calculate where this row extends to in pixels int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1, miniMe.getHeight() - 1); - + int colIndex = 0; int pixelCol = 0; for (int alignmentCol : cols) @@ -106,21 +139,19 @@ public class OverviewRenderer { break; } - + // calculate where this column extends to in pixels - int endCol = Math.min( - Math.round((colIndex + 1) * pixelsPerCol) - 1, + int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, miniMe.getWidth() - 1); - + // don't do expensive colour determination if we're not going to use it // NB this is important to avoid performance issues in the overview // panel if (pixelCol <= endCol) { - rgbcolor = getColumnColourFromSequence(seq, - alignmentCol, - finder); - + rgbcolor = getColumnColourFromSequence(allGroups, seq, + alignmentCol); + // fill in the appropriate number of pixels for (int row = pixelRow; row <= endRow; ++row) { @@ -129,46 +160,118 @@ public class OverviewRenderer miniMe.setRGB(col, row, rgbcolor); } } - + + // store last update value + lastUpdate = sendProgressUpdate( + (pixelCol + 1) * (endRow - pixelRow), totalPixels, + lastRowUpdate, lastUpdate); + pixelCol = endCol + 1; } colIndex++; } - pixelRow = endRow + 1; + + if (pixelRow != endRow + 1) + { + // store row offset and last update value + lastRowUpdate = sendProgressUpdate(endRow + 1, alignmentHeight, 0, + lastUpdate); + lastUpdate = lastRowUpdate; + pixelRow = endRow + 1; + } seqIndex++; } - return applyMask(hiddenImage, miniMe); + overlayHiddenRegions(rows, cols); + // final update to progress bar if present + if (redraw) + { + sendProgressUpdate(pixelRow - 1, alignmentHeight, 0, 0); + } + else + { + sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0, 0); + } + return miniMe; } /* - * Find the colour of a sequence at a specified column position + * Calculate progress update value and fire event + * @param rowOffset number of rows to offset calculation by + * @return new rowOffset - return value only to be used when at end of a row */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - int lastcol, FeatureColourFinder fcfinder) + private int sendProgressUpdate(int position, int maximum, int rowOffset, + int lastUpdate) { - Color color = Color.white; + int newUpdate = rowOffset + + Math.round(MAX_PROGRESS * ((float) position / maximum)); + if (newUpdate > lastUpdate) + { + changeSupport.firePropertyChange(UPDATE, rowOffset, newUpdate); + return newUpdate; + } + return newUpdate; + } + + /* + * Find the RGB value of the colour of a sequence at a specified column position + * + * @param seq + * sequence to get colour for + * @param lastcol + * column position to get colour for + * @return colour of sequence at this position, as RGB + */ + int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq, + int lastcol) + { + Color color = resColFinder.GAP_COLOUR; if ((seq != null) && (seq.getLength() > lastcol)) { - color = sr.getResidueColour(seq, lastcol, fcfinder); + color = resColFinder.getResidueColour(true, shader, allGroups, seq, + lastcol, finder); } return color.getRGB(); } - private BufferedImage applyMask(BufferedImage mask, BufferedImage image) + /** + * Overlay the hidden regions on the overview image + * + * @param rows + * collection of rows the overview is built over + * @param cols + * collection of columns the overview is built over + */ + private void overlayHiddenRegions(AlignmentRowsCollectionI rows, + AlignmentColsCollectionI cols) { - Graphics2D g = (Graphics2D) image.getGraphics(); - g.setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.5f)); - g.drawImage(mask, 0, 0, image.getWidth(), image.getHeight(), null); - return image; + if (cols.hasHidden() || rows.hasHidden()) + { + BufferedImage mask = buildHiddenImage(rows, cols, miniMe.getWidth(), + miniMe.getHeight()); + + Graphics2D g = (Graphics2D) miniMe.getGraphics(); + g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + TRANSPARENCY)); + g.drawImage(mask, 0, 0, miniMe.getWidth(), miniMe.getHeight(), null); + } } - /* - * Build a masking image of hidden columns and rows to be applied on top - * of the main overview image. + /** + * Build a masking image of hidden columns and rows to be applied on top of + * the main overview image. + * + * @param rows + * collection of rows the overview is built over + * @param cols + * collection of columns the overview is built over + * @param width + * width of overview in pixels + * @param height + * height of overview in pixels + * @return BufferedImage containing mask of hidden regions */ private BufferedImage buildHiddenImage(AlignmentRowsCollectionI rows, AlignmentColsCollectionI cols, int width, int height) @@ -180,13 +283,13 @@ public class OverviewRenderer int colIndex = 0; int pixelCol = 0; - Color hidden = Color.DARK_GRAY; + Color hidden = resColFinder.getHiddenColour(); Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics(); // set background to transparent - g2d.setComposite(AlphaComposite.Clear); - g2d.fillRect(0, 0, width, height); + // g2d.setComposite(AlphaComposite.Clear); + // g2d.fillRect(0, 0, width, height); // set next colour to opaque g2d.setComposite(AlphaComposite.Src); @@ -250,15 +353,13 @@ public class OverviewRenderer * the graphics object to draw on * @param anno * alignment annotation information - * @param charWidth - * alignment character width value * @param y * y-position for the annotation graph * @param cols * the collection of columns used in the overview panel */ - public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth, - int y, AlignmentColsCollectionI cols) + public void drawGraph(Graphics g, AlignmentAnnotation anno, int y, + AlignmentColsCollectionI cols) { Annotation[] annotations = anno.annotations; g.setColor(Color.white); @@ -271,16 +372,17 @@ public class OverviewRenderer { if (redraw) { + changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, 0); break; } + if (alignmentCol >= annotations.length) { break; // no more annotations to draw here } else { - int endCol = Math.min( - Math.round((colIndex + 1) * pixelsPerCol) - 1, + int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, miniMe.getWidth() - 1); if (annotations[alignmentCol] != null) @@ -294,7 +396,8 @@ public class OverviewRenderer g.setColor(annotations[alignmentCol].colour); } - height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y); + height = (int) ((annotations[alignmentCol].value / anno.graphMax) + * y); if (height > y) { height = y; @@ -302,12 +405,22 @@ public class OverviewRenderer g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height); } + pixelCol = endCol + 1; colIndex++; } } + changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, + MAX_PROGRESS); } + /** + * Allows redraw flag to be set + * + * @param b + * value to set redraw to: true = redraw is occurring, false = no + * redraw + */ public void setRedraw(boolean b) { synchronized (this) @@ -315,4 +428,14 @@ public class OverviewRenderer redraw = b; } } + + public void addPropertyChangeListener(RendererListenerI listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(RendererListenerI listener) + { + changeSupport.removePropertyChangeListener(listener); + } }