X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=e9b4de4055e1d4f67d1cccd276e2a3950d4b20e9;hb=2a86b2b3d7b5e8ad3f23d7895637cbfb24685fac;hp=1fb2d89f59910ee88e243bcd91e6cdce34330e6d;hpb=3f03cc818538d68c829869c6341112c44cf648d9;p=jalview.git diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java index 1fb2d89..e9b4de4 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; @@ -34,15 +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 { // transparency of hidden cols/seqs overlay private final float TRANSPARENCY = 0.5f; - private FeatureColourFinder finder; + public static final String UPDATE = "OverviewUpdate"; + + private static final int MAX_PROGRESS = 100; - private jalview.api.SequenceRenderer sr; + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + private FeatureColourFinder finder; // image to render on private BufferedImage miniMe; @@ -53,17 +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); } @@ -83,6 +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; + + int lastRowUpdate = 0; + int lastUpdate = 0; + changeSupport.firePropertyChange(UPDATE, -1, 0); for (int alignmentRow : rows) { @@ -93,7 +123,10 @@ public class OverviewRenderer // 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); @@ -108,8 +141,7 @@ public class OverviewRenderer } // 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 @@ -117,9 +149,8 @@ public class OverviewRenderer // 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) @@ -129,38 +160,77 @@ 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++; } 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 sendProgressUpdate(int position, int maximum, int rowOffset, + int lastUpdate) + { + 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 - * @param fcfinder - * FeatureColourFinder to use * @return colour of sequence at this position, as RGB */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - int lastcol, FeatureColourFinder fcfinder) + int getColumnColourFromSequence(SequenceGroup[] allGroups, + SequenceI seq, int lastcol) { - Color color = Color.white; + 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(); @@ -213,7 +283,7 @@ public class OverviewRenderer int colIndex = 0; int pixelCol = 0; - Color hidden = Color.DARK_GRAY.darker(); + Color hidden = resColFinder.getHiddenColour(); Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics(); @@ -283,15 +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); @@ -304,16 +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) @@ -327,7 +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; @@ -335,10 +405,13 @@ public class OverviewRenderer g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height); } + pixelCol = endCol + 1; colIndex++; } } + changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, + MAX_PROGRESS); } /** @@ -355,4 +428,14 @@ public class OverviewRenderer redraw = b; } } + + public void addPropertyChangeListener(RendererListenerI listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(RendererListenerI listener) + { + changeSupport.removePropertyChangeListener(listener); + } }