X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=1fb2d89f59910ee88e243bcd91e6cdce34330e6d;hb=3f03cc818538d68c829869c6341112c44cf648d9;hp=75b81987f11790c41297788a4347ef5111ec9509;hpb=a714684d20bb1b8423e0e63d6f3257c2bffa850b;p=jalview.git diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java index 75b8198..1fb2d89 100644 --- a/src/jalview/renderer/OverviewRenderer.java +++ b/src/jalview/renderer/OverviewRenderer.java @@ -26,14 +26,20 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.SequenceI; import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.renderer.seqfeatures.FeatureRenderer; import jalview.viewmodel.OverviewDimensions; +import java.awt.AlphaComposite; import java.awt.Color; import java.awt.Graphics; +import java.awt.Graphics2D; import java.awt.image.BufferedImage; public class OverviewRenderer { + // transparency of hidden cols/seqs overlay + private final float TRANSPARENCY = 0.5f; + private FeatureColourFinder finder; private jalview.api.SequenceRenderer sr; @@ -47,11 +53,14 @@ public class OverviewRenderer // raw number of pixels to allocate to each row private float pixelsPerSeq; + // flag to indicate whether to halt drawing + private volatile boolean redraw = false; + public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer, - FeatureColourFinder colfinder, OverviewDimensions od) + FeatureRenderer fr, OverviewDimensions od) { sr = seqRenderer; - finder = colfinder; + finder = new FeatureColourFinder(fr); pixelsPerCol = od.getPixelsPerCol(); pixelsPerSeq = od.getPixelsPerSeq(); @@ -74,52 +83,78 @@ public class OverviewRenderer int rgbcolor = Color.white.getRGB(); int seqIndex = 0; int pixelRow = 0; + for (int alignmentRow : rows) { + if (redraw) + { + break; + } + // get details of this alignment row - boolean hidden = rows.isHidden(alignmentRow); SequenceI seq = rows.getSequence(alignmentRow); - + // 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) { + if (redraw) + { + break; + } + // calculate where this column extends to in pixels int endCol = Math.min( Math.round((colIndex + 1) * pixelsPerCol) - 1, miniMe.getWidth() - 1); - - // determine the colour based on the sequence and column position - rgbcolor = getColumnColourFromSequence(seq, - hidden || cols.isHidden(alignmentCol), alignmentCol, finder); - - // fill in the appropriate number of pixels - for (int row = pixelRow; row <= endRow; ++row) + + // 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) { - for (int col = pixelCol; col <= endCol; ++col) + rgbcolor = getColumnColourFromSequence(seq, + alignmentCol, + finder); + + // fill in the appropriate number of pixels + for (int row = pixelRow; row <= endRow; ++row) { - miniMe.setRGB(col, row, rgbcolor); + for (int col = pixelCol; col <= endCol; ++col) + { + miniMe.setRGB(col, row, rgbcolor); + } } + + pixelCol = endCol + 1; } - - pixelCol = endCol + 1; colIndex++; } pixelRow = endRow + 1; seqIndex++; } + + overlayHiddenRegions(rows, cols); return miniMe; } - /* + /** * Find 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, - boolean isHidden, int lastcol, FeatureColourFinder fcfinder) + int lastcol, FeatureColourFinder fcfinder) { Color color = Color.white; @@ -128,12 +163,117 @@ public class OverviewRenderer color = sr.getResidueColour(seq, lastcol, fcfinder); } - if (isHidden) + return color.getRGB(); + } + + /** + * 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) + { + if (cols.hasHidden() || rows.hasHidden()) { - color = color.darker().darker(); + 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); } + } - return color.getRGB(); + /** + * 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) + { + // new masking image + BufferedImage hiddenImage = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); + + int colIndex = 0; + int pixelCol = 0; + + Color hidden = Color.DARK_GRAY.darker(); + + Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics(); + + // set background to transparent + g2d.setComposite(AlphaComposite.Clear); + g2d.fillRect(0, 0, width, height); + + // set next colour to opaque + g2d.setComposite(AlphaComposite.Src); + + for (int alignmentCol : cols) + { + if (redraw) + { + break; + } + + // calculate where this column extends to in pixels + int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, + hiddenImage.getWidth() - 1); + + if (pixelCol <= endCol) + { + // determine the colour based on the sequence and column position + if (cols.isHidden(alignmentCol)) + { + g2d.setColor(hidden); + g2d.fillRect(pixelCol, 0, endCol - pixelCol + 1, height); + } + + pixelCol = endCol + 1; + } + colIndex++; + + } + + int seqIndex = 0; + int pixelRow = 0; + for (int alignmentRow : rows) + { + if (redraw) + { + break; + } + + // calculate where this row extends to in pixels + int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1, + miniMe.getHeight() - 1); + + // get details of this alignment row + if (rows.isHidden(alignmentRow)) + { + g2d.setColor(hidden); + g2d.fillRect(0, pixelRow, width, endRow - pixelRow + 1); + } + pixelRow = endRow + 1; + seqIndex++; + } + + return hiddenImage; } /** @@ -162,6 +302,10 @@ public class OverviewRenderer int pixelCol = 0; for (int alignmentCol : cols) { + if (redraw) + { + break; + } if (alignmentCol >= annotations.length) { break; // no more annotations to draw here @@ -196,4 +340,19 @@ public class OverviewRenderer } } } + + /** + * 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) + { + redraw = b; + } + } }