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;
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;
import java.beans.PropertyChangeSupport;
public class OverviewRenderer
{
+ // transparency of hidden cols/seqs overlay
+ private final float TRANSPARENCY = 0.5f;
+
+ private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+
public static final String UPDATE = "OverviewUpdate";
private static final int MAX_PROGRESS = 100;
private FeatureColourFinder finder;
- private jalview.api.SequenceRenderer sr;
-
// image to render on
private BufferedImage miniMe;
// 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();
{
break;
}
-
+
// get details of this alignment row
- boolean hidden = rows.isHidden(alignmentRow);
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)
{
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)
{
- // determine the colour based on the sequence and column position
- rgbcolor = getColumnColourFromSequence(seq,
- hidden || cols.isHidden(alignmentCol), alignmentCol,
- finder);
-
+ rgbcolor = getColumnColourFromSequence(allGroups, seq,
+ alignmentCol, finder);
+
// fill in the appropriate number of pixels
for (int row = pixelRow; row <= endRow; ++row)
{
sendProgressUpdate((pixelCol + 1) * (endRow - pixelRow),
totalPixels, lastRowUpdate);
+
pixelCol = endCol + 1;
}
colIndex++;
seqIndex++;
}
+ overlayHiddenRegions(rows, cols);
// final update to progress bar if present
if (redraw)
{
/*
* 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)
+ private int getColumnColourFromSequence(SequenceGroup[] allGroups,
+ jalview.datamodel.SequenceI seq,
+ int lastcol, FeatureColourFinder fcfinder)
{
Color color = Color.white;
if ((seq != null) && (seq.getLength() > lastcol))
{
- color = sr.getResidueColour(seq, lastcol, fcfinder);
+ color = resColFinder.getResidueColour(true, shader, allGroups, 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 = resColFinder.getHiddenColour();
+
+ 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;
}
/**
}
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)
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;
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)
git://source.jalview.org / jalview.git / blobdiff