*/
package jalview.renderer.seqfeatures;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.util.List;
+
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.util.Comparison;
+import jalview.util.ReverseListIterator;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
public class FeatureRenderer extends FeatureRendererModel
{
private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
.getInstance(AlphaComposite.SRC_OVER, 1.0f);
- protected SequenceI lastSeq;
-
- private volatile SequenceFeature[] lastSequenceFeatures;
-
- int sfSize;
-
/**
* Constructor given a viewport
*
g.setColor(featureColour);
- g.fillRect((i - start) * charWidth, y1, charWidth,
- charHeight);
+ g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
if (colourOnly || !validCharWidth)
{
continue;
}
+ /*
+ * JAL-3045 text is always drawn over features, even if
+ * 'Show Text' is unchecked in the format menu
+ */
g.setColor(Color.white);
int charOffset = (charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (charWidth * (i - start)), pady);
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
}
return true;
}
g.setColor(Color.black);
int charOffset = (charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (charWidth * (i - start)), pady);
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
}
return true;
}
return null;
}
- SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
- if (seq != lastSeq)
- {
- lastSeq = seq;
- lastSequenceFeatures = sequenceFeatures;
- if (lastSequenceFeatures != null)
- {
- sfSize = lastSequenceFeatures.length;
- }
- }
- else
- {
- if (lastSequenceFeatures != sequenceFeatures)
- {
- lastSequenceFeatures = sequenceFeatures;
- if (lastSequenceFeatures != null)
- {
- sfSize = lastSequenceFeatures.length;
- }
- }
- }
-
- if (lastSequenceFeatures == null || sfSize == 0)
+ // column is 'base 1' but getCharAt is an array index (ie from 0)
+ if (Comparison.isGap(seq.getCharAt(column - 1)))
{
+ /*
+ * returning null allows the colour scheme to provide gap colour
+ * - normally white, but can be customised
+ */
return null;
}
- if (Comparison.isGap(lastSeq.getCharAt(column)))
- {
- return Color.white;
- }
-
Color renderedColour = null;
if (transparency == 1.0f)
{
/*
* simple case - just find the topmost rendered visible feature colour
*/
- renderedColour = findFeatureColour(seq, seq.findPosition(column));
+ renderedColour = findFeatureColour(seq, column);
}
else
{
* transparency case - draw all visible features in render order to
* build up a composite colour on the graphics context
*/
- renderedColour = drawSequence(g, lastSeq, column, column, 0, true);
+ renderedColour = drawSequence(g, seq, column, column, 0, true);
}
return renderedColour;
}
final SequenceI seq, int start, int end, int y1,
boolean colourOnly)
{
- SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
- if (sequenceFeatures == null || sequenceFeatures.length == 0)
+ /*
+ * if columns are all gapped, or sequence has no features, nothing to do
+ */
+ ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
+ if (visiblePositions == null || !seq.getFeatures().hasFeatures()
+ && !av.isShowComplementFeatures())
{
return null;
}
updateFeatures();
- if (lastSeq == null || seq != lastSeq
- || sequenceFeatures != lastSequenceFeatures)
- {
- lastSeq = seq;
- lastSequenceFeatures = sequenceFeatures;
- }
-
if (transparency != 1f && g != null)
{
Graphics2D g2 = (Graphics2D) g;
transparency));
}
- int startPos = lastSeq.findPosition(start);
- int endPos = lastSeq.findPosition(end);
-
- sfSize = lastSequenceFeatures.length;
Color drawnColour = null;
/*
+ * draw 'complement' features below ours if configured to do so
+ */
+ if (av.isShowComplementFeatures()
+ && !av.isShowComplementFeaturesOnTop())
+ {
+ drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+ colourOnly, visiblePositions, drawnColour);
+ }
+
+ /*
* iterate over features in ordering of their rendering (last is on top)
*/
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
continue;
}
- // loop through all features in sequence to find
- // current feature to render
- for (int sfindex = 0; sfindex < sfSize; sfindex++)
+ FeatureColourI fc = getFeatureStyle(type);
+ List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
+ visiblePositions.getBegin(), visiblePositions.getEnd(), type);
+
+ if (overlaps.size() > 1 && fc.isSimpleColour())
{
- final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
- if (!sequenceFeature.type.equals(type))
+ filterFeaturesForDisplay(overlaps);
+ }
+
+ for (SequenceFeature sf : overlaps)
+ {
+ Color featureColour = getColor(sf, fc);
+ if (featureColour == null)
{
+ /*
+ * feature excluded by filters, or colour threshold
+ */
continue;
}
/*
- * a feature type may be flagged as shown but the group
- * an instance of it belongs to may be hidden
+ * if feature starts/ends outside the visible range,
+ * restrict to visible positions (or if a contact feature,
+ * to a single position)
*/
- if (featureGroupNotShown(sequenceFeature))
+ int visibleStart = sf.getBegin();
+ if (visibleStart < visiblePositions.getBegin())
{
- continue;
+ visibleStart = sf.isContactFeature() ? sf.getEnd()
+ : visiblePositions.getBegin();
}
-
- /*
- * check feature overlaps the target range
- * TODO: efficient retrieval of features overlapping a range
- */
- if (sequenceFeature.getBegin() > endPos
- || sequenceFeature.getEnd() < startPos)
+ int visibleEnd = sf.getEnd();
+ if (visibleEnd > visiblePositions.getEnd())
{
- continue;
+ visibleEnd = sf.isContactFeature() ? sf.getBegin()
+ : visiblePositions.getEnd();
}
- Color featureColour = getColour(sequenceFeature);
- boolean isContactFeature = sequenceFeature.isContactFeature();
+ int featureStartCol = seq.findIndex(visibleStart);
+ int featureEndCol = sf.begin == sf.end ? featureStartCol
+ : seq.findIndex(visibleEnd);
+
+ // Color featureColour = getColour(sequenceFeature);
+
+ boolean isContactFeature = sf.isContactFeature();
if (isContactFeature)
{
- boolean drawn = renderFeature(g, seq,
- seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.begin) - 1, featureColour,
- start, end, y1, colourOnly);
- drawn |= renderFeature(g, seq,
- seq.findIndex(sequenceFeature.end) - 1,
- seq.findIndex(sequenceFeature.end) - 1, featureColour,
- start, end, y1, colourOnly);
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureStartCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ drawn |= renderFeature(g, seq, featureEndCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
if (drawn)
{
drawnColour = featureColour;
}
}
- else if (showFeature(sequenceFeature))
+ else
{
+ /*
+ * showing feature score by height of colour
+ * is not implemented as a selectable option
+ *
if (av.isShowSequenceFeaturesHeight()
&& !Float.isNaN(sequenceFeature.score))
{
}
else
{
- boolean drawn = renderFeature(g, seq,
- seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.end) - 1, featureColour,
- start, end, y1, colourOnly);
- if (drawn)
- {
- drawnColour = featureColour;
- }
+ */
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
}
+ /*}*/
}
}
}
+ /*
+ * draw 'complement' features above ours if configured to do so
+ */
+ if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
+ {
+ drawnColour = drawComplementFeatures(g, seq, start, end, y1,
+ colourOnly, visiblePositions, drawnColour);
+ }
+
if (transparency != 1.0f && g != null)
{
/*
}
/**
- * Answers true if the feature belongs to a feature group which is not
- * currently displayed, else false
+ * Find any features on the CDS/protein complement of the sequence region and
+ * draw them, with visibility and colouring as configured in the complementary
+ * viewport
*
- * @param sequenceFeature
+ * @param g
+ * @param seq
+ * @param start
+ * @param end
+ * @param y1
+ * @param colourOnly
+ * @param visiblePositions
+ * @param drawnColour
* @return
*/
- protected boolean featureGroupNotShown(
- final SequenceFeature sequenceFeature)
+ Color drawComplementFeatures(final Graphics g, final SequenceI seq,
+ int start, int end, int y1, boolean colourOnly,
+ ContiguousI visiblePositions, Color drawnColour)
{
- return featureGroups != null
- && sequenceFeature.featureGroup != null
- && sequenceFeature.featureGroup.length() != 0
- && featureGroups.containsKey(sequenceFeature.featureGroup)
- && !featureGroups.get(sequenceFeature.featureGroup)
- .booleanValue();
+ AlignViewportI comp = av.getCodingComplement();
+ FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
+ .getFeatureRenderer();
+
+ final int visibleStart = visiblePositions.getBegin();
+ final int visibleEnd = visiblePositions.getEnd();
+
+ for (int pos = visibleStart; pos <= visibleEnd; pos++)
+ {
+ int column = seq.findIndex(pos);
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
+ {
+ FeatureColourI fc = fr2.getFeatureStyle(sf.getType());
+ Color featureColour = fr2.getColor(sf, fc);
+ renderFeature(g, seq, column - 1, column - 1, featureColour,
+ start, end, y1, colourOnly);
+ drawnColour = featureColour;
+ }
+ }
+ }
+ return drawnColour;
}
/**
@Override
public void featuresAdded()
{
- lastSeq = null;
findAllFeatures();
}
/**
- * Returns the sequence feature colour rendered at the given sequence
- * position, or null if none found. The feature of highest render order (i.e.
- * on top) is found, subject to both feature type and feature group being
- * visible, and its colour returned.
+ * Returns the sequence feature colour rendered at the given column position,
+ * or null if none found. The feature of highest render order (i.e. on top) is
+ * found, subject to both feature type and feature group being visible, and
+ * its colour returned. This method is suitable when no feature transparency
+ * applied (only the topmost visible feature colour is rendered).
+ * <p>
+ * Note this method does not check for a gap in the column so would return the
+ * colour for features enclosing a gapped column. Check for gap before calling
+ * if different behaviour is wanted.
*
* @param seq
- * @param pos
+ * @param column
+ * (1..)
* @return
*/
- Color findFeatureColour(SequenceI seq, int pos)
+ Color findFeatureColour(SequenceI seq, int column)
{
- SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
- if (sequenceFeatures == null || sequenceFeatures.length == 0)
- {
- return null;
- }
-
/*
* check for new feature added while processing
*/
updateFeatures();
/*
+ * show complement features on top (if configured to show them)
+ */
+ if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop())
+ {
+ Color col = findComplementFeatureColour(seq, column);
+ if (col != null)
+ {
+ return col;
+ }
+ }
+
+ /*
* inspect features in reverse renderOrder (the last in the array is
* displayed on top) until we find one that is rendered at the position
*/
- for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+ for (int renderIndex = renderOrder.length
+ - 1; renderIndex >= 0; renderIndex--)
{
String type = renderOrder[renderIndex];
if (!showFeatureOfType(type))
continue;
}
- for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+ /*
+ * find features of this type, and the colour of the _last_ one
+ * (the one that would be drawn on top) that has a colour
+ */
+ List<SequenceFeature> overlaps = seq.findFeatures(column, column,
+ type);
+ for (int i = overlaps.size() - 1 ; i >= 0 ; i--)
{
- SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
- if (!sequenceFeature.type.equals(type))
+ SequenceFeature sequenceFeature = overlaps.get(i);
+ if (!featureGroupNotShown(sequenceFeature))
{
- continue;
+ Color col = getColour(sequenceFeature);
+ if (col != null)
+ {
+ return col;
+ }
}
+ }
+ }
- if (featureGroupNotShown(sequenceFeature))
- {
- continue;
- }
+ /*
+ * show complement features underneath (if configured to show them)
+ */
+ Color col = null;
+ if (av.isShowComplementFeatures()
+ && !av.isShowComplementFeaturesOnTop())
+ {
+ col = findComplementFeatureColour(seq, column);
+ }
- /*
- * check the column position is within the feature range
- * (or is one of the two contact positions for a contact feature)
- */
- boolean featureIsAtPosition = sequenceFeature.begin <= pos
- && sequenceFeature.end >= pos;
- if (sequenceFeature.isContactFeature())
- {
- featureIsAtPosition = sequenceFeature.begin == pos
- || sequenceFeature.end == pos;
- }
- if (featureIsAtPosition)
+ return col;
+ }
+
+ Color findComplementFeatureColour(SequenceI seq, int column)
+ {
+ AlignViewportI complement = av.getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq,
+ seq.findPosition(column - 1));
+ if (mf == null)
+ {
+ return null;
+ }
+ ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
+ mf.features);
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (!fr2.featureGroupNotShown(sf))
+ {
+ Color col = fr2.getColour(sf);
+ if (col != null)
{
- return getColour(sequenceFeature);
+ return col;
}
}
}
-
- /*
- * no displayed feature found at position
- */
return null;
}
}
git://source.jalview.org / jalview.git / blobdiff