X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=c1bccb89bf19f1bdbb8a54b5d00a3496bb87188f;hb=08b87509ada06ac8614424247346daef4054b41a;hp=f16522fcf0931894658a763091bca5213d7b7c44;hpb=353109c11d706b29ae5bc9606f0e12223aa45a98;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index f16522f..c1bccb8 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -22,10 +22,11 @@ package jalview.renderer.seqfeatures; import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; -import jalview.datamodel.Range; +import jalview.datamodel.ContiguousI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.util.Comparison; +import jalview.util.Platform; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.AlphaComposite; @@ -33,6 +34,7 @@ import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; +import java.util.ArrayList; import java.util.List; public class FeatureRenderer extends FeatureRendererModel @@ -40,6 +42,13 @@ public class FeatureRenderer extends FeatureRendererModel private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite .getInstance(AlphaComposite.SRC_OVER, 1.0f); + /* + * persistent list used by JalviewJS; not threadsafe for Java + */ + private List overlaps = (Platform.isJS() + ? new ArrayList<>() + : null); + /** * Constructor given a viewport * @@ -90,11 +99,13 @@ public class FeatureRenderer extends FeatureRendererModel int pady = (y1 + charHeight) - charHeight / 5; FontMetrics fm = g.getFontMetrics(); + char s = '\0'; for (int i = featureStart; i <= featureEnd; i++) { - char s = seq.getCharAt(i); - if (Comparison.isGap(s)) + // colourOnly is just for Overview -- no need to check this again + + if (!colourOnly && Comparison.isGap(s = seq.getCharAt(i))) { continue; } @@ -103,7 +114,12 @@ public class FeatureRenderer extends FeatureRendererModel g.fillRect((i - start) * charWidth, y1, charWidth, charHeight); - if (colourOnly || !validCharWidth) + if (colourOnly) + { + return true; + } + + if (!validCharWidth) { continue; } @@ -117,6 +133,9 @@ public class FeatureRenderer extends FeatureRendererModel } /** + * + * BH - this method is never called? + * * Renders the sequence using the given SCORE feature colour between the given * start and end columns. Returns true if at least one column is drawn, else * false (the feature range does not overlap the start and end positions). @@ -211,12 +230,8 @@ public class FeatureRenderer extends FeatureRendererModel @Override public Color findFeatureColour(SequenceI seq, int column, Graphics g) { - if (!av.isShowSequenceFeatures()) - { - return null; - } - - if (Comparison.isGap(seq.getCharAt(column))) + // 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 @@ -251,7 +266,7 @@ public class FeatureRenderer extends FeatureRendererModel * applies), or null if no feature is drawn in the range given. * * @param g - * the graphics context to draw on (may be null if colourOnly==true) + * the graphics context to draw on (null if no transparency applies) * @param seq * @param start * start column @@ -271,18 +286,22 @@ public class FeatureRenderer extends FeatureRendererModel /* * if columns are all gapped, or sequence has no features, nothing to do */ - Range visiblePositions = seq.findPositions(start+1, end+1); - if (visiblePositions == null || !seq.getFeatures().hasFeatures()) + ContiguousI visiblePositions; + if (!seq.getFeatures().hasFeatures() || (visiblePositions = seq + .findPositions(start + 1, end + 1)) == null) { return null; } + int vp0 = visiblePositions.getBegin(); + int vp1 = visiblePositions.getEnd(); + updateFeatures(); - if (transparency != 1f && g != null) + if (transparency != 1f) { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + ((Graphics2D) g).setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER, transparency)); } @@ -291,26 +310,34 @@ public class FeatureRenderer extends FeatureRendererModel /* * iterate over features in ordering of their rendering (last is on top) */ - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + for (int renderIndex = 0, n = renderOrder.length; renderIndex < n; renderIndex++) { String type = renderOrder[renderIndex]; - if (!showFeatureOfType(type)) + if (!seq.hasFeatures(type) || !showFeatureOfType(type)) { continue; } FeatureColourI fc = getFeatureStyle(type); - List overlaps = seq.getFeatures().findFeatures( - visiblePositions.getBegin(), visiblePositions.getEnd(), type); + List overlaps = seq.getFeatures().findFeatures(vp0, + vp1, type); - filterFeaturesForDisplay(overlaps, fc); + // colourOnly (i.e. Overview) can only be here if translucent, so + // there is no need to check for filtering + if (!colourOnly && fc.isSimpleColour()) + { + filterFeaturesForDisplay(overlaps); + } - for (SequenceFeature sf : overlaps) + for (int i = overlaps.size(); --i >= 0;) { - Color featureColour = fc.getColor(sf); + SequenceFeature sf = overlaps.get(i); + Color featureColour = getColor(sf, fc); if (featureColour == null) { - // score feature outwith threshold for colouring + /* + * feature excluded by visibility settings, filters, or colour threshold + */ continue; } @@ -319,22 +346,22 @@ public class FeatureRenderer extends FeatureRendererModel * restrict to visible positions (or if a contact feature, * to a single position) */ - int visibleStart = sf.getBegin(); - if (visibleStart < visiblePositions.getBegin()) + int sf0 = sf.getBegin(); + int sf1 = sf.getEnd(); + int visibleStart = sf0; + if (visibleStart < vp0) { - visibleStart = sf.isContactFeature() ? sf.getEnd() - : visiblePositions.getBegin(); + visibleStart = sf.isContactFeature() ? sf1 : vp0; } - int visibleEnd = sf.getEnd(); - if (visibleEnd > visiblePositions.getEnd()) + int visibleEnd = sf1; + if (visibleEnd > vp1) { - visibleEnd = sf.isContactFeature() ? sf.getBegin() - : visiblePositions.getEnd(); + visibleEnd = sf.isContactFeature() ? sf0 : vp1; } int featureStartCol = seq.findIndex(visibleStart); - int featureEndCol = sf.begin == sf.end ? featureStartCol : seq - .findIndex(visibleEnd); + int featureEndCol = (sf.begin == sf.end ? featureStartCol + : seq.findIndex(visibleEnd)); // Color featureColour = getColour(sequenceFeature); @@ -375,26 +402,24 @@ public class FeatureRenderer extends FeatureRendererModel else { */ - boolean drawn = renderFeature(g, seq, - featureStartCol - 1, - featureEndCol - 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; + } /*}*/ } } } - if (transparency != 1.0f && g != null) + if (transparency != 1.0f) { /* * reset transparency */ - Graphics2D g2 = (Graphics2D) g; - g2.setComposite(NO_TRANSPARENCY); + ((Graphics2D) g).setComposite(NO_TRANSPARENCY); } return drawnColour; @@ -427,7 +452,7 @@ public class FeatureRenderer extends FeatureRendererModel * (1..) * @return */ - Color findFeatureColour(SequenceI seq, int column) + private Color findFeatureColour(SequenceI seq, int column) { /* * check for new feature added while processing @@ -438,22 +463,33 @@ public class FeatureRenderer extends FeatureRendererModel * 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; --renderIndex >= 0;) { String type = renderOrder[renderIndex]; - if (!showFeatureOfType(type)) + if (!seq.hasFeatures(type) || !showFeatureOfType(type)) { continue; } - List overlaps = seq.findFeatures(column, column, - type); - for (SequenceFeature sequenceFeature : overlaps) + /* + * field overlaps is used by JalviewJS to avoid object creation; + * not thread-safe for Java (Javascript is single-threaded) + */ + if (overlaps != null) { - if (!featureGroupNotShown(sequenceFeature)) + overlaps.clear(); + } + List list = seq.findFeatures(column, type, overlaps); + if (list.size() > 0) + { + for (int i = 0, n = list.size(); i < n; i++) { - Color col = getColour(sequenceFeature); + SequenceFeature sf = list.get(i); + if (featureGroupNotShown(sf)) + { + continue; + } + Color col = getColour(sf); if (col != null) { return col;