X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=e66b7d5189753053692555297a9c9bb1d11b2451;hb=5c041c1e56a818e673f4a141520a4becf81ae801;hp=4e81e69841f544460c14197e339476d36a887d70;hpb=011b6facdd2bc4e179d95833613a39d0778b5681;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 4e81e69..e66b7d5 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -20,9 +20,17 @@ */ package jalview.renderer.seqfeatures; +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.Range; +import jalview.datamodel.ContiguousI; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; @@ -31,13 +39,6 @@ import jalview.util.Comparison; import jalview.util.ReverseListIterator; 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; - public class FeatureRenderer extends FeatureRendererModel { private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite @@ -111,6 +112,10 @@ public class FeatureRenderer extends FeatureRendererModel 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), @@ -275,9 +280,9 @@ 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() - && !av.isShowComplementFeatures())) + ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1); + if (visiblePositions == null || !seq.getFeatures().hasFeatures() + && !av.isShowComplementFeatures()) { return null; } @@ -294,6 +299,16 @@ public class FeatureRenderer extends FeatureRendererModel 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++) @@ -308,7 +323,7 @@ public class FeatureRenderer extends FeatureRendererModel List overlaps = seq.getFeatures().findFeatures( visiblePositions.getBegin(), visiblePositions.getEnd(), type); - if (fc.isSimpleColour()) + if (overlaps.size() > 1 && fc.isSimpleColour()) { filterFeaturesForDisplay(overlaps); } @@ -343,8 +358,8 @@ public class FeatureRenderer extends FeatureRendererModel } 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); @@ -385,41 +400,25 @@ 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 configured to do so, find and show complement's features + * draw 'complement' features above ours if configured to do so */ - if (av.isShowComplementFeatures()) + if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop()) { - AlignViewportI comp = av.getCodingComplement(); - FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp) - .getFeatureRenderer(); - for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++) - { - int column = seq.findIndex(pos); - List features = fr2 - .findComplementFeaturesAtResidue(seq, pos); - for (SequenceFeature sf : 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; - } - } + drawnColour = drawComplementFeatures(g, seq, start, end, y1, + colourOnly, visiblePositions, drawnColour); } if (transparency != 1.0f && g != null) @@ -435,6 +434,51 @@ public class FeatureRenderer extends FeatureRendererModel } /** + * 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 g + * @param seq + * @param start + * @param end + * @param y1 + * @param colourOnly + * @param visiblePositions + * @param drawnColour + * @return + */ + Color drawComplementFeatures(final Graphics g, final SequenceI seq, + int start, int end, int y1, boolean colourOnly, + ContiguousI visiblePositions, Color drawnColour) + { + 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; + } + + /** * Called when alignment in associated view has new/modified features to * discover and display. * @@ -471,27 +515,12 @@ public class FeatureRenderer extends FeatureRendererModel /* * show complement features on top (if configured to show them) */ - if (av.isShowComplementFeatures()) + if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop()) { - AlignViewportI complement = av.getCodingComplement(); - AlignFrame af = Desktop.getAlignFrameFor(complement); - FeatureRendererModel fr2 = af.getFeatureRenderer(); - List features = fr2.findComplementFeaturesAtResidue( - seq, seq.findPosition(column - 1)); - - ReverseListIterator it = new ReverseListIterator<>( - features); - while (it.hasNext()) + Color col = findComplementFeatureColour(seq, column); + if (col != null) { - SequenceFeature sf = it.next(); - if (!fr2.featureGroupNotShown(sf)) - { - Color col = fr2.getColour(sf); - if (col != null) - { - return col; - } - } + return col; } } @@ -508,10 +537,15 @@ public class FeatureRenderer extends FeatureRendererModel continue; } + /* + * 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 overlaps = seq.findFeatures(column, column, type); - for (SequenceFeature sequenceFeature : overlaps) + for (int i = overlaps.size() - 1 ; i >= 0 ; i--) { + SequenceFeature sequenceFeature = overlaps.get(i); if (!featureGroupNotShown(sequenceFeature)) { Color col = getColour(sequenceFeature); @@ -524,8 +558,43 @@ public class FeatureRenderer extends FeatureRendererModel } /* - * no displayed feature found at position + * show complement features underneath (if configured to show them) */ + Color col = null; + if (av.isShowComplementFeatures() + && !av.isShowComplementFeaturesOnTop()) + { + col = findComplementFeatureColour(seq, column); + } + + 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 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 col; + } + } + } return null; } }