X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=fe80e63721aeac42a2567a85488bc77bc979bafa;hb=7baccbacc20ff22336ca8c94935f6124b5e5a135;hp=fc8731d750db99db2d24315c20d2b4c427e1ba60;hpb=3740241b6d0dfa109dc81847afe58f17497c39e8;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index fc8731d..fe80e63 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -20,23 +20,25 @@ */ 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; import jalview.gui.Desktop; 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 @@ -110,6 +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), @@ -274,8 +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()) + ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1); + if (visiblePositions == null || !seq.getFeatures().hasFeatures() + && !av.isShowComplementFeatures()) { return null; } @@ -292,6 +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++) @@ -306,7 +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); } @@ -317,7 +334,7 @@ public class FeatureRenderer extends FeatureRendererModel if (featureColour == null) { /* - * feature excluded by visibility settings, filters, or colour threshold + * feature excluded by filters, or colour threshold */ continue; } @@ -396,6 +413,15 @@ public class FeatureRenderer extends FeatureRendererModel } } + /* + * 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) { /* @@ -409,6 +435,52 @@ 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. * @@ -445,24 +517,12 @@ 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)); - // todo: ensure ordered by feature render order - for (SequenceFeature sf : features) + Color col = findComplementFeatureColour(seq, column); + if (col != null) { - if (!fr2.featureGroupNotShown(sf)) - { - Color col = fr2.getColour(sf); - if (col != null) - { - return col; - } - } + return col; } } @@ -479,10 +539,15 @@ 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); @@ -495,8 +560,43 @@ 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; } }