X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=e66b7d5189753053692555297a9c9bb1d11b2451;hb=5c041c1e56a818e673f4a141520a4becf81ae801;hp=8f4f13951d7ac91d9b340f19c7b6971bdf8a090e;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 8f4f139..e66b7d5 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -20,13 +20,6 @@ */ package jalview.renderer.seqfeatures; -import jalview.api.AlignViewportI; -import jalview.api.FeatureColourI; -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; @@ -34,6 +27,18 @@ 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 @@ -100,18 +105,21 @@ public class FeatureRenderer extends FeatureRendererModel 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; } @@ -199,8 +207,8 @@ public class FeatureRenderer extends FeatureRendererModel 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; } @@ -216,9 +224,14 @@ public class FeatureRenderer extends FeatureRendererModel 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))) { - return Color.white; + /* + * returning null allows the colour scheme to provide gap colour + * - normally white, but can be customised + */ + return null; } Color renderedColour = null; @@ -264,7 +277,12 @@ public class FeatureRenderer extends FeatureRendererModel final SequenceI seq, int start, int end, int y1, boolean colourOnly) { - if (!seq.getFeatures().hasFeatures()) + /* + * 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; } @@ -281,6 +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++) @@ -292,28 +320,51 @@ public class FeatureRenderer extends FeatureRendererModel } FeatureColourI fc = getFeatureStyle(type); - List overlaps = seq.findFeatures(start + 1, end + 1, - type); + List overlaps = seq.getFeatures().findFeatures( + visiblePositions.getBegin(), visiblePositions.getEnd(), type); - filterFeaturesForDisplay(overlaps, fc); + if (overlaps.size() > 1 && fc.isSimpleColour()) + { + 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(sf)) + int visibleStart = sf.getBegin(); + if (visibleStart < visiblePositions.getBegin()) { - continue; + visibleStart = sf.isContactFeature() ? sf.getEnd() + : visiblePositions.getBegin(); + } + int visibleEnd = sf.getEnd(); + if (visibleEnd > visiblePositions.getEnd()) + { + visibleEnd = sf.isContactFeature() ? sf.getBegin() + : visiblePositions.getEnd(); } - Color featureColour = fc.getColor(sf); + int featureStartCol = seq.findIndex(visibleStart); + int featureEndCol = sf.begin == sf.end ? featureStartCol + : seq.findIndex(visibleEnd); + + // Color featureColour = getColour(sequenceFeature); + boolean isContactFeature = sf.isContactFeature(); - int featureStartCol = seq.findIndex(sf.begin); - int featureEndCol = sf.begin == sf.end ? featureStartCol : seq - .findIndex(sf.end); if (isContactFeature) { boolean drawn = renderFeature(g, seq, featureStartCol - 1, @@ -327,7 +378,7 @@ public class FeatureRenderer extends FeatureRendererModel drawnColour = featureColour; } } - else if (showFeature(sf)) + else { /* * showing feature score by height of colour @@ -349,19 +400,27 @@ 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; + } /*}*/ } } } + /* + * 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) { /* @@ -375,6 +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. * @@ -389,7 +493,8 @@ public class FeatureRenderer extends FeatureRendererModel * 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. + * its colour returned. This method is suitable when no feature transparency + * applied (only the topmost visible feature colour is rendered). *

* 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 @@ -408,10 +513,23 @@ public class FeatureRenderer extends FeatureRendererModel 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)) @@ -419,20 +537,64 @@ 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)) { - return getColour(sequenceFeature); + Color col = getColour(sequenceFeature); + if (col != null) + { + return col; + } } } } - + /* - * 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; } }