X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=4e81e69841f544460c14197e339476d36a887d70;hb=011b6facdd2bc4e179d95833613a39d0778b5681;hp=d6be4c251a4899e9a20a55029820920f4991eb1e;hpb=9ccd0ca3146f4b7fe41b7d7bc307501d2ccd9a31;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index d6be4c2..4e81e69 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -21,9 +21,14 @@ package jalview.renderer.seqfeatures; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; +import jalview.datamodel.Range; 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; @@ -99,8 +104,7 @@ 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) { @@ -109,8 +113,8 @@ public class FeatureRenderer extends FeatureRendererModel 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; } @@ -198,8 +202,8 @@ 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; } @@ -215,9 +219,14 @@ 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; @@ -226,7 +235,7 @@ public class FeatureRenderer extends FeatureRendererModel /* * simple case - just find the topmost rendered visible feature colour */ - renderedColour = findFeatureColour(seq, seq.findPosition(column)); + renderedColour = findFeatureColour(seq, column); } else { @@ -263,7 +272,12 @@ 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 + */ + Range visiblePositions = seq.findPositions(start+1, end+1); + if (visiblePositions == null || (!seq.getFeatures().hasFeatures() + && !av.isShowComplementFeatures())) { return null; } @@ -277,9 +291,6 @@ public class FeatureRenderer extends FeatureRendererModel transparency)); } - int startPos = seq.findPosition(start); - int endPos = seq.findPosition(end);// todo a performant overload of this! - Color drawnColour = null; /* @@ -293,38 +304,66 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - List overlaps = seq.findFeatures(startPos, endPos, - type); - for (SequenceFeature sequenceFeature : overlaps) + FeatureColourI fc = getFeatureStyle(type); + List overlaps = seq.getFeatures().findFeatures( + visiblePositions.getBegin(), visiblePositions.getEnd(), type); + + if (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(sequenceFeature)) + 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 = 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 @@ -347,8 +386,8 @@ public class FeatureRenderer extends FeatureRendererModel { */ boolean drawn = renderFeature(g, seq, - seq.findIndex(sequenceFeature.begin) - 1, - seq.findIndex(sequenceFeature.end) - 1, featureColour, + featureStartCol - 1, + featureEndCol - 1, featureColour, start, end, y1, colourOnly); if (drawn) { @@ -359,6 +398,30 @@ public class FeatureRenderer extends FeatureRendererModel } } + /* + * if configured to do so, find and show complement's features + */ + if (av.isShowComplementFeatures()) + { + 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; + } + } + } + if (transparency != 1.0f && g != null) { /* @@ -383,16 +446,22 @@ public class FeatureRenderer extends FeatureRendererModel } /** - * 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). + *

+ * 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) { /* * check for new feature added while processing @@ -400,10 +469,38 @@ public class FeatureRenderer extends FeatureRendererModel updateFeatures(); /* + * show complement features on top (if configured to show them) + */ + if (av.isShowComplementFeatures()) + { + 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()) + { + SequenceFeature sf = it.next(); + if (!fr2.featureGroupNotShown(sf)) + { + Color col = fr2.getColour(sf); + 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)) @@ -411,16 +508,21 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - List overlaps = seq.findFeatures(pos, pos, type); + List overlaps = seq.findFeatures(column, column, + type); for (SequenceFeature sequenceFeature : overlaps) { if (!featureGroupNotShown(sequenceFeature)) { - return getColour(sequenceFeature); + Color col = getColour(sequenceFeature); + if (col != null) + { + return col; + } } } } - + /* * no displayed feature found at position */