X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=f16522fcf0931894658a763091bca5213d7b7c44;hb=353109c11d706b29ae5bc9606f0e12223aa45a98;hp=5dce2b86df6281d6fdfe620d952261fe1d94de3d;hpb=480d7b96f089281a3caf77d2a4e5adec09dc5bfa;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 5dce2b8..f16522f 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -21,6 +21,7 @@ package jalview.renderer.seqfeatures; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; import jalview.datamodel.Range; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -100,8 +101,7 @@ 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) { @@ -110,8 +110,8 @@ 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; } @@ -199,8 +199,8 @@ 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; } @@ -218,7 +218,11 @@ public class FeatureRenderer extends FeatureRendererModel if (Comparison.isGap(seq.getCharAt(column))) { - return Color.white; + /* + * returning null allows the colour scheme to provide gap colour + * - normally white, but can be customised + */ + return null; } Color renderedColour = null; @@ -227,7 +231,7 @@ 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 { @@ -264,7 +268,11 @@ 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()) { return null; } @@ -278,15 +286,6 @@ public class FeatureRenderer extends FeatureRendererModel transparency)); } - /* - * get range of sequence positions within column range - */ - Range seqRange = seq.findPositions(start, end); - if (seqRange == null) - { - return null; - } - Color drawnColour = null; /* @@ -300,41 +299,61 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - List overlaps = seq.findFeatures(seqRange.start, - seqRange.end, type); - for (SequenceFeature sequenceFeature : overlaps) + FeatureColourI fc = getFeatureStyle(type); + List overlaps = seq.getFeatures().findFeatures( + visiblePositions.getBegin(), visiblePositions.getEnd(), type); + + filterFeaturesForDisplay(overlaps, fc); + + for (SequenceFeature sf : overlaps) { + Color featureColour = fc.getColor(sf); + if (featureColour == null) + { + // score feature outwith threshold for colouring + 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(); + } + + int featureStartCol = seq.findIndex(visibleStart); + int featureEndCol = sf.begin == sf.end ? featureStartCol : seq + .findIndex(visibleEnd); + + // Color featureColour = getColour(sequenceFeature); - Color featureColour = getColour(sequenceFeature); - boolean isContactFeature = sequenceFeature.isContactFeature(); + boolean isContactFeature = sf.isContactFeature(); - // todo overload findIndex using Location data - int featureStartCol = seq.findIndex(sequenceFeature.begin); - int featureEndCol = seq.findIndex(sequenceFeature.end); if (isContactFeature) { - 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); + 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 @@ -393,16 +412,22 @@ 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 @@ -413,7 +438,8 @@ 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 + - 1; renderIndex >= 0; renderIndex--) { String type = renderOrder[renderIndex]; if (!showFeatureOfType(type)) @@ -421,16 +447,21 @@ 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 */