X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=795cd3681e4ea9a059604ee6cf58462c41e64c69;hb=b83eff8c672cede0305da3c76823dab414749dde;hp=f826a88cb2784bd75f6ade974f39ef35e35be943;hpb=17bea66b37be69a173f6b1ea73c8544bd4c6e2b1;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index f826a88..795cd36 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -21,6 +21,8 @@ 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.util.Comparison; @@ -31,18 +33,13 @@ 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 .getInstance(AlphaComposite.SRC_OVER, 1.0f); - protected SequenceI lastSeq; - - private volatile SequenceFeature[] lastSequenceFeatures; - - int sfSize; - /** * Constructor given a viewport * @@ -104,8 +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) { @@ -114,8 +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; } @@ -203,19 +199,14 @@ 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; } /** - * This is used by Structure Viewers and the Overview Window to get the - * feature colour of the rendered sequence - * - * @param seq - * @param column - * @return + * {@inheritDoc} */ @Override public Color findFeatureColour(SequenceI seq, int column, Graphics g) @@ -225,61 +216,48 @@ public class FeatureRenderer extends FeatureRendererModel return null; } - SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); - if (seq != lastSeq) - { - lastSeq = seq; - lastSequenceFeatures = sequenceFeatures; - if (lastSequenceFeatures != null) - { - sfSize = lastSequenceFeatures.length; - } - } - else - { - if (lastSequenceFeatures != sequenceFeatures) - { - lastSequenceFeatures = sequenceFeatures; - if (lastSequenceFeatures != null) - { - sfSize = lastSequenceFeatures.length; - } - } - } - - if (lastSequenceFeatures == null || sfSize == 0) + // column is 'base 1' but getCharAt is an array index (ie from 0) + if (Comparison.isGap(seq.getCharAt(column - 1))) { + /* + * returning null allows the colour scheme to provide gap colour + * - normally white, but can be customised + */ return null; } - if (Comparison.isGap(lastSeq.getCharAt(column))) - { - return Color.white; - } - Color renderedColour = null; if (transparency == 1.0f) { - renderedColour = findFeatureColour(seq, seq.findPosition(column)); + /* + * simple case - just find the topmost rendered visible feature colour + */ + renderedColour = findFeatureColour(seq, column); } else { - renderedColour = drawSequence(g, lastSeq, column, column, 0, true); + /* + * transparency case - draw all visible features in render order to + * build up a composite colour on the graphics context + */ + renderedColour = drawSequence(g, seq, column, column, 0, true); } return renderedColour; } /** * Draws the sequence features on the graphics context, or just determines the - * colour that would be drawn (if flag offscreenrender is true). + * colour that would be drawn (if flag colourOnly is true). Returns the last + * colour drawn (which may not be the effective colour if transparency + * applies), or null if no feature is drawn in the range given. * * @param g * the graphics context to draw on (may be null if colourOnly==true) * @param seq * @param start - * start column (or sequence position in offscreenrender mode) + * start column * @param end - * end column (not used in offscreenrender mode) + * end column * @param y1 * vertical offset at which to draw on the graphics * @param colourOnly @@ -291,21 +269,17 @@ public class FeatureRenderer extends FeatureRendererModel final SequenceI seq, int start, int end, int y1, boolean colourOnly) { - SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); - if (sequenceFeatures == null || sequenceFeatures.length == 0) + /* + * 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; } updateFeatures(); - if (lastSeq == null || seq != lastSeq - || sequenceFeatures != lastSequenceFeatures) - { - lastSeq = seq; - lastSequenceFeatures = sequenceFeatures; - } - if (transparency != 1f && g != null) { Graphics2D g2 = (Graphics2D) g; @@ -313,10 +287,6 @@ public class FeatureRenderer extends FeatureRendererModel transparency)); } - int startPos = lastSeq.findPosition(start); - int endPos = lastSeq.findPosition(end); - - sfSize = lastSequenceFeatures.length; Color drawnColour = null; /* @@ -330,55 +300,71 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - // loop through all features in sequence to find - // current feature to render - for (int sfindex = 0; sfindex < sfSize; sfindex++) + FeatureColourI fc = getFeatureStyle(type); + List overlaps = seq.getFeatures().findFeatures( + visiblePositions.getBegin(), visiblePositions.getEnd(), type); + + if (fc.isSimpleColour()) + { + filterFeaturesForDisplay(overlaps); + } + + for (SequenceFeature sf : overlaps) { - final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex]; - if (!sequenceFeature.type.equals(type)) + Color featureColour = getColor(sf, fc); + if (featureColour == null) { + /* + * feature excluded by visibility settings, 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(); } - - /* - * check feature overlaps the target range - * TODO: efficient retrieval of features overlapping a range - */ - if (sequenceFeature.getBegin() > endPos - || sequenceFeature.getEnd() < startPos) + int visibleEnd = sf.getEnd(); + if (visibleEnd > visiblePositions.getEnd()) { - continue; + 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 + * is not implemented as a selectable option + * if (av.isShowSequenceFeaturesHeight() && !Float.isNaN(sequenceFeature.score)) { @@ -394,15 +380,16 @@ public class FeatureRenderer extends FeatureRendererModel } else { + */ 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) { drawnColour = featureColour; } - } + /*}*/ } } } @@ -420,24 +407,6 @@ public class FeatureRenderer extends FeatureRendererModel } /** - * Answers true if the feature belongs to a feature group which is not - * currently displayed, else false - * - * @param sequenceFeature - * @return - */ - protected boolean featureGroupNotShown( - final SequenceFeature sequenceFeature) - { - return featureGroups != null - && sequenceFeature.featureGroup != null - && sequenceFeature.featureGroup.length() != 0 - && featureGroups.containsKey(sequenceFeature.featureGroup) - && !featureGroups.get(sequenceFeature.featureGroup) - .booleanValue(); - } - - /** * Called when alignment in associated view has new/modified features to * discover and display. * @@ -445,35 +414,38 @@ public class FeatureRenderer extends FeatureRendererModel @Override public void featuresAdded() { - lastSeq = null; findAllFeatures(); } /** - * 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) { - SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); - if (sequenceFeatures == null || sequenceFeatures.length == 0) - { - return null; - } - - // updateFeatures(); + /* + * check for new feature added while processing + */ + updateFeatures(); /* * 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)) @@ -481,33 +453,21 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++) + List overlaps = seq.findFeatures(column, column, + type); + for (SequenceFeature sequenceFeature : overlaps) { - SequenceFeature sequenceFeature = sequenceFeatures[sfindex]; - if (!sequenceFeature.type.equals(type)) - { - continue; - } - - if (featureGroupNotShown(sequenceFeature)) + if (!featureGroupNotShown(sequenceFeature)) { - continue; - } - - boolean featureIsAtPosition = sequenceFeature.begin <= pos - && sequenceFeature.end >= pos; - if (sequenceFeature.isContactFeature()) - { - featureIsAtPosition = sequenceFeature.begin == pos - || sequenceFeature.end == pos; - } - if (featureIsAtPosition) - { - return getColour(sequenceFeature); + Color col = getColour(sequenceFeature); + if (col != null) + { + return col; + } } } } - + /* * no displayed feature found at position */