X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=13885b45370b005378ac348fdbf7edca256bc3a2;hb=4f77328104498504339216829abf5ea87e2791ec;hp=9988076f7fbc5821164145e182003d6b9907863a;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 9988076..13885b4 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -26,7 +26,6 @@ import jalview.datamodel.ContiguousI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.util.Comparison; -import jalview.util.Platform; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.AlphaComposite; @@ -34,7 +33,6 @@ import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; -import java.util.ArrayList; import java.util.List; public class FeatureRenderer extends FeatureRendererModel @@ -92,13 +90,11 @@ public class FeatureRenderer extends FeatureRendererModel int pady = (y1 + charHeight) - charHeight / 5; FontMetrics fm = g.getFontMetrics(); - char s = '\0'; for (int i = featureStart; i <= featureEnd; i++) { + char s = seq.getCharAt(i); - // colourOnly is just for Overview -- no need to check this again - - if (!colourOnly && Comparison.isGap(s = seq.getCharAt(i))) + if (Comparison.isGap(s)) { continue; } @@ -107,12 +103,7 @@ public class FeatureRenderer extends FeatureRendererModel g.fillRect((i - start) * charWidth, y1, charWidth, charHeight); - if (colourOnly) - { - return true; - } - - if (!validCharWidth) + if (colourOnly || !validCharWidth) { continue; } @@ -126,9 +117,6 @@ public class FeatureRenderer extends FeatureRendererModel } /** - * - * BH - this method is never called? - * * Renders the sequence using the given SCORE feature colour between the given * start and end columns. Returns true if at least one column is drawn, else * false (the feature range does not overlap the start and end positions). @@ -223,12 +211,10 @@ public class FeatureRenderer extends FeatureRendererModel @Override public Color findFeatureColour(SequenceI seq, int column, Graphics g) { - // BH 2019.08.01 - // this is already checked in FeatureColorFinder - // if (!av.isShowSequenceFeatures()) - // { - // return null; - // } + if (!av.isShowSequenceFeatures()) + { + return null; + } // column is 'base 1' but getCharAt is an array index (ie from 0) if (Comparison.isGap(seq.getCharAt(column - 1))) @@ -266,8 +252,7 @@ public class FeatureRenderer extends FeatureRendererModel * applies), or null if no feature is drawn in the range given. * * @param g - * the graphics context to draw on (may be null only if t == 1 from - * colourOnly==true) + * the graphics context to draw on (may be null if colourOnly==true) * @param seq * @param start * start column @@ -284,27 +269,21 @@ public class FeatureRenderer extends FeatureRendererModel final SequenceI seq, int start, int end, int y1, boolean colourOnly) { - // from SeqCanvas and OverviewRender /* * if columns are all gapped, or sequence has no features, nothing to do */ - ContiguousI visiblePositions; - if (!seq.getFeatures().hasFeatures() || (visiblePositions = seq - .findPositions(start + 1, end + 1)) == null) + ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1); + if (visiblePositions == null || !seq.getFeatures().hasFeatures()) { return null; } - int vp0 = visiblePositions.getBegin(); - int vp1 = visiblePositions.getEnd(); - updateFeatures(); - if (transparency != 1f) // g cannot be null here if trans == 1f - BH // && g - // != null) + if (transparency != 1f && g != null) { - ((Graphics2D) g).setComposite( - AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, transparency)); } @@ -313,28 +292,25 @@ public class FeatureRenderer extends FeatureRendererModel /* * iterate over features in ordering of their rendering (last is on top) */ - for (int renderIndex = 0, n = renderOrder.length; renderIndex < n; renderIndex++) + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) { String type = renderOrder[renderIndex]; - if (!seq.hasFeatures(type) || !showFeatureOfType(type)) + if (!showFeatureOfType(type)) { continue; } FeatureColourI fc = getFeatureStyle(type); - List overlaps = seq.getFeatures().findFeatures(vp0, - vp1, type); + List overlaps = seq.getFeatures().findFeatures( + visiblePositions.getBegin(), visiblePositions.getEnd(), type); - // colourOnly (i.e. Overview) can only be here if translucent, so - // there is no need to check for filtering - if (!colourOnly && fc.isSimpleColour()) + if (fc.isSimpleColour()) { filterFeaturesForDisplay(overlaps); } - for (int i = overlaps.size(); --i >= 0;) + for (SequenceFeature sf : overlaps) { - SequenceFeature sf = overlaps.get(i); Color featureColour = getColor(sf, fc); if (featureColour == null) { @@ -349,22 +325,22 @@ public class FeatureRenderer extends FeatureRendererModel * restrict to visible positions (or if a contact feature, * to a single position) */ - int sf0 = sf.getBegin(); - int sf1 = sf.getEnd(); - int visibleStart = sf0; - if (visibleStart < vp0) + int visibleStart = sf.getBegin(); + if (visibleStart < visiblePositions.getBegin()) { - visibleStart = sf.isContactFeature() ? sf1 : vp0; + visibleStart = sf.isContactFeature() ? sf.getEnd() + : visiblePositions.getBegin(); } - int visibleEnd = sf1; - if (visibleEnd > vp1) + int visibleEnd = sf.getEnd(); + if (visibleEnd > visiblePositions.getEnd()) { - visibleEnd = sf.isContactFeature() ? sf0 : vp1; + visibleEnd = sf.isContactFeature() ? sf.getBegin() + : visiblePositions.getEnd(); } int featureStartCol = seq.findIndex(visibleStart); - int featureEndCol = (sf.begin == sf.end ? featureStartCol - : seq.findIndex(visibleEnd)); + int featureEndCol = sf.begin == sf.end ? featureStartCol : seq + .findIndex(visibleEnd); // Color featureColour = getColour(sequenceFeature); @@ -405,24 +381,26 @@ 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; + } /*}*/ } } } - if (transparency != 1.0f) + if (transparency != 1.0f && g != null) { /* * reset transparency */ - ((Graphics2D) g).setComposite(NO_TRANSPARENCY); + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(NO_TRANSPARENCY); } return drawnColour; @@ -439,10 +417,6 @@ public class FeatureRenderer extends FeatureRendererModel findAllFeatures(); } - private List overlaps = (Platform.isJS() - ? new ArrayList<>() - : null); - /** * 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 @@ -454,18 +428,12 @@ public class FeatureRenderer extends FeatureRendererModel * colour for features enclosing a gapped column. Check for gap before calling * if different behaviour is wanted. * - * BH 2019.07.30 - * - * Adds a result ArrayList to parameters in order to avoid an unnecessary - * construction of that for every pixel checked. - * - * * @param seq * @param column * (1..) * @return */ - private Color findFeatureColour(SequenceI seq, int column) + Color findFeatureColour(SequenceI seq, int column) { /* * check for new feature added while processing @@ -476,29 +444,22 @@ 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; --renderIndex >= 0;) + for (int renderIndex = renderOrder.length + - 1; renderIndex >= 0; renderIndex--) { String type = renderOrder[renderIndex]; - if (!seq.hasFeatures(type) || !showFeatureOfType(type)) + if (!showFeatureOfType(type)) { continue; } - if (overlaps != null) + List overlaps = seq.findFeatures(column, column, + type); + for (SequenceFeature sequenceFeature : overlaps) { - overlaps.clear(); - } - List list = seq.findFeatures(column, type, overlaps); - if (list.size() > 0) - { - for (int i = 0, n = list.size(); i < n; i++) + if (!featureGroupNotShown(sequenceFeature)) { - SequenceFeature sf = list.get(i); - if (featureGroupNotShown(sf)) - { - continue; - } - Color col = getColour(sf); + Color col = getColour(sequenceFeature); if (col != null) { return col;