From adc06771b3c3eeaac8f54514f00d7c3c692b8844 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 16 Nov 2016 15:45:13 +0000 Subject: [PATCH] JAL-2323 render disulfide bond correctly on overview and structure --- .../renderer/seqfeatures/FeatureRenderer.java | 110 +++++++++++++------- .../seqfeatures/FeatureRendererModel.java | 9 +- 2 files changed, 82 insertions(+), 37 deletions(-) diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index b007365..07d97d0 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -188,15 +188,20 @@ public class FeatureRenderer extends FeatureRendererModel } /** - * This is used by the Molecule Viewer and Overview to get the accurate colour - * of the rendered sequence + * This is used by Structure Viewers and the Overview Window to get the + * feature colour of the rendered sequence, returned as an RGB value + * + * @param defaultColour + * @param seq + * @param column + * @return */ - public synchronized int findFeatureColour(int initialCol, + public synchronized int findFeatureColour(int defaultColour, final SequenceI seq, int column) { if (!av.isShowSequenceFeatures()) { - return initialCol; + return defaultColour; } SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); @@ -223,7 +228,7 @@ public class FeatureRenderer extends FeatureRendererModel if (lastSequenceFeatures == null || sfSize == 0) { - return initialCol; + return defaultColour; } if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) @@ -244,7 +249,7 @@ public class FeatureRenderer extends FeatureRendererModel if (offscreenImage != null) { - offscreenImage.setRGB(0, 0, initialCol); + offscreenImage.setRGB(0, 0, defaultColour); drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0); return offscreenImage.getRGB(0, 0); @@ -255,7 +260,7 @@ public class FeatureRenderer extends FeatureRendererModel if (currentColour == null) { - return initialCol; + return defaultColour; } else { @@ -275,6 +280,19 @@ public class FeatureRenderer extends FeatureRendererModel int epos; + /** + * Draws the sequence on the graphics context, or just determines the colour + * that would be drawn (if flag offscreenrender is true). + * + * @param g + * @param seq + * @param start + * start column (or sequence position in offscreenrender mode) + * @param end + * end column (not used in offscreenrender mode) + * @param y1 + * vertical offset at which to draw on the graphics + */ public synchronized void drawSequence(Graphics g, final SequenceI seq, int start, int end, int y1) { @@ -312,12 +330,9 @@ public class FeatureRenderer extends FeatureRendererModel } sfSize = lastSequenceFeatures.length; - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + for (String type : renderOrder) { - type = renderOrder[renderIndex]; - - if (type == null || !showFeatureOfType(type)) + if (!showFeatureOfType(type)) { continue; } @@ -332,16 +347,16 @@ public class FeatureRenderer extends FeatureRendererModel continue; } - if (featureGroups != null - && sequenceFeature.featureGroup != null - && sequenceFeature.featureGroup.length() != 0 - && featureGroups.containsKey(sequenceFeature.featureGroup) - && !featureGroups.get(sequenceFeature.featureGroup) - .booleanValue()) + if (featureGroupNotShown(sequenceFeature)) { continue; } + /* + * check feature overlaps the visible part of the alignment, + * unless doing offscreenRender (to the Overview window or a + * structure viewer) which is not limited + */ if (!offscreenRender && (sequenceFeature.getBegin() > epos || sequenceFeature .getEnd() < spos)) @@ -349,35 +364,42 @@ public class FeatureRenderer extends FeatureRendererModel continue; } + Color featureColour = getColour(sequenceFeature); + boolean isDisulfideBond = "disulfide bond".equals(sequenceFeature.type); if (offscreenRender && offscreenImage == null) { - if (sequenceFeature.begin <= start - && sequenceFeature.end >= start) + /* + * offscreen mode with no image (image is only needed if transparency + * is applied to feature colours) - just check feature is rendered at + * the requested position (start == sequence position in this mode) + */ + boolean featureIsAtPosition = sequenceFeature.begin <= start + && sequenceFeature.end >= start; + if (isDisulfideBond) + { + featureIsAtPosition = sequenceFeature.begin == start + || sequenceFeature.end == start; + } + if (featureIsAtPosition) { // this is passed out to the overview and other sequence renderers // (e.g. molecule viewer) to get displayed colour for rendered // sequence - currentColour = new Integer(getColour(sequenceFeature).getRGB()); + currentColour = new Integer(featureColour.getRGB()); // used to be retreived from av.featuresDisplayed // currentColour = av.featuresDisplayed // .get(sequenceFeatures[sfindex].type); } } - else if (sequenceFeature.type.equals("disulfide bond")) + else if (isDisulfideBond) { renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, - seq.findIndex(sequenceFeature.begin) - 1, - getColour(sequenceFeature) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); + seq.findIndex(sequenceFeature.begin) - 1, featureColour, + start, end, y1); renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1, - seq.findIndex(sequenceFeature.end) - 1, - getColour(sequenceFeature) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); + seq.findIndex(sequenceFeature.end) - 1, featureColour, + start, end, y1); } else if (showFeature(sequenceFeature)) @@ -388,19 +410,17 @@ public class FeatureRenderer extends FeatureRendererModel renderScoreFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.end) - 1, - getColour(sequenceFeature), start, end, y1, + featureColour, start, end, y1, normaliseScore(sequenceFeature)); } else { renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, seq.findIndex(sequenceFeature.end) - 1, - getColour(sequenceFeature), start, end, y1); + featureColour, start, end, y1); } } - } - } if (transparency != 1.0f && g != null) @@ -412,6 +432,24 @@ 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. * diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 4ac4804..7ff9adf 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -564,9 +564,16 @@ public abstract class FeatureRendererModel implements return fc.isColored(sequenceFeature); } + /** + * Answers true if the feature type is currently selected to be displayed, + * else false + * + * @param type + * @return + */ protected boolean showFeatureOfType(String type) { - return av.getFeaturesDisplayed().isVisible(type); + return type == null ? false : av.getFeaturesDisplayed().isVisible(type); } @Override -- 1.7.10.2