X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=b007365df8ac769a34a1310a28f1d67d54000085;hb=167ce32fb49494a4d6ae03ffdb430f05f4d93f76;hp=909ee103bf86fe485b6f0155f1a1c2ff0ba3a1d0;hpb=72b3f05a1157da32ada5aea139139996dddea219;p=jalview.git diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 909ee10..b007365 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -1,7 +1,29 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.renderer.seqfeatures; +import jalview.api.AlignViewportI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.AlphaComposite; import java.awt.Color; @@ -10,8 +32,7 @@ import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.image.BufferedImage; -public class FeatureRenderer extends - jalview.viewmodel.seqfeatures.FeatureRendererModel +public class FeatureRenderer extends FeatureRendererModel { FontMetrics fm; @@ -20,28 +41,6 @@ public class FeatureRenderer extends boolean offscreenRender = false; - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param sg - * DOCUMENT ME! - * @param start - * DOCUMENT ME! - * @param end - * DOCUMENT ME! - * @param x1 - * DOCUMENT ME! - * @param y1 - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param height - * DOCUMENT ME! - */ protected SequenceI lastSeq; char s; @@ -52,6 +51,18 @@ public class FeatureRenderer extends boolean av_validCharWidth, av_isShowSeqFeatureHeight; + private Integer currentColour; + + /** + * Constructor given a viewport + * + * @param viewport + */ + public FeatureRenderer(AlignViewportI viewport) + { + this.av = viewport; + } + protected void updateAvConfig() { av_charHeight = av.getCharHeight(); @@ -164,54 +175,53 @@ public class FeatureRenderer extends charOffset = (av_charWidth - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), charOffset + (av_charWidth * (i - start)), pady); - } } } BufferedImage offscreenImage; + @Override public Color findFeatureColour(Color initialCol, SequenceI seq, int res) { return new Color(findFeatureColour(initialCol.getRGB(), seq, res)); } /** - * This is used by the Molecule Viewer and Overview to get the accurate - * colourof the rendered sequence + * This is used by the Molecule Viewer and Overview to get the accurate colour + * of the rendered sequence */ - public synchronized int findFeatureColour(int initialCol, final SequenceI seq, - int column) + public synchronized int findFeatureColour(int initialCol, + final SequenceI seq, int column) { if (!av.isShowSequenceFeatures()) { return initialCol; } - final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq - .getDatasetSequence() : seq; + SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); if (seq != lastSeq) { lastSeq = seq; - sequenceFeatures = aseq.getSequenceFeatures(); - if (sequenceFeatures != null) + lastSequenceFeatures = sequenceFeatures; + if (lastSequenceFeatures != null) { - sfSize = sequenceFeatures.length; + sfSize = lastSequenceFeatures.length; } } else { - if (sequenceFeatures != lastSeq.getSequenceFeatures()) + if (lastSequenceFeatures != sequenceFeatures) { - sequenceFeatures = lastSeq.getSequenceFeatures(); - if (sequenceFeatures != null) + lastSequenceFeatures = sequenceFeatures; + if (lastSequenceFeatures != null) { - sfSize = sequenceFeatures.length; + sfSize = lastSequenceFeatures.length; } } } - if (sequenceFeatures == null || sfSize == 0) + if (lastSequenceFeatures == null || sfSize == 0) { return initialCol; } @@ -249,13 +259,13 @@ public class FeatureRenderer extends } else { - return ((Integer) currentColour).intValue(); + return currentColour.intValue(); } } } - private volatile SequenceFeature[] sequenceFeatures; + private volatile SequenceFeature[] lastSequenceFeatures; int sfSize; @@ -268,10 +278,8 @@ public class FeatureRenderer extends public synchronized void drawSequence(Graphics g, final SequenceI seq, int start, int end, int y1) { - final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq - .getDatasetSequence() : seq; - if (aseq.getSequenceFeatures() == null - || aseq.getSequenceFeatures().length == 0) + SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures(); + if (sequenceFeatures == null || sequenceFeatures.length == 0) { return; } @@ -284,10 +292,10 @@ public class FeatureRenderer extends updateFeatures(); if (lastSeq == null || seq != lastSeq - || aseq.getSequenceFeatures() != sequenceFeatures) + || sequenceFeatures != lastSequenceFeatures) { lastSeq = seq; - sequenceFeatures = aseq.getSequenceFeatures(); + lastSequenceFeatures = sequenceFeatures; } if (transparency != 1 && g != null) @@ -303,7 +311,7 @@ public class FeatureRenderer extends epos = lastSeq.findPosition(end); } - sfSize = sequenceFeatures.length; + sfSize = lastSequenceFeatures.length; String type; for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) { @@ -318,25 +326,24 @@ public class FeatureRenderer extends // current feature to render for (sfindex = 0; sfindex < sfSize; sfindex++) { - if (!sequenceFeatures[sfindex].type.equals(type)) + final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex]; + if (!sequenceFeature.type.equals(type)) { continue; } if (featureGroups != null - && sequenceFeatures[sfindex].featureGroup != null - && sequenceFeatures[sfindex].featureGroup.length() != 0 - && featureGroups - .containsKey(sequenceFeatures[sfindex].featureGroup) - && !((Boolean) featureGroups - .get(sequenceFeatures[sfindex].featureGroup)) + && sequenceFeature.featureGroup != null + && sequenceFeature.featureGroup.length() != 0 + && featureGroups.containsKey(sequenceFeature.featureGroup) + && !featureGroups.get(sequenceFeature.featureGroup) .booleanValue()) { continue; } if (!offscreenRender - && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + && (sequenceFeature.getBegin() > epos || sequenceFeature .getEnd() < spos)) { continue; @@ -344,56 +351,51 @@ public class FeatureRenderer extends if (offscreenRender && offscreenImage == null) { - if (sequenceFeatures[sfindex].begin <= start - && sequenceFeatures[sfindex].end >= start) + if (sequenceFeature.begin <= start + && sequenceFeature.end >= start) { // 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(sequenceFeatures[sfindex]).getRGB()); + currentColour = new Integer(getColour(sequenceFeature).getRGB()); // used to be retreived from av.featuresDisplayed // currentColour = av.featuresDisplayed // .get(sequenceFeatures[sfindex].type); } } - else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) + else if (sequenceFeature.type.equals("disulfide bond")) { - - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - getColour(sequenceFeatures[sfindex]) + 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); - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]) + 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); } - else if (showFeature(sequenceFeatures[sfindex])) + else if (showFeature(sequenceFeature)) { if (av_isShowSeqFeatureHeight - && sequenceFeatures[sfindex].score != Float.NaN) + && !Float.isNaN(sequenceFeature.score)) { renderScoreFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]), start, end, y1, - normaliseScore(sequenceFeatures[sfindex])); + seq.findIndex(sequenceFeature.begin) - 1, + seq.findIndex(sequenceFeature.end) - 1, + getColour(sequenceFeature), start, end, y1, + normaliseScore(sequenceFeature)); } else { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]), start, end, y1); + renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1, + seq.findIndex(sequenceFeature.end) - 1, + getColour(sequenceFeature), start, end, y1); } } @@ -401,7 +403,7 @@ public class FeatureRenderer extends } - if (transparency != 1.0f && g != null && transparencyAvailable) + if (transparency != 1.0f && g != null) { Graphics2D g2 = (Graphics2D) g; g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, @@ -409,24 +411,12 @@ public class FeatureRenderer extends } } - boolean transparencyAvailable = true; - - protected void setTransparencyAvailable(boolean isTransparencyAvailable) - { - transparencyAvailable = isTransparencyAvailable; - } - - @Override - public boolean isTransparencyAvailable() - { - return transparencyAvailable; - } - /** * Called when alignment in associated view has new/modified features to * discover and display. * */ + @Override public void featuresAdded() { lastSeq = null;