X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=cc2c04870fa801287daaf6f0cf32e33ed912a7d8;hb=33b4764ff9d75a0e966c3c8b4b7956f54431221f;hp=09dccfec441f4478df02a8c32f56a41a4265d4c9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 09dccfe..cc2c048 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * 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 @@ -18,6 +18,7 @@ package jalview.gui; import java.util.*; +import java.util.concurrent.ConcurrentHashMap; import java.awt.*; import java.awt.event.*; @@ -36,7 +37,7 @@ import jalview.schemes.GraduatedColor; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer implements jalview.api.FeatureRenderer { AlignmentPanel ap; @@ -53,11 +54,11 @@ public class FeatureRenderer int charOffset; - Hashtable featureColours = new Hashtable(); + Map featureColours = new ConcurrentHashMap(); // A higher level for grouping features of a // particular type - Hashtable featureGroups = new Hashtable(); + Map featureGroups = new ConcurrentHashMap(); // This is actually an Integer held in the hashtable, // Retrieved using the key feature type @@ -79,19 +80,24 @@ public class FeatureRenderer { this.ap = ap; this.av = ap.av; + if (ap != null && ap.seqPanel != null && ap.seqPanel.seqCanvas != null + && ap.seqPanel.seqCanvas.fr != null) + { + transferSettings(ap.seqPanel.seqCanvas.fr); + } } public class FeatureRendererSettings implements Cloneable { String[] renderOrder; - Hashtable featureGroups; + Map featureGroups; - Hashtable featureColours; + Map featureColours; float transparency; - Hashtable featureOrder; + Map featureOrder; public FeatureRendererSettings(String[] renderOrder, Hashtable featureGroups, Hashtable featureColours, @@ -105,13 +111,47 @@ public class FeatureRenderer this.featureOrder = featureOrder; } + /** + * create an independent instance of the feature renderer settings + * + * @param fr + */ public FeatureRendererSettings(FeatureRenderer fr) { - this.renderOrder = fr.renderOrder; - this.featureGroups = fr.featureGroups; - this.featureColours = fr.featureColours; + renderOrder = null; + featureGroups = new ConcurrentHashMap(); + featureColours = new ConcurrentHashMap(); + featureOrder = new ConcurrentHashMap(); + if (fr.renderOrder != null) + { + this.renderOrder = new String[fr.renderOrder.length]; + System.arraycopy(fr.renderOrder, 0, renderOrder, 0, + fr.renderOrder.length); + } + if (fr.featureGroups != null) + { + this.featureGroups = new ConcurrentHashMap(fr.featureGroups); + } + if (fr.featureColours != null) + { + this.featureColours = new ConcurrentHashMap(fr.featureColours); + } + Iterator en = fr.featureColours.keySet().iterator(); + while (en.hasNext()) + { + Object next = en.next(); + Object val = featureColours.get(next); + if (val instanceof GraduatedColor) + { + featureColours + .put(next, new GraduatedColor((GraduatedColor) val)); + } + } this.transparency = fr.transparency; - this.featureOrder = fr.featureOrder; + if (fr.featureOrder != null) + { + this.featureOrder = new ConcurrentHashMap(fr.featureOrder); + } } } @@ -128,14 +168,43 @@ public class FeatureRenderer this.transparency = fr.transparency; this.featureOrder = fr.featureOrder; } - + /** + * update from another feature renderer + * @param fr settings to copy + */ public void transferSettings(FeatureRenderer fr) { - this.renderOrder = fr.renderOrder; - this.featureGroups = fr.featureGroups; - this.featureColours = fr.featureColours; - this.transparency = fr.transparency; - this.featureOrder = fr.featureOrder; + FeatureRendererSettings frs = new FeatureRendererSettings(fr); + this.renderOrder = frs.renderOrder; + this.featureGroups = frs.featureGroups; + this.featureColours = frs.featureColours; + this.transparency = frs.transparency; + this.featureOrder = frs.featureOrder; + if (av != null && av != fr.av) + { + // copy over the displayed feature settings + if (fr.av != null) + { + if (fr.av.featuresDisplayed != null) + { + // update display settings + if (av.featuresDisplayed == null) + { + av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed); + } + else + { + av.featuresDisplayed.clear(); + Enumeration en = fr.av.featuresDisplayed.keys(); + while (en.hasMoreElements()) + { + av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE); + } + + } + } + } + } } BufferedImage offscreenImage; @@ -151,7 +220,8 @@ public class FeatureRenderer * This is used by the Molecule Viewer and Overview to get the accurate * colourof the rendered sequence */ - public int findFeatureColour(int initialCol, SequenceI seq, int column) + public synchronized int findFeatureColour(int initialCol, SequenceI seq, + int column) { if (!av.showSequenceFeatures) { @@ -195,7 +265,8 @@ public class FeatureRenderer } currentColour = null; - + // TODO: non-threadsafe - each rendering thread needs its own instance of + // the feature renderer - or this should be synchronized. offscreenRender = true; if (offscreenImage != null) @@ -362,16 +433,16 @@ public class FeatureRenderer else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) { - renderFeature(g, seq, seq - .findIndex(sequenceFeatures[sfindex].begin) - 1, seq - .findIndex(sequenceFeatures[sfindex].begin) - 1, + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, getColour(sequenceFeatures[sfindex]) // 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, + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, getColour(sequenceFeatures[sfindex]) // new Color(((Integer) av.featuresDisplayed // .get(sequenceFeatures[sfindex].type)).intValue()) @@ -383,17 +454,17 @@ public class FeatureRenderer if (av.showSeqFeaturesHeight && sequenceFeatures[sfindex].score != Float.NaN) { - renderScoreFeature(g, seq, seq - .findIndex(sequenceFeatures[sfindex].begin) - 1, seq - .findIndex(sequenceFeatures[sfindex].end) - 1, + renderScoreFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, getColour(sequenceFeatures[sfindex]), start, end, y1, normaliseScore(sequenceFeatures[sfindex])); } else { - renderFeature(g, seq, seq - .findIndex(sequenceFeatures[sfindex].begin) - 1, seq - .findIndex(sequenceFeatures[sfindex].end) - 1, + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, getColour(sequenceFeatures[sfindex]), start, end, y1); } } @@ -625,9 +696,10 @@ public class FeatureRenderer { minmax = new Hashtable(); } - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - SequenceFeature[] features = av.alignment.getSequenceAt(i) + SequenceFeature[] features = alignment.getSequenceAt(i) .getDatasetSequence().getSequenceFeatures(); if (features == null) @@ -1062,7 +1134,7 @@ public class FeatureRenderer panel = new JPanel(); panel.add(new JLabel("Description: ", JLabel.RIGHT)); - description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); panel.add(new JScrollPane(description)); @@ -1329,7 +1401,7 @@ public class FeatureRenderer { String type = data[i][0].toString(); setColour(type, data[i][1]); // todo : typesafety - feature color - // interface object + // interface object if (((Boolean) data[i][2]).booleanValue()) { av.featuresDisplayed.put(type, new Integer(getColour(type) @@ -1342,7 +1414,7 @@ public class FeatureRenderer } - Hashtable featureOrder = null; + Map featureOrder = null; /** * analogous to colour - store a normalized ordering for all feature types in