X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=28ecc860f7b7af20dbcd96e404e87ba685336bb9;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=d613a30fd4ec831b58fc083c32cc9339e98bc796;hpb=cbc4934969890599b7360f9ff698b9ceebb9933c;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index d613a30..28ecc86 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,23 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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.gui; import java.util.*; +import java.util.concurrent.ConcurrentHashMap; import java.awt.*; import java.awt.event.*; @@ -29,6 +31,7 @@ import javax.swing.*; import jalview.datamodel.*; import jalview.schemes.GraduatedColor; +import jalview.util.MessageManager; /** * DOCUMENT ME! @@ -53,11 +56,11 @@ public class FeatureRenderer implements jalview.api.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 +82,24 @@ public class FeatureRenderer implements jalview.api.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, @@ -113,27 +121,27 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer public FeatureRendererSettings(FeatureRenderer fr) { renderOrder = null; - featureGroups = new Hashtable(); - featureColours = new Hashtable(); - featureOrder = new Hashtable(); + 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, - renderOrder.length); + fr.renderOrder.length); } if (fr.featureGroups != null) { - this.featureGroups = new Hashtable(fr.featureGroups); + this.featureGroups = new ConcurrentHashMap(fr.featureGroups); } if (fr.featureColours != null) { - this.featureColours = new Hashtable(fr.featureColours); + this.featureColours = new ConcurrentHashMap(fr.featureColours); } - Enumeration en = fr.featureColours.keys(); - while (en.hasMoreElements()) + Iterator en = fr.featureColours.keySet().iterator(); + while (en.hasNext()) { - Object next = en.nextElement(); + Object next = en.next(); Object val = featureColours.get(next); if (val instanceof GraduatedColor) { @@ -144,7 +152,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer this.transparency = fr.transparency; if (fr.featureOrder != null) { - this.featureOrder = new Hashtable(fr.featureOrder); + this.featureOrder = new ConcurrentHashMap(fr.featureOrder); } } } @@ -162,7 +170,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer this.transparency = fr.transparency; this.featureOrder = fr.featureOrder; } - + /** + * update from another feature renderer + * @param fr settings to copy + */ public void transferSettings(FeatureRenderer fr) { FeatureRendererSettings frs = new FeatureRendererSettings(fr); @@ -171,7 +182,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer this.featureColours = frs.featureColours; this.transparency = frs.transparency; this.featureOrder = frs.featureOrder; - if (av != null && av!=fr.av) + if (av != null && av != fr.av) { // copy over the displayed feature settings if (fr.av != null) @@ -195,7 +206,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } } } - } + } } BufferedImage offscreenImage; @@ -211,7 +222,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer * This is used by the Molecule Viewer and Overview to get the accurate * colourof the rendered sequence */ - public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column) + public synchronized int findFeatureColour(int initialCol, SequenceI seq, + int column) { if (!av.showSequenceFeatures) { @@ -255,7 +267,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } currentColour = null; - // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized. + // TODO: non-threadsafe - each rendering thread needs its own instance of + // the feature renderer - or this should be synchronized. offscreenRender = true; if (offscreenImage != null) @@ -685,9 +698,10 @@ public class FeatureRenderer implements jalview.api.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) @@ -1049,7 +1063,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer { panel = new JPanel(new GridLayout(4, 1)); tmp = new JPanel(); - tmp.add(new JLabel("Select Feature: ")); + tmp.add(new JLabel(MessageManager.getString("label.select_feature"))); overlaps = new JComboBox(); for (int i = 0; i < features.length; i++) { @@ -1099,17 +1113,17 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel("Name: ", JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT)); tmp.add(name); tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel("Group: ", JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.group")+":", JLabel.RIGHT)); tmp.add(source); tmp = new JPanel(); panel.add(tmp); - tmp.add(new JLabel("Colour: ", JLabel.RIGHT)); + tmp.add(new JLabel(MessageManager.getString("label.colour"), JLabel.RIGHT)); tmp.add(colour); colour.setPreferredSize(new Dimension(150, 15)); colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9)); @@ -1121,8 +1135,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer bigPanel.add(panel, BorderLayout.NORTH); panel = new JPanel(); - panel.add(new JLabel("Description: ", JLabel.RIGHT)); - description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + panel.add(new JLabel(MessageManager.getString("label.description"), JLabel.RIGHT)); + description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); panel.add(new JScrollPane(description)); @@ -1131,9 +1145,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer bigPanel.add(panel, BorderLayout.SOUTH); panel = new JPanel(); - panel.add(new JLabel(" Start:", JLabel.RIGHT)); + panel.add(new JLabel(MessageManager.getString("label.start"), JLabel.RIGHT)); panel.add(start); - panel.add(new JLabel(" End:", JLabel.RIGHT)); + panel.add(new JLabel(MessageManager.getString("label.end"), JLabel.RIGHT)); panel.add(end); bigPanel.add(panel, BorderLayout.CENTER); } @@ -1402,7 +1416,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } - Hashtable featureOrder = null; + Map featureOrder = null; /** * analogous to colour - store a normalized ordering for all feature types in