X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=5a96ff50d7959b3d494fa1a4edd8e267664ae977;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=09dccfec441f4478df02a8c32f56a41a4265d4c9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index 09dccfe..5a96ff5
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,23 +1,27 @@
/*
- * 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 2.8.2b1)
+ * 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.
- *
+ * 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 .
+ * 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 +33,7 @@ import javax.swing.*;
import jalview.datamodel.*;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -36,7 +41,7 @@ import jalview.schemes.GraduatedColor;
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
AlignmentPanel ap;
@@ -53,11 +58,11 @@ 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 +84,24 @@ 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 +115,47 @@ 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);
+ }
}
}
@@ -129,13 +173,45 @@ public class FeatureRenderer
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 +227,8 @@ 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 +272,8 @@ 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 +440,16 @@ 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 +461,17 @@ 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 +703,10 @@ 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)
@@ -861,8 +940,7 @@ public class FeatureRenderer
return ((GraduatedColor) fc).getMaxColor();
}
}
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + featureType);
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),featureType}));
}
/**
@@ -886,8 +964,7 @@ public class FeatureRenderer
return ((GraduatedColor) fc).findColor(feature);
}
}
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + feature.getType());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),feature.getType()}));
}
private boolean showFeature(SequenceFeature sequenceFeature)
@@ -947,7 +1024,7 @@ public class FeatureRenderer
if (fcol instanceof Color)
{
Color col = JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour", ((Color) fcol));
+ MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
if (col != null)
{
fcol = col;
@@ -989,7 +1066,7 @@ public class 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++)
{
@@ -1039,17 +1116,19 @@ public class 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));
@@ -1061,8 +1140,9 @@ public class 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));
@@ -1071,9 +1151,11 @@ public class 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);
}
@@ -1134,12 +1216,12 @@ public class FeatureRenderer
{ "OK", "Cancel" };
}
- String title = newFeatures ? "Create New Sequence Feature(s)"
- : "Amend/Delete Features for " + sequences[0].getName();
+ String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options, "OK");
+ JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
@@ -1329,7 +1411,7 @@ 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 +1424,7 @@ public class FeatureRenderer
}
- Hashtable featureOrder = null;
+ Map featureOrder = null;
/**
* analogous to colour - store a normalized ordering for all feature types in