X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=d2d9c9c335b072dcecca03ac87010cd8627e846c;hb=aec85d6dfc1dd5970a50a53dc9d161635d1e9960;hp=0aee327f4e673575b5c5b7e0016636028a6773da;hpb=49bb27409f71165b4d2daa6c38142a6466bb3946;p=jalview.git
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index 0aee327..d2d9c9c
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.
- *
+ * 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;
@@ -30,6 +33,7 @@ import javax.swing.*;
import jalview.datamodel.*;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -53,7 +57,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
FontMetrics fm;
int charOffset;
-
+
Map featureColours = new ConcurrentHashMap();
// A higher level for grouping features of a
@@ -80,6 +84,11 @@ 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
@@ -121,7 +130,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
{
this.renderOrder = new String[fr.renderOrder.length];
System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
- renderOrder.length);
+ fr.renderOrder.length);
}
if (fr.featureGroups != null)
{
@@ -164,6 +173,12 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
this.featureOrder = fr.featureOrder;
}
+ /**
+ * update from another feature renderer
+ *
+ * @param fr
+ * settings to copy
+ */
public void transferSettings(FeatureRenderer fr)
{
FeatureRendererSettings frs = new FeatureRendererSettings(fr);
@@ -172,7 +187,7 @@ 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)
@@ -196,7 +211,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
}
}
}
- }
+ }
}
BufferedImage offscreenImage;
@@ -212,7 +227,8 @@ 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)
{
@@ -256,7 +272,8 @@ 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)
@@ -686,7 +703,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
{
minmax = new Hashtable();
}
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceFeature[] features = alignment.getSequenceAt(i)
@@ -923,8 +940,7 @@ public class FeatureRenderer implements jalview.api.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}));
}
/**
@@ -948,8 +964,7 @@ public class FeatureRenderer implements jalview.api.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)
@@ -1009,7 +1024,7 @@ public class FeatureRenderer implements jalview.api.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;
@@ -1051,7 +1066,7 @@ 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++)
{
@@ -1101,17 +1116,19 @@ 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));
@@ -1123,7 +1140,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
- panel.add(new JLabel("Description: ", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.description"),
+ JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
panel.add(new JScrollPane(description));
@@ -1133,9 +1151,11 @@ 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);
}
@@ -1196,12 +1216,12 @@ public class FeatureRenderer implements jalview.api.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();