X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=c1363d788d2c2647677b9fe2a1db829160ea6df2;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=8b891e59e4d7fd9298732f7d26f6cbdf50898a0f;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index 8b891e5..c1363d7
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,19 +1,22 @@
/*
- * 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
+ * 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.appletgui;
@@ -24,9 +27,7 @@ import java.awt.event.*;
import jalview.datamodel.*;
import jalview.schemes.*;
-import java.awt.Rectangle;
-
-import javax.swing.BoxLayout;
+import jalview.util.MessageManager;
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
@@ -83,19 +84,20 @@ public class AnnotationColourChooser extends Panel implements
setDefaultMinMax();
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.predefinedColours);
- if (!acg.predefinedColours)
+ currentColours.setState(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
+ // seqAssociated.setState(acg.isSeqAssociated());
}
- adjusting = true;
-
Vector list = new Vector();
int index = 1;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
@@ -112,9 +114,12 @@ public class AnnotationColourChooser extends Panel implements
annotations.addItem(list.elementAt(i).toString());
}
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold"));
if (oldcs instanceof AnnotationColourGradient)
{
@@ -123,17 +128,16 @@ public class AnnotationColourChooser extends Panel implements
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.select("No Threshold");
+ threshold.select(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.select("Above Threshold");
+ threshold.select(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.select("Below Threshold");
+ threshold.select(1);
break;
default:
- throw new Error(
- "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ throw new Error(MessageManager.getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -145,7 +149,8 @@ public class AnnotationColourChooser extends Panel implements
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 560,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 560,
175);
validate();
}
@@ -173,21 +178,21 @@ public class AnnotationColourChooser extends Panel implements
private void jbInit() throws Exception
{
minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setLabel("Min Colour");
+ minColour.setLabel(MessageManager.getString("label.min_colour"));
minColour.addActionListener(this);
maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setLabel("Max Colour");
+ maxColour.setLabel(MessageManager.getString("label.max_colour"));
maxColour.addActionListener(this);
thresholdIsMin.addItemListener(this);
- ok.setLabel("OK");
+ ok.setLabel(MessageManager.getString("action.ok"));
ok.addActionListener(this);
- cancel.setLabel("Cancel");
+ cancel.setLabel(MessageManager.getString("action.cancel"));
cancel.addActionListener(this);
- defColours.setLabel("Defaults");
+ defColours.setLabel(MessageManager.getString("action.set_defaults"));
defColours.addActionListener(this);
annotations.addItemListener(this);
@@ -200,11 +205,13 @@ public class AnnotationColourChooser extends Panel implements
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel("Use Original Colours");
+ currentColours.setLabel(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel("Threshold is min/max");
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
@@ -402,11 +409,11 @@ public class AnnotationColourChooser extends Panel implements
.getSelectedIndex()];
int aboveThreshold = -1;
- if (threshold.getSelectedItem().equals("Above Threshold"))
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedItem().equals("Below Threshold"))
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
@@ -460,13 +467,14 @@ public class AnnotationColourChooser extends Panel implements
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.getState();
av.setGlobalColourScheme(acg);
+ // TODO: per group colour propagation not always desired
if (av.getAlignment().getGroups() != null)
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
@@ -493,6 +501,7 @@ public class AnnotationColourChooser extends Panel implements
}
// update colours in linked windows
+ ap.alignmentChanged();
ap.paintAlignment(true);
}