X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=ec609a7d021a76949b9029734547e0ddd44c0064;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c9e9ee4859b8cdd7d337fcfc07de9688e321fbf0;hpb=e5ecde79316259cf913da454373e9f5ee7488798;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index c9e9ee4..ec609a7 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,31 +1,53 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
@@ -81,28 +103,33 @@ public class AnnotationColourChooser extends Panel implements
setDefaultMinMax();
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.isPredefinedColours());
- if (!acg.isPredefinedColours())
+ 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++)
{
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
+ {
list.addElement(label);
+ }
else
+ {
list.addElement(label + "_" + (index++));
+ }
}
for (int i = 0; i < list.size(); i++)
@@ -110,9 +137,12 @@ 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)
{
@@ -121,17 +151,18 @@ 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.");
+ MessageManager
+ .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -143,7 +174,8 @@ public class AnnotationColourChooser extends Panel implements
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 560,
175);
validate();
}
@@ -198,11 +230,13 @@ public class AnnotationColourChooser extends Panel implements
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel(MessageManager.getString("label.use_original_colours"));
+ currentColours.setLabel(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
@@ -302,7 +336,6 @@ public class AnnotationColourChooser extends Panel implements
}
else if (evt.getSource() == ok)
{
- changeColour();
frame.setVisible(false);
}
else if (evt.getSource() == cancel)
@@ -339,14 +372,14 @@ public class AnnotationColourChooser extends Panel implements
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
if (currentColours.getState()
&& !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
ap.paintAlignment(false);
}
}
@@ -400,11 +433,11 @@ 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;
}
@@ -465,6 +498,7 @@ public class AnnotationColourChooser extends Panel implements
av.setGlobalColourScheme(acg);
+ // TODO: per group colour propagation not always desired
if (av.getAlignment().getGroups() != null)
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
@@ -491,6 +525,7 @@ public class AnnotationColourChooser extends Panel implements
}
// update colours in linked windows
+ ap.alignmentChanged();
ap.paintAlignment(true);
}