X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=3c552a412dace3dabb1e438ce32c4e63c66f5a6f;hb=50ff87bdae1829a7a7471ec393142ae659b40a11;hp=61ef75f062905738a5f807298124b4c094cb43a9;hpb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;p=jalview.git
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 61ef75f..3c552a4 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,38 +1,57 @@
/*
- * 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 2.8.2)
+ * 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;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import net.miginfocom.swing.MigLayout;
-
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import net.miginfocom.swing.MigLayout;
public class AnnotationColourChooser extends JPanel
{
@@ -49,8 +68,10 @@ public class AnnotationColourChooser extends JPanel
jalview.datamodel.AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
+
/**
- * enabled if the user is dragging the slider - try to keep updates to a minimun
+ * enabled if the user is dragging the slider - try to keep updates to a
+ * minimun
*/
boolean sliderDragging = false;
@@ -73,15 +94,18 @@ public class AnnotationColourChooser extends JPanel
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
valueChanged(!sliderDragging);
}
}
@@ -91,21 +115,23 @@ public class AnnotationColourChooser extends JPanel
@Override
public void mousePressed(MouseEvent e)
{
- sliderDragging=true;
+ sliderDragging = true;
super.mousePressed(e);
}
@Override
public void mouseDragged(MouseEvent e)
{
- sliderDragging=true;
+ sliderDragging = true;
super.mouseDragged(e);
}
+
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (sliderDragging)
{
- sliderDragging=false;
+ sliderDragging = false;
valueChanged(true);
}
ap.paintAlignment(true);
@@ -120,24 +146,29 @@ public class AnnotationColourChooser extends JPanel
// Always get default shading from preferences.
setDefaultMinMax();
+ adjusting = true;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.predefinedColours);
- if (!acg.predefinedColours)
+ currentColours.setSelected(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
seqAssociated.setSelected(acg.isSeqAssociated());
+
}
- adjusting = true;
annotations = new JComboBox(
getAnnotationItems(seqAssociated.isSelected()));
- 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)
{
@@ -146,17 +177,16 @@ public class AnnotationColourChooser extends JPanel
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedItem("No Threshold");
+ threshold.setSelectedIndex(0);
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedItem("Above Threshold");
+ threshold.setSelectedIndex(1);
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
- threshold.setSelectedItem("Below Threshold");
+ threshold.setSelectedIndex(2);
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_about_thereshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -200,7 +230,7 @@ public class AnnotationColourChooser extends JPanel
if (!list.contains(label))
{
anmap[list.size()] = i;
- list.addElement(label);
+ list.add(label);
}
else
@@ -208,15 +238,16 @@ public class AnnotationColourChooser extends JPanel
if (!isSeqAssociated)
{
anmap[list.size()] = i;
- list.addElement(label + "_" + (index++));
+ list.add(label + "_" + (index++));
}
}
}
seqAssociated.setEnabled(enableSeqAss);
- annmap = new int[list.size()];
- System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+ this.annmap = new int[list.size()];
+ System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
return list;
}
+
private void setDefaultMinMax()
{
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
@@ -241,9 +272,10 @@ public class AnnotationColourChooser extends JPanel
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
- minColour.setToolTipText("Minimum Colour");
+ minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (minColour.isEnabled())
@@ -255,9 +287,10 @@ public class AnnotationColourChooser extends JPanel
maxColour.setFont(JvSwingUtils.getLabelFont());
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.setToolTipText("Maximum Colour");
+ maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (maxColour.isEnabled())
@@ -270,6 +303,7 @@ public class AnnotationColourChooser extends JPanel
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
@@ -279,6 +313,7 @@ public class AnnotationColourChooser extends JPanel
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
@@ -286,8 +321,8 @@ public class AnnotationColourChooser extends JPanel
});
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
- defColours
- .setToolTipText("Reset min and max colours to defaults from user preferences.");
+ defColours.setToolTipText(MessageManager
+ .getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
@@ -300,6 +335,7 @@ public class AnnotationColourChooser extends JPanel
annotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotations_actionPerformed(e);
@@ -307,6 +343,7 @@ public class AnnotationColourChooser extends JPanel
});
threshold.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
threshold_actionPerformed(e);
@@ -314,6 +351,7 @@ public class AnnotationColourChooser extends JPanel
});
thresholdValue.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
thresholdValue_actionPerformed(e);
@@ -329,9 +367,11 @@ public class AnnotationColourChooser extends JPanel
thresholdValue.setColumns(7);
currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
- currentColours.setText(MessageManager.getString("label.use_original_colours"));
+ currentColours.setText(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
currentColours_actionPerformed(e);
@@ -339,9 +379,11 @@ public class AnnotationColourChooser extends JPanel
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setText(MessageManager
+ .getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
thresholdIsMin_actionPerformed(actionEvent);
@@ -349,7 +391,8 @@ public class AnnotationColourChooser extends JPanel
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
+ seqAssociated.setText(MessageManager
+ .getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
@@ -455,7 +498,7 @@ public class AnnotationColourChooser extends JPanel
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
if (col != null)
{
minColour.setBackground(col);
@@ -467,7 +510,7 @@ public class AnnotationColourChooser extends JPanel
public void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
if (col != null)
{
maxColour.setBackground(col);
@@ -488,11 +531,11 @@ public class AnnotationColourChooser extends JPanel
.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;
}
@@ -550,7 +593,7 @@ public class AnnotationColourChooser extends JPanel
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
@@ -662,7 +705,7 @@ public class AnnotationColourChooser extends JPanel
{
changeColour();
}
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
propagateSeqAssociatedThreshold(updateAllAnnotation);
ap.paintAlignment(false);
}
@@ -674,7 +717,8 @@ public class AnnotationColourChooser extends JPanel
{
return;
}
- // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+ // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation
+ // is false, since we only need to provide a quick visual indicator
float thr = currentAnnotation.threshold.value;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)