/*
- * 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.
- *
+ *
* 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+
import java.awt.Dimension;
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
+ */
+ boolean sliderDragging = false;
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
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()
{
if (!adjusting)
{
thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
- valueChanged();
+ valueChanged(!sliderDragging);
}
}
});
slider.addMouseListener(new MouseAdapter()
{
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ sliderDragging=true;
+ super.mousePressed(e);
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent e)
+ {
+ sliderDragging=true;
+ super.mouseDragged(e);
+ }
public void mouseReleased(MouseEvent evt)
{
+ if (sliderDragging)
+ {
+ sliderDragging=false;
+ valueChanged(true);
+ }
ap.paintAlignment(true);
}
});
// 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)
{
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(
System.arraycopy(anmap, 0, annmap, 0, annmap.length);
return list;
}
-
private void setDefaultMinMax()
{
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
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()
{
public void mousePressed(MouseEvent e)
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()
{
public void mousePressed(MouseEvent e)
}
});
ok.setOpaque(false);
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
cancel.setOpaque(false);
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
defColours.setOpaque(false);
- defColours.setText("Defaults");
+ defColours.setText(MessageManager.getString("action.set_defaults"));
defColours
- .setToolTipText("Reset min and max colours to defaults from user preferences.");
+ .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
thresholdValue.setColumns(7);
currentColours.setFont(JvSwingUtils.getLabelFont());
currentColours.setOpaque(false);
- currentColours.setText("Use Original Colours");
+ currentColours.setText(MessageManager.getString("label.use_original_colours"));
currentColours.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText("Threshold is Min/Max");
+ thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText("Per-sequence only");
+ seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
.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;
}
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
}
}
- public void valueChanged()
+ public void valueChanged(boolean updateAllAnnotation)
{
if (currentColours.isSelected()
&& !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
-
currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation);
ap.paintAlignment(false);
}
+ private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+ {
+ if (currentAnnotation.sequenceRef == null
+ || currentAnnotation.threshold == null)
+ {
+ return;
+ }
+ // 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++)
+ {
+ AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+ if (aa.label.equals(currentAnnotation.label))
+ {
+ aa.threshold.value = thr;
+ }
+ }
+ }
+
public void currentColours_actionPerformed(ActionEvent e)
{
if (currentColours.isSelected())
git://source.jalview.org / jalview.git / blobdiff