/*
- * 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 <http://www.gnu.org/licenses/>.
+ * 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;
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;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
slider.addChangeListener(new ChangeListener()
{
@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);
}
+
public void mouseReleased(MouseEvent evt)
{
if (sliderDragging)
{
- sliderDragging=false;
+ sliderDragging = false;
valueChanged(true);
}
ap.paintAlignment(true);
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ 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());
-
+
}
annotations = new JComboBox(
getAnnotationItems(seqAssociated.isSelected()));
- 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"));
+ 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)
{
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());
System.arraycopy(anmap, 0, annmap, 0, annmap.length);
return list;
}
+
private void setDefaultMinMax()
{
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
});
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
- defColours
- .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+ defColours.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(MessageManager.getString("label.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(MessageManager.getString("label.threshold_minmax"));
+ 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(MessageManager.getString("label.per_sequence_only"));
+ seqAssociated.setText(MessageManager
+ .getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
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);
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);
.getSelectedIndex()]];
int aboveThreshold = -1;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
{
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++)