X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=7226eb06b6e2cbcfca5d50dd415ae4a64a5182c6;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=f53f55a453c9858325bad4e68ee72061e2647f87;hpb=42a69102cb90f11498687980f3592ef96a3cf9ea;p=jalview.git
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index f53f55a..7226eb0
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,19 +1,22 @@
/*
- * 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.
- *
+ * 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;
@@ -30,6 +33,8 @@ import net.miginfocom.swing.MigLayout;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+
import java.awt.Dimension;
public class AnnotationColourChooser extends JPanel
@@ -48,13 +53,19 @@ public class AnnotationColourChooser extends JPanel
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)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- for (SequenceGroup sg:ap.av.getAlignment().getGroups())
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs != null)
{
@@ -67,7 +78,9 @@ 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()
{
@@ -76,14 +89,33 @@ public class AnnotationColourChooser extends JPanel
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);
}
});
@@ -95,44 +127,51 @@ 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());
+ minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
seqAssociated.setSelected(acg.isSeqAssociated());
+
}
- adjusting = true;
- annotations = new JComboBox(getAnnotationItems(seqAssociated.isSelected()));
+ 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)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
annotations.setSelectedItem(acg.getAnnotation());
- switch (acg.getAboveThreshold()) {
+ 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.");
+ default:
+ throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
- thresholdValue.setText(""+acg.getAnnotationThreshold());
+ thresholdValue.setText("" + acg.getAnnotationThreshold());
}
try
@@ -150,29 +189,36 @@ public class AnnotationColourChooser extends JPanel
}
- private Vector getAnnotationItems(boolean isSeqAssociated) {
+ private Vector getAnnotationItems(boolean isSeqAssociated)
+ {
Vector list = new Vector();
int index = 1;
int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss=false;
+ boolean enableSeqAss = false;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
{
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef==null)
+ if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
{
if (isSeqAssociated)
- {
+ {
continue;
- }
- } else {
- enableSeqAss=true;
+ }
+ }
+ else
+ {
+ enableSeqAss = true;
}
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
- {anmap[list.size()] = i;
+ {
+ anmap[list.size()] = i;
list.addElement(label);
-
- }else {
- if (!isSeqAssociated) {
+
+ }
+ else
+ {
+ if (!isSeqAssociated)
+ {
anmap[list.size()] = i;
list.addElement(label + "_" + (index++));
}
@@ -180,13 +226,16 @@ public class AnnotationColourChooser extends JPanel
}
seqAssociated.setEnabled(enableSeqAss);
annmap = new int[list.size()];
- System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+ System.arraycopy(anmap, 0, annmap, 0, annmap.length);
return list;
}
+
private void setDefaultMinMax()
{
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
}
public AnnotationColourChooser()
@@ -205,7 +254,7 @@ 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()
{
public void mousePressed(MouseEvent e)
@@ -219,7 +268,7 @@ 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()
{
public void mousePressed(MouseEvent e)
@@ -231,7 +280,7 @@ public class AnnotationColourChooser extends JPanel
}
});
ok.setOpaque(false);
- ok.setText("OK");
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -240,7 +289,7 @@ public class AnnotationColourChooser extends JPanel
}
});
cancel.setOpaque(false);
- cancel.setText("Cancel");
+ cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -249,18 +298,19 @@ public class AnnotationColourChooser extends JPanel
}
});
defColours.setOpaque(false);
- defColours.setText("Defaults");
- defColours.setToolTipText("Reset min and max colours to defaults from user preferences.");
+ defColours.setText(MessageManager.getString("action.set_defaults"));
+ defColours.setToolTipText(MessageManager
+ .getString("label.reset_min_max_colours_to_defaults"));
defColours.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
resetColours_actionPerformed(arg0);
}
});
-
+
annotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -292,7 +342,8 @@ public class AnnotationColourChooser extends JPanel
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)
@@ -302,7 +353,8 @@ public class AnnotationColourChooser extends JPanel
});
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)
@@ -312,19 +364,20 @@ public class AnnotationColourChooser extends JPanel
});
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()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
seqAssociated_actionPerformed(arg0);
}
});
-
+
this.setLayout(borderLayout1);
- jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]"));
+ jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
@@ -339,7 +392,7 @@ public class AnnotationColourChooser extends JPanel
colpanel.add(maxColour);
jPanel2.add(colpanel, "wrap");
jPanel2.add(threshold);
- jPanel2.add(defColours,"skip 1, wrap");
+ jPanel2.add(defColours, "skip 1, wrap");
jPanel2.add(thresholdIsMin);
jPanel2.add(slider, "grow");
jPanel2.add(thresholdValue, "grow");
@@ -350,22 +403,28 @@ public class AnnotationColourChooser extends JPanel
protected void seqAssociated_actionPerformed(ActionEvent arg0)
{
- adjusting=true;
+ adjusting = true;
String cursel = (String) annotations.getSelectedItem();
- boolean isvalid=false,isseqs=seqAssociated.isSelected();
+ boolean isvalid = false, isseqs = seqAssociated.isSelected();
this.annotations.removeAllItems();
- for (String anitem:getAnnotationItems(seqAssociated.isSelected()))
+ for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
{
- if (anitem.equals( cursel) || (isseqs && cursel.startsWith(anitem)))
+ if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
{
- isvalid=true;
- cursel=anitem;
+ isvalid = true;
+ cursel = anitem;
}
this.annotations.addItem(anitem);
}
- adjusting=false;
- if (isvalid) { this.annotations.setSelectedItem(cursel); } else {
- if (annotations.getItemCount()>0) {
+ adjusting = false;
+ if (isvalid)
+ {
+ this.annotations.setSelectedItem(cursel);
+ }
+ else
+ {
+ if (annotations.getItemCount() > 0)
+ {
annotations.setSelectedIndex(0);
}
}
@@ -378,23 +437,27 @@ public class AnnotationColourChooser extends JPanel
}
JComboBox annotations;
+
int[] annmap;
+
JPanel minColour = new JPanel();
JPanel maxColour = new JPanel();
+
JButton defColours = new JButton();
+
JButton ok = new JButton();
JButton cancel = new JButton();
JPanel jPanel1 = new JPanel();
+
JPanel jPanel2 = new JPanel();
-
+
BorderLayout borderLayout1 = new BorderLayout();
JComboBox threshold = new JComboBox();
-
JSlider slider = new JSlider();
JTextField thresholdValue = new JTextField(20);
@@ -402,13 +465,13 @@ public class AnnotationColourChooser extends JPanel
JCheckBox currentColours = new JCheckBox();
JCheckBox thresholdIsMin = new JCheckBox();
-
+
JCheckBox seqAssociated = new JCheckBox();
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);
@@ -420,7 +483,7 @@ 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);
@@ -441,11 +504,11 @@ 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;
}
@@ -503,7 +566,7 @@ public class AnnotationColourChooser extends JPanel
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
@@ -512,8 +575,8 @@ public class AnnotationColourChooser extends JPanel
if (av.getAlignment().getGroups() != null)
{
-
- for (SequenceGroup sg:ap.av.getAlignment().getGroups())
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs == null)
{
@@ -524,7 +587,8 @@ public class AnnotationColourChooser extends JPanel
{
sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
aboveThreshold);
- ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
}
else
@@ -532,13 +596,15 @@ public class AnnotationColourChooser extends JPanel
sg.cs = new AnnotationColourGradient(currentAnnotation,
minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
- ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
}
}
}
ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of updated colours.
+ // ensure all associated views (overviews, structures, etc) are notified of
+ // updated colours.
ap.paintAlignment(true);
}
@@ -556,7 +622,7 @@ public class AnnotationColourChooser extends JPanel
public void cancel_actionPerformed(ActionEvent e)
{
reset();
- // ensure all original colouring is propagated to listeners.
+ // ensure all original colouring is propagated to listeners.
ap.paintAlignment(true);
try
{
@@ -571,8 +637,8 @@ public class AnnotationColourChooser extends JPanel
av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
-
- for (SequenceGroup sg:ap.av.getAlignment().getGroups())
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
@@ -605,18 +671,39 @@ public class AnnotationColourChooser extends JPanel
}
}
- 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())