/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
+import jalview.analysis.AAFrequency;
+import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import java.awt.event.MouseEvent;
import java.util.Vector;
-public class UserDefinedColours extends Panel implements ActionListener,
- AdjustmentListener, FocusListener
+public class UserDefinedColours extends Panel
+ implements ActionListener, AdjustmentListener, FocusListener
{
AlignmentPanel ap;
Button selectedButton;
- Vector oldColours = new Vector();
+ Vector<Color> oldColours = new Vector<Color>();
ColourSchemeI oldColourScheme;
String originalLabel;
- Object originalColour;
+ FeatureColourI originalColour;
int R = 0, G = 0, B = 0;
if (seqGroup != null)
{
- oldColourScheme = seqGroup.cs;
+ oldColourScheme = seqGroup.getColourScheme();
}
else
{
public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
{
caller = fr;
- originalColour = fr.colourPanel.getBackground();
+ originalColour = new FeatureColour(fr.colourPanel.getBackground());
originalLabel = "Feature Colour";
setForDialog("Select Feature Colour", alignframe);
setTargetColour(fr.colourPanel.getBackground());
*
* @param caller
* - handles events
- * @param col1
+ * @param col
* - original colour
* @param alignframe
* - the parent Frame for the dialog
* @param title
* - window title
*/
- public UserDefinedColours(Component caller, Color col1, Frame alignframe,
+ public UserDefinedColours(Component caller, Color col, Frame alignframe,
String title)
{
this.caller = caller;
- originalColour = col1;
+ originalColour = new FeatureColour(col);
originalLabel = title;
setForDialog(title, alignframe);
- setTargetColour(col1);
+ setTargetColour(col);
dialog.setVisible(true);
}
*/
public UserDefinedColours(Object caller, String label, Color colour)
{
- this(caller, label, colour, colour);
+ this(caller, label, new FeatureColour(colour), colour);
}
/**
* @param graduatedColor
*/
public UserDefinedColours(FeatureSettings me, String type,
- GraduatedColor graduatedColor)
+ FeatureColourI graduatedColor)
{
- this(me, type, graduatedColor, graduatedColor.getMaxColor());
+ this(me, type, graduatedColor, graduatedColor.getMaxColour());
}
- private UserDefinedColours(Object caller, String label, Object ocolour,
- Color colour)
+ private UserDefinedColours(Object caller, String label,
+ FeatureColourI ocolour, Color colour)
{
this.caller = caller;
originalColour = ocolour;
// // not 1.1 compatible!
// dialog = new Dialog(((JVDialog)alignframe), title, true);
// } else {
- throw new Error(
- MessageManager
- .getString("label.error_unsupported_owwner_user_colour_scheme"));
+ throw new Error(MessageManager.getString(
+ "label.error_unsupported_owwner_user_colour_scheme"));
}
dialog.add(this);
int height = 160 + alignframe.getInsets().top + getInsets().bottom;
int width = 400;
- dialog.setBounds(alignframe.getBounds().x
- + (alignframe.getSize().width - width) / 2,
+ dialog.setBounds(
+ alignframe.getBounds().x
+ + (alignframe.getSize().width - width) / 2,
alignframe.getBounds().y
- + (alignframe.getSize().height - height) / 2, width,
- height);
+ + (alignframe.getSize().height - height) / 2,
+ width, height);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
final Object source = evt.getSource();
}
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (evt.getSource() == rScroller)
{
final Button button = new Button();
Color col = Color.white;
- if (oldColourScheme != null)
+ if (oldColourScheme != null && oldColourScheme.isSimple())
{
- try
- {
- col = oldColourScheme.findColour(aa.charAt(0), -1, null);
- } catch (Exception ex)
- {
- }
+ col = oldColourScheme.findColour(aa.charAt(0), 0, null, null, 0f);
}
button.setBackground(col);
oldColours.addElement(col);
button.setFont(new java.awt.Font("Verdana", 1, 10));
button.addMouseListener(new java.awt.event.MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
colourButtonPressed(e);
{
if (caller instanceof FeatureSettings)
{
- ((FeatureSettings) caller).setUserColour(originalLabel, getColor());
+ ((FeatureSettings) caller).setUserColour(originalLabel,
+ new FeatureColour(getColor()));
}
else if (caller instanceof AnnotationColourChooser)
{
}
else if (caller instanceof FeatureRenderer)
{
- ((FeatureRenderer) caller).colourPanel.updateColor(getColor());
+ ((FeatureRenderer) caller).colourPanel
+ .updateColor(new FeatureColour(getColor()));
}
else if (caller instanceof FeatureColourChooser)
{
}
UserColourScheme ucs = new UserColourScheme(newColours);
- if (ap != null)
- {
- ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
- }
+ // if (ap != null)
+ // {
+ // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ // }
if (ap != null)
{
if (seqGroup != null)
{
- seqGroup.cs = ucs;
+ seqGroup.cs = new ResidueShader(ucs);
+ seqGroup.getGroupColourScheme().setThreshold(0,
+ ap.av.isIgnoreGapsConsensus());
}
else
{
ap.av.setGlobalColourScheme(ucs);
+ ap.av.getResidueShading().setThreshold(0,
+ ap.av.isIgnoreGapsConsensus());
}
ap.seqPanel.seqCanvas.img = null;
ap.paintAlignment(true);
if (originalLabel.equals("Min Colour"))
{
((AnnotationColourChooser) caller)
- .minColour_actionPerformed((Color) originalColour);
+ .minColour_actionPerformed(originalColour.getColour());
}
else
{
((AnnotationColourChooser) caller)
- .maxColour_actionPerformed((Color) originalColour);
+ .maxColour_actionPerformed(originalColour.getColour());
}
}
else if (caller instanceof FeatureRenderer)
if (originalLabel.indexOf("inimum") > -1)
{
((FeatureColourChooser) caller)
- .minColour_actionPerformed((Color) originalColour);
+ .minColour_actionPerformed(originalColour.getColour());
}
else
{
((FeatureColourChooser) caller)
- .maxColour_actionPerformed((Color) originalColour);
+ .maxColour_actionPerformed(originalColour.getColour());
}
}
if (dialog != null)
return;
}
- Color[] newColours = new Color[24];
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = (Color) oldColours.elementAt(i);
- buttonPanel.getComponent(i).setBackground(newColours[i]);
- }
-
- UserColourScheme ucs = new UserColourScheme(newColours);
-
if (ap != null)
{
if (seqGroup != null)
{
- seqGroup.cs = ucs;
+ seqGroup.cs = new ResidueShader(oldColourScheme);
+ if (oldColourScheme instanceof PIDColourScheme
+ || oldColourScheme instanceof Blosum62ColourScheme)
+ {
+ seqGroup.cs.setConsensus(AAFrequency.calculate(
+ seqGroup.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
+ }
}
else
{
- ap.av.setGlobalColourScheme(ucs);
+ ap.av.setGlobalColourScheme(oldColourScheme);
}
ap.paintAlignment(true);
}
- else if (jmol != null)
- {
- jmol.setJalviewColourScheme(ucs);
- }
- else if (pdbcanvas != null)
- {
- pdbcanvas.pdb.setColours(ucs);
- }
frame.setVisible(false);
}
git://source.jalview.org / jalview.git / blobdiff