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JAL-2386 simplify changeColour (doesn't change colour thresholds)
[jalview.git]
/
src
/
jalview
/
appletgui
/
APopupMenu.java
diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
1f3d318
..
018b227
100644
(file)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-42,7
+42,8
@@
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.ColourSchemeI;
+import jalview.schemes.CollectionColourScheme;
+import jalview.schemes.CollectionColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.JalviewColourScheme;
@@
-329,20
+330,21
@@
public class APopupMenu extends java.awt.PopupMenu implements
*
* @param cs
*/
*
* @param cs
*/
- protected void setSelectedColour(ColourSchemeI cs)
+ protected void setSelectedColour(CollectionColourSchemeI cs)
{
{
- if (cs == null)
+ if (cs == null || cs.getColourScheme() == null)
{
noColour.setState(true);
}
else
{
{
noColour.setState(true);
}
else
{
+ String name = cs.getColourScheme().getSchemeName();
for (int i = 0; i < colourMenu.getItemCount(); i++)
{
MenuItem item = colourMenu.getItem(i);
if (item instanceof CheckboxMenuItem)
{
for (int i = 0; i < colourMenu.getItemCount(); i++)
{
MenuItem item = colourMenu.getItem(i);
if (item instanceof CheckboxMenuItem)
{
- if (cs.getSchemeName().equals(item.getName()))
+ if (name.equals(item.getName()))
{
((CheckboxMenuItem) item).setState(true);
}
{
((CheckboxMenuItem) item).setState(true);
}
@@
-565,7
+567,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
BLOSUM62Colour_actionPerformed();
}
{
BLOSUM62Colour_actionPerformed();
}
- else if (source == PIDColour)
+ else if (evt.getSource() == PIDColour)
{
PIDColour_actionPerformed();
}
{
PIDColour_actionPerformed();
}
@@
-958,6
+960,8
@@
public class APopupMenu extends java.awt.PopupMenu implements
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
@@
-1092,6
+1096,9
@@
public class APopupMenu extends java.awt.PopupMenu implements
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.addActionListener(this);
+
editMenu.add(copy);
copy.addActionListener(this);
editMenu.add(cut);
editMenu.add(copy);
copy.addActionListener(this);
editMenu.add(cut);
@@
-1140,61
+1147,63
@@
public class APopupMenu extends java.awt.PopupMenu implements
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
+ sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg,
+ ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
refresh();
}
protected void zappoColour_actionPerformed()
{
- getGroup().cs = new ZappoColourScheme();
+ getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
refresh();
}
protected void taylorColour_actionPerformed()
{
refresh();
}
protected void taylorColour_actionPerformed()
{
- getGroup().cs = new TaylorColourScheme();
+ getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
- getGroup().cs = new HydrophobicColourScheme();
+ getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
refresh();
}
protected void helixColour_actionPerformed()
{
refresh();
}
protected void helixColour_actionPerformed()
{
- getGroup().cs = new HelixColourScheme();
+ getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
refresh();
}
protected void strandColour_actionPerformed()
{
refresh();
}
protected void strandColour_actionPerformed()
{
- getGroup().cs = new StrandColourScheme();
+ getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
refresh();
}
protected void turnColour_actionPerformed()
{
refresh();
}
protected void turnColour_actionPerformed()
{
- getGroup().cs = new TurnColourScheme();
+ getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
refresh();
}
protected void buriedColour_actionPerformed()
{
refresh();
}
protected void buriedColour_actionPerformed()
{
- getGroup().cs = new BuriedColourScheme();
+ getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
- getGroup().cs = new NucleotideColourScheme();
+ getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
- getGroup().cs = new PurinePyrimidineColourScheme();
+ getGroup().cs = new CollectionColourScheme(
+ new PurinePyrimidineColourScheme());
refresh();
}
refresh();
}
@@
-1236,7
+1245,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
+ sg.cs = new CollectionColourScheme(new PIDColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
@@
-1246,7
+1255,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
SequenceGroup sg = getGroup();
{
SequenceGroup sg = getGroup();
- sg.cs = new Blosum62ColourScheme();
+ sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
@@
-1270,10
+1279,12
@@
public class APopupMenu extends java.awt.PopupMenu implements
if (conservationColour.getState())
{
if (conservationColour.getState())
{
- sg.cs.setConservation(Conservation.calculateConservation("Group", sg
+ Conservation conservation = Conservation.calculateConservation(
+ "Group", sg
.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
.getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
.getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
- false));
+ false);
+ sg.getGroupColourScheme().setConservation(conservation);
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}