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JAL-2401 fix for NPE on selectedButtons, tweak for button appearance
[jalview.git]
/
src
/
jalview
/
appletgui
/
APopupMenu.java
diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
6882c6c
..
4ae0ed2
100644
(file)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-39,11
+39,11
@@
import jalview.io.DataSourceType;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
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.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;
@@
-112,8
+112,14
@@
public class APopupMenu extends java.awt.PopupMenu implements
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ MenuItem modifyPID = new MenuItem();
+
protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
+ MenuItem modifyConservation = new MenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
final AlignmentPanel ap;
MenuItem unGroupMenuItem = new MenuItem();
final AlignmentPanel ap;
MenuItem unGroupMenuItem = new MenuItem();
@@
-256,6
+262,8
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
conservationColour.setState(sg.cs.conservationApplied());
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
conservationColour.setState(sg.cs.conservationApplied());
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
}
}
setSelectedColour(sg.cs);
}
}
setSelectedColour(sg.cs);
@@
-322,7
+330,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
*
* @param cs
*/
*
* @param cs
*/
- protected void setSelectedColour(CollectionColourSchemeI cs)
+ protected void setSelectedColour(ResidueShaderI cs)
{
if (cs == null || cs.getColourScheme() == null)
{
{
if (cs == null || cs.getColourScheme() == null)
{
@@
-636,6
+644,14
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
userDefinedColour_actionPerformed();
}
{
userDefinedColour_actionPerformed();
}
+ else if (source == modifyConservation)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == modifyPID)
+ {
+ abovePIDColour_itemStateChanged();
+ }
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
@@
-901,14
+917,14
@@
public class APopupMenu extends java.awt.PopupMenu implements
void addPDB()
{
Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
void addPDB()
{
Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
- if (pdbs != null&& !pdbs.isEmpty())
+ if (pdbs != null && !pdbs.isEmpty())
{
PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
{
PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
- null, ap, DataSourceType.URL);
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
}
else
{
}
else
{
@@
-924,7
+940,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
@@
-944,6
+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);
@@
-999,8
+1017,10
@@
public class APopupMenu extends java.awt.PopupMenu implements
colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
colourMenu.add(conservationColour);
colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
noColour.setLabel(MessageManager.getString("label.none"));
noColour.addItemListener(this);
noColour.setLabel(MessageManager.getString("label.none"));
noColour.addItemListener(this);
@@
-1066,9
+1086,18
@@
public class APopupMenu extends java.awt.PopupMenu implements
abovePIDColour.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addItemListener(this);
abovePIDColour.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
conservationColour.setLabel(MessageManager
conservationColour.setLabel(MessageManager
- .getString("label.conservation"));
+ .getString("action.by_conservation"));
conservationColour.addItemListener(this);
conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
+
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.addActionListener(this);
editMenu.add(copy);
copy.addActionListener(this);
editMenu.add(copy);
copy.addActionListener(this);
@@
-1118,62
+1147,62
@@
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 CollectionColourScheme(new ClustalxColourScheme(sg,
+ sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
refresh();
}
protected void taylorColour_actionPerformed()
{
refresh();
}
protected void taylorColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
refresh();
}
protected void helixColour_actionPerformed()
{
refresh();
}
protected void helixColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
refresh();
}
protected void strandColour_actionPerformed()
{
refresh();
}
protected void strandColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
refresh();
}
protected void turnColour_actionPerformed()
{
refresh();
}
protected void turnColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
refresh();
}
protected void buriedColour_actionPerformed()
{
refresh();
}
protected void buriedColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(
+ getGroup().cs = new ResidueShader(
new PurinePyrimidineColourScheme());
refresh();
}
new PurinePyrimidineColourScheme());
refresh();
}
@@
-1201,11
+1230,11
@@
public class APopupMenu extends java.awt.PopupMenu implements
else
// remove PIDColouring
{
else
// remove PIDColouring
{
+ SliderPanel.hidePIDSlider();
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
-
+ modifyPID.setEnabled(abovePIDColour.getState());
refresh();
refresh();
-
}
protected void userDefinedColour_actionPerformed()
}
protected void userDefinedColour_actionPerformed()
@@
-1216,7
+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 CollectionColourScheme(new PIDColourScheme());
+ sg.cs = new ResidueShader(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();
@@
-1226,7
+1255,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
SequenceGroup sg = getGroup();
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
+ sg.cs = new ResidueShader(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()));
@@
-1262,9
+1291,10
@@
public class APopupMenu extends java.awt.PopupMenu implements
else
// remove ConservationColouring
{
else
// remove ConservationColouring
{
+ SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
sg.cs.setConservation(null);
}
-
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
refresh();
}