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JAL-2570 don't zap group colour scheme when mapping over split frame
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
18e7d1a
..
c0b4ff0
100644
(file)
--- a/
src/jalview/appletgui/AppletJmol.java
+++ b/
src/jalview/appletgui/AppletJmol.java
@@
-24,8
+24,8
@@
import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
import jalview.io.DataSourceType;
import jalview.io.DataSourceType;
+import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
@@
-61,7
+61,6
@@
import java.awt.event.KeyListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
@@
-94,27
+93,29
@@
public class AppletJmol extends EmbmenuFrame implements
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
- MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
+ MenuItem zappo = new MenuItem(
+ MessageManager.getString("label.colourScheme_zappo"));
- MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
+ MenuItem taylor = new MenuItem(
+ MessageManager.getString("label.colourScheme_taylor"));
MenuItem hydro = new MenuItem(
MenuItem hydro = new MenuItem(
- MessageManager.getString("label.hydrophobicity"));
+ MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
MenuItem helix = new MenuItem(
- MessageManager.getString("label.helix_propensity"));
+ MessageManager.getString("label.colourScheme_helix_propensity"));
MenuItem strand = new MenuItem(
MenuItem strand = new MenuItem(
- MessageManager.getString("label.strand_propensity"));
+ MessageManager.getString("label.colourScheme_strand_propensity"));
MenuItem turn = new MenuItem(
MenuItem turn = new MenuItem(
- MessageManager.getString("label.turn_propensity"));
+ MessageManager.getString("label.colourScheme_turn_propensity"));
MenuItem buried = new MenuItem(
MenuItem buried = new MenuItem(
- MessageManager.getString("label.buried_index"));
+ MessageManager.getString("label.colourScheme_buried_index"));
MenuItem purinepyrimidine = new MenuItem(
MenuItem purinepyrimidine = new MenuItem(
- MessageManager.getString("label.purine_pyrimidine"));
+ MessageManager.getString("label.colourScheme_purine/pyrimidine"));
MenuItem user = new MenuItem(
MessageManager.getString("label.user_defined_colours"));
MenuItem user = new MenuItem(
MessageManager.getString("label.user_defined_colours"));
@@
-182,7
+183,7
@@
public class AppletJmol extends EmbmenuFrame implements
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
- new String[][] { chains }, protocol);
+ protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
@@
-291,12
+292,9
@@
public class AppletJmol extends EmbmenuFrame implements
closeViewer();
}
});
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable<String, String>());
- pdbentry.getProperty().put("protocol", protocol.toString());
- }
+ pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
if (pdbentry.getFile() != null)
+
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol == DataSourceType.PASTE)
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol == DataSourceType.PASTE)
@@
-374,7
+372,7
@@
public class AppletJmol extends EmbmenuFrame implements
jmb.loadInline(string);
}
jmb.loadInline(string);
}
- void setChainMenuItems(Vector<String> chains)
+ void setChainMenuItems(List<String> chains)
{
chainMenu.removeAll();
{
chainMenu.removeAll();
@@
-588,12
+586,12
@@
public class AppletJmol extends EmbmenuFrame implements
public void updateTitleAndMenus()
{
public void updateTitleAndMenus()
{
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ if (jmb.hasFileLoadingError())
{
repaint();
return;
}
{
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());