Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 8374721..c0b4ff0 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,10 +20,11 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
@@ -60,7 +61,6 @@ import java.awt.event.KeyListener;
 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;
 
@@ -93,27 +93,29 @@ public class AppletJmol extends EmbmenuFrame implements
   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(
-          MessageManager.getString("label.hydrophobicity"));
+          MessageManager.getString("label.colourScheme_hydrophobic"));
 
   MenuItem helix = new MenuItem(
-          MessageManager.getString("label.helix_propensity"));
+          MessageManager.getString("label.colourScheme_helix_propensity"));
 
   MenuItem strand = new MenuItem(
-          MessageManager.getString("label.strand_propensity"));
+          MessageManager.getString("label.colourScheme_strand_propensity"));
 
   MenuItem turn = new MenuItem(
-          MessageManager.getString("label.turn_propensity"));
+          MessageManager.getString("label.colourScheme_turn_propensity"));
 
   MenuItem buried = new MenuItem(
-          MessageManager.getString("label.buried_index"));
+          MessageManager.getString("label.colourScheme_buried_index"));
 
   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"));
@@ -176,16 +178,16 @@ public class AppletJmol extends EmbmenuFrame implements
   }
 
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol)
+          AlignmentPanel ap, DataSourceType protocol)
   {
     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)
     {
-      if (protocol.equals(AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
         pdbentry.setId("PASTED PDB"
                 + (chains == null ? "_" : chains.toString()));
@@ -196,7 +198,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
 
-    if (jalview.bin.JalviewLite.debug)
+    if (JalviewLite.debug)
     {
       System.err
               .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
@@ -290,22 +292,19 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-    if (pdbentry.getProperty() == null)
-    {
-      pdbentry.setProperty(new Hashtable());
-      pdbentry.getProperty().put("protocol", protocol);
-    }
+    pdbentry.setProperty("protocol", protocol);
     if (pdbentry.getFile() != null)
+    
     {
       // import structure data from pdbentry.getFile based on given protocol
-      if (protocol.equals(AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
         // TODO: JAL-623 : correctly record file contents for matching up later
         // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
         loadInline(pdbentry.getFile());
       }
-      else if (protocol.equals(AppletFormatAdapter.FILE)
-              || protocol.equals(AppletFormatAdapter.URL))
+      else if (protocol == DataSourceType.FILE
+              || protocol == DataSourceType.URL)
       {
         jmb.viewer.openFile(pdbentry.getFile());
       }
@@ -373,7 +372,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector<String> chains)
+  void setChainMenuItems(List<String> chains)
   {
     chainMenu.removeAll();
 
@@ -587,12 +586,12 @@ public class AppletJmol extends EmbmenuFrame implements
 
   public void updateTitleAndMenus()
   {
-    if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+    if (jmb.hasFileLoadingError())
     {
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
     jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());