notes re JAL-623 and JAL-583, new api methods for adding several structure/seq mappin...

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3707cfa..e45bd28 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -98,7 +98,19 @@ public class AppletJmol extends EmbmenuFrame implements
    * datasource protocol for access to PDBEntry
    */
   String protocol = null;
-
+  /**
+   * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary.
+   * @param pdbentries each pdb file (at least one needed)
+   * @param boundseqs each set of sequences for each pdb file (must match number of pdb files)
+   * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level)
+   * @param align true/false
+   * @param ap associated alignment
+   * @param protocol how to get pdb data
+   */
+  public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol)
+  {
+    throw new Error("Not yet implemented.");
+  }
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           AlignmentPanel ap, String protocol)
   {
@@ -203,12 +215,18 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-
+    if (pdbentry.getProperty()==null)
+    {
+      pdbentry.setProperty(new Hashtable());
+      pdbentry.getProperty().put("protocol", protocol);
+    }
     if (pdbentry.getFile() != null)
     {
       // import structure data from pdbentry.getFile based on given protocol
       if (protocol.equals(AppletFormatAdapter.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)
@@ -276,7 +294,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void loadInline(String string)
   {
     loadedInline = true;
-    jmb.viewer.openStringInline(string);
+    jmb.loadInline(string);
   }
 
   void setChainMenuItems(Vector chains)