JAL-3551 save structure viewer session refactorings, PyMol added

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index fe5c980..17433c5 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,28 +20,12 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.FeatureRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.IProgressIndicator;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureCommandsI.SuperposeData;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
 import java.awt.Container;
 import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.BitSet;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
@@ -55,6 +39,19 @@ import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
 import org.jmol.viewer.Viewer;
 
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
@@ -125,19 +122,21 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public List<String> executeCommand(String command, boolean getReply)
+  public List<String> executeCommand(StructureCommandI command,
+          boolean getReply)
   {
     if (command == null)
     {
       return null;
     }
+    String cmd = command.getCommand();
     jmolHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command))
+    if (lastCommand == null || !lastCommand.equals(cmd))
     {
-      jmolViewer.evalStringQuiet(command + "\n");
+      jmolViewer.evalStringQuiet(cmd + "\n");
     }
     jmolHistory(true);
-    lastCommand = command;
+    lastCommand = cmd;
     return null;
   }
 
@@ -425,7 +424,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
               .append(toks.nextToken());
       sb.append("|").append(label).append("\"");
-      executeCommand(sb.toString(), false);
+      executeCommand(new StructureCommand(sb.toString()), false);
     }
   }
 
@@ -712,14 +711,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         }
         if (matches)
         {
-          // add an entry for every chain in the model
-          for (int i = 0; i < pdb.getChains().size(); i++)
-          {
-            String chid = pdb.getId() + ":"
-                    + pdb.getChains().elementAt(i).id;
-            addChainFile(chid, fileName);
-            getChainNames().add(chid);
-          }
+          stashFoundChains(pdb, fileName);
           notifyLoaded = true;
         }
       }
@@ -955,20 +947,20 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  protected int getModelNoForFile(String pdbFile)
+  protected String getModelIdForFile(String pdbFile)
   {
     if (modelFileNames == null)
     {
-      return -1;
+      return "";
     }
     for (int i = 0; i < modelFileNames.length; i++)
     {
       if (modelFileNames[i].equalsIgnoreCase(pdbFile))
       {
-        return i;
+        return String.valueOf(i + 1);
       }
     }
-    return -1;
+    return "";
   }
 
   @Override
@@ -976,4 +968,22 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     return ViewerType.JMOL;
   }
+
+  @Override
+  protected String getModelId(int pdbfnum, String file)
+  {
+    return String.valueOf(pdbfnum + 1);
+  }
+
+  /**
+   * Returns ".spt" - the Jmol session file extension
+   * 
+   * @return
+   * @see https://chemapps.stolaf.edu/jmol/docs/#writemodel
+   */
+  @Override
+  public String getSessionFileExtension()
+  {
+    return ".spt";
+  }
 }