Merge branch 'develop' into patch/JAL-3921_jmol_session_save

[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 dde7643..f51252c 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -26,6 +26,8 @@ import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
@@ -163,28 +165,49 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public void createImage(String file, String type, int quality)
   {
-    System.out.println("JMOL CREATE IMAGE");
+    jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
   }
 
   @Override
   public String createImage(String fileName, String type,
           Object textOrBytes, int quality)
   {
-    System.out.println("JMOL CREATE IMAGE");
+    jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
     return null;
   }
 
   @Override
   public String eval(String strEval)
   {
-    // System.out.println(strEval);
+    // jalview.bin.Console.outPrintln(strEval);
     // "# 'eval' is implemented only for the applet.";
     return null;
   }
 
   // End StructureListener
   // //////////////////////////
-
+  
+  ////////////////////////////
+  // HETATM get
+  //
+  
+  @Override
+  public Map<String,String> getHetatmNames()
+  {
+    HashMap<String,String> hetlist=new HashMap();
+    for (int mc=0;mc<jmolViewer.ms.mc; mc++)
+    {
+      Map<String,String> hets = jmolViewer.ms.getHeteroList(mc);
+      if (hets!=null)
+      {
+        hetlist.putAll(hets);
+      }
+    }
+    return hetlist;
+  }
+  //
+  ////////////////////////////
+  
   @Override
   public float[][] functionXY(String functionName, int x, int y)
   {
@@ -267,16 +290,30 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
-      boolean useScriptWait = atoms.size() > 1;
       if (resetLastRes.length() > 0)
       {
-        jmolScript(resetLastRes.toString(), useScriptWait);
+        jmolScript(resetLastRes.toString());
         resetLastRes.setLength(0);
       }
+      StringBuilder highlightCommands=null;
       for (AtomSpec atom : atoms)
       {
-        highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
-                atom.getChain(), atom.getPdbFile(), useScriptWait);
+        StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+                atom.getChain(), atom.getPdbFile());
+        if (thisAtom!=null) {
+          if (highlightCommands==null)
+          {
+            highlightCommands=thisAtom;                  
+          } else {
+            highlightCommands.append(thisAtom);
+          }
+        }
+      }
+      if (highlightCommands!=null)
+      {
+        jmolHistory(false);
+        jmolScript(highlightCommands.toString());
+        jmolHistory(true);
       }
       // Highlight distances between atoms with a 'measure' command - not yet
       // working
@@ -306,17 +343,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   // jmol/ssm only
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile, boolean useScriptWait)
+  private StringBuilder highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     String modelId = getModelIdForFile(pdbfile);
     if (modelId.isEmpty())
     {
-      return;
+      return null;
     }
 
-    jmolHistory(false, useScriptWait);
-
     StringBuilder selection = new StringBuilder(32);
     StringBuilder cmd = new StringBuilder(64);
     selection.append("select ").append(String.valueOf(pdbResNum));
@@ -333,8 +368,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     resetLastRes.append(selection).append(";wireframe 0;").append(selection)
             .append(" and not hetero; spacefill 0;");
 
-    jmolScript(cmd.toString(), useScriptWait);
-    jmolHistory(true, useScriptWait);
+    return cmd;
   }
 
   private boolean debug = true;
@@ -476,7 +510,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastMessage = strInfo;
     if (data != null)
     {
-      System.err.println("Ignoring additional hover info: " + data
+      jalview.bin.Console.errPrintln("Ignoring additional hover info: " + data
               + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
@@ -497,7 +531,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
      */
     if (strData != null)
     {
-      System.err.println("Ignoring additional pick data string " + strData);
+      jalview.bin.Console.errPrintln("Ignoring additional pick data string " + strData);
     }
     int chainSeparator = strInfo.indexOf(":");
     int p = 0;
@@ -599,7 +633,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                 (data == null) ? ((String) null) : (String) data[1]);
         break;
       case ERROR:
-        // System.err.println("Ignoring error callback.");
+        // jalview.bin.Console.errPrintln("Ignoring error callback.");
         break;
       case SYNC:
       case RESIZE:
@@ -609,13 +643,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
       case CLICK:
       default:
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Unhandled callback " + type + " " + data[1].toString());
         break;
       }
     } catch (Exception e)
     {
-      System.err.println("Squashed Jmol callback handler error:");
+      jalview.bin.Console.errPrintln("Squashed Jmol callback handler error:");
       e.printStackTrace();
     }
   }
@@ -864,7 +898,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void setCallbackFunction(String callbackType,
           String callbackFunction)
   {
-    System.err.println("Ignoring set-callback request to associate "
+    jalview.bin.Console.errPrintln("Ignoring set-callback request to associate "
             + callbackType + " with function " + callbackFunction);
 
   }
@@ -938,7 +972,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           String buttonsToShow)
   {
 
-    System.err.println("Allocating Jmol Viewer: " + commandOptions);
+    jalview.bin.Console.errPrintln("Allocating Jmol Viewer: " + commandOptions);
 
     if (commandOptions == null)
     {
@@ -956,7 +990,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       console = createJmolConsole(consolePanel, buttonsToShow);
     } catch (Throwable e)
     {
-      System.err.println("Could not create Jmol application console. "
+      jalview.bin.Console.errPrintln("Could not create Jmol application console. "
               + e.getMessage());
       e.printStackTrace();
     }