X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=dc18369aa2678804f1061b59b12552d9b3cc661b;hb=ecc31307701d785d41f503484fa5a823580ea79f;hp=903d9b7c53faed57f0b58f2490c44f61758de5d2;hpb=931c66e5efd8c066326b6db713b4db498657ebe6;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 903d9b7..dc18369 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -45,7 +45,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AppJmol;
@@ -122,9 +122,22 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private String jmolScript(String script)
   {
-    Cache.log.debug(">>Jmol>> " + script);
-    String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
-    Cache.log.debug("<<Jmol<< " + s);
+    return jmolScript(script, false);
+  }
+
+  private String jmolScript(String script, boolean useScriptWait)
+  {
+    Console.debug(">>Jmol>> " + script);
+    String s;
+    if (useScriptWait)
+    {
+      s = jmolViewer.scriptWait(script);
+    }
+    else
+    {
+      s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+    }
+    Console.debug("<<Jmol<< " + s);
 
     return s;
   }
@@ -150,21 +163,21 @@ 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;
   }
@@ -259,26 +272,63 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         jmolScript(resetLastRes.toString());
         resetLastRes.setLength(0);
       }
+      StringBuilder highlightCommands=null;
       for (AtomSpec atom : atoms)
       {
-        highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+        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
+      // if (atoms.size() >= 2)
+      // {
+      // StringBuilder sb = new StringBuilder();
+      // for (int a = 0; a < atoms.size(); a++)
+      // {
+      // AtomSpec speca = atoms.get(a);
+      // String a_model = getModelIdForFile(speca.getPdbFile());
+      // for (int b = a + 1; b < atoms.size(); b++)
+      // {
+      // AtomSpec specb = atoms.get(b);
+      // String b_model = getModelIdForFile(speca.getPdbFile());
+      // sb.append("measure ALL (" + speca.getAtomIndex() + " and */"
+      // + a_model + ") (" + specb.getAtomIndex() + " and */"
+      // + b_model + ");");
+      // }
+      // }
+      // jmolHistory(false, useScriptWait);
+      // jmolScript(sb.toString(), useScriptWait);
+      // jmolHistory(true, useScriptWait);
+      // }
+
     }
+
   }
 
   // jmol/ssm only
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+  private StringBuilder highlightAtom(int atomIndex, int pdbResNum, String chain,
           String pdbfile)
   {
     String modelId = getModelIdForFile(pdbfile);
     if (modelId.isEmpty())
     {
-      return;
+      return null;
     }
 
-    jmolHistory(false);
-
     StringBuilder selection = new StringBuilder(32);
     StringBuilder cmd = new StringBuilder(64);
     selection.append("select ").append(String.valueOf(pdbResNum));
@@ -295,15 +345,20 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     resetLastRes.append(selection).append(";wireframe 0;").append(selection)
             .append(" and not hetero; spacefill 0;");
 
-    jmolScript(cmd.toString());
-    jmolHistory(true);
+    return cmd;
   }
 
   private boolean debug = true;
 
   private void jmolHistory(boolean enable)
   {
-    jmolScript("History " + ((debug || enable) ? "on" : "off"));
+    jmolHistory(enable, false);
+  }
+
+  private void jmolHistory(boolean enable, boolean useScriptWait)
+  {
+    jmolScript("History " + ((debug || enable) ? "on" : "off"),
+            useScriptWait);
   }
 
   public void loadInline(String string)
@@ -432,7 +487,7 @@ 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);
@@ -453,7 +508,7 @@ 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;
@@ -555,7 +610,7 @@ 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:
@@ -565,13 +620,13 @@ 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();
     }
   }
@@ -820,7 +875,7 @@ 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);
 
   }
@@ -894,7 +949,7 @@ 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)
     {
@@ -912,7 +967,7 @@ 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();
     }