From 05ee59c456b1b0032dd14fabe3fbaeb8569c93cb Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 18 Aug 2010 10:16:36 +0000
Subject: [PATCH] thread safe construction of Jmol instance and hack to
 translate invalid jmol state statements.

---
 src/jalview/gui/Jalview2XML.java |   55 +++++++++++++++++++++++++++++++-------
 1 file changed, 45 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1a6024e..4b6879c 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -19,6 +19,7 @@ package jalview.gui;
 
 import java.awt.Rectangle;
 import java.io.*;
+import java.lang.reflect.InvocationTargetException;
 import java.net.*;
 import java.util.*;
 import java.util.jar.*;
@@ -578,13 +579,14 @@ public class Jalview2XML
           {
             if (frames[f] instanceof AppJmol)
             {
+              // TODO: revise schema to allow many:one PDB id binding to viewer
               jmol = (AppJmol) frames[f];
-              if (!jmol.pdbentry.getId().equals(entry.getId())
+              if (!jmol.jmb.pdbentry[0].getId().equals(entry.getId())
                       && !(entry.getId().length() > 4 && entry.getId()
                               .toLowerCase().startsWith(
-                                      jmol.pdbentry.getId().toLowerCase())))
+                                      jmol.jmb.pdbentry[0].getId().toLowerCase())))
                 continue;
-              matchedFile = jmol.pdbentry.getFile(); // record the file so we
+              matchedFile = jmol.jmb.pdbentry[0].getFile(); // record the file so we
               // can get at it if the ID
               // match is ambiguous (e.g.
               // 1QIP==1qipA)
@@ -595,14 +597,14 @@ public class Jalview2XML
               state.setWidth(jmol.getWidth());
               state.setHeight(jmol.getHeight());
               state.setViewId(jmol.getViewId());
-              String statestring = jmol.viewer.getStateInfo();
+              String statestring = jmol.jmb.viewer.getStateInfo();
               if (state != null)
               {
                 state.setContent(statestring.replaceAll("\n", ""));
               }
-              for (int s = 0; s < jmol.sequence.length; s++)
+              for (int s = 0; s < jmol.jmb.sequence.length; s++)
               {
-                if (jal.findIndex(jmol.sequence[s]) > -1)
+                if (jal.findIndex(jmol.jmb.sequence[s]) > -1)
                 {
                   pdb.addStructureState(state);
                 }
@@ -2534,9 +2536,42 @@ public class Jalview2XML
 
                 if (newFileLoc != null)
                 {
-                  new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
-                          newFileLoc.toString(), new java.awt.Rectangle(x,
-                                  y, width, height), sviewid);
+                  int histbug = newFileLoc.indexOf("history = ");
+                  histbug+=10;
+                  int diff = histbug==-1 ? -1 : newFileLoc.indexOf(";",histbug); 
+                  String val = (diff==-1) ? null : newFileLoc.substring(histbug,diff); 
+                  if (val!=null && val.length()>=4)
+                  {
+                    if (val.contains("e")) {
+                      if (val.trim().equals("true")) {
+                        val = "1";
+                      } else {
+                        val = "0";
+                      }
+                      newFileLoc.replace(histbug, diff, val);
+                    }
+                  }
+                  final String pdbf=pdbFile, id=ids[p].getId(), fileloc=newFileLoc.toString(),vid=sviewid;
+                  final SequenceI[] sq=seq;
+                  final AlignFrame alf = af;
+                  final java.awt.Rectangle rect = new java.awt.Rectangle(x,
+                          y, width, height);
+                  try {
+                  javax.swing.SwingUtilities.invokeAndWait(new Runnable() {
+                    public void run() {
+                      new AppJmol(pdbf, id, sq, alf.alignPanel,
+                              fileloc, rect, vid);
+                    }
+                  });
+                  }
+                  catch (InvocationTargetException ex)
+                  {
+                    System.err.println("Unexpected error when opening Jmol view.");
+                    ex.printStackTrace();
+                  } catch (InterruptedException e)
+                  {
+                    // e.printStackTrace();
+                  }
                 }
 
               }
@@ -2553,7 +2588,7 @@ public class Jalview2XML
                         .setMapping(seq, null, pdbFile,
                                 jalview.io.AppletFormatAdapter.FILE);
 
-                ((AppJmol) comp).addSequence(seq);
+                ((AppJmol) comp).jmb.addSequence(seq);
               }
             }
           }
-- 
1.7.10.2