X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=8cecf6eba5f3d47abb24fbe2590fd6c5003df90f;hb=6bf5604d306cbcd55289639967411ddbafcac682;hp=11354780db60bcc46903a963149c18020442690e;hpb=9644afe3c10e90365290d4b249d32635bccfad7f;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 1135478..8cecf6e 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,20 +20,20 @@
  */
 package jalview.ext.jmol;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
 import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
@@ -44,7 +44,6 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
-import java.security.AccessControlException;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Hashtable;
@@ -135,15 +134,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * prepare the view for a given set of models/chains. chainList contains
    * strings of the form 'pdbfilename:Chaincode'
-   * 
-   * @param chainList
-   *          list of chains to make visible
    */
-  public void centerViewer(Vector<String> chainList)
+  public void centerViewer()
   {
     StringBuilder cmd = new StringBuilder(128);
     int mlength, p;
-    for (String lbl : chainList)
+    for (String lbl : chainsToShow)
     {
       mlength = 0;
       do
@@ -159,7 +155,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       cmd.setLength(cmd.length() - 4);
     }
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
+    String command = "select *;restrict " + cmd + ";cartoon;center " + cmd;
+    evalStateCommand(command);
   }
 
   public void closeViewer()
@@ -478,36 +475,47 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
+  
   /**
    * Sends a set of colour commands to the structure viewer
    * 
-   * @param colourBySequenceCommands
+   * @param commands
    */
   @Override
-  protected void colourBySequence(
-          StructureMappingcommandSet[] colourBySequenceCommands)
+  protected void colourBySequence(final String[] commands)
   {
-    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+    if (colourby != null)
     {
-      for (String cbyseq : cpdbbyseq.commands)
+      colourby.interrupt();
+      colourby = null;
+    }
+    colourby = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
       {
-        executeWhenReady(cbyseq);
+        for (String cmd : commands)
+        {
+          executeWhenReady(cmd);
+        }
       }
-    }
+    });
+    colourby.start();
   }
 
   /**
    * @param files
-   * @param sr
    * @param viewPanel
    * @return
    */
   @Override
-  protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+  protected String[] getColourBySequenceCommands(
+          String[] files, AlignmentViewPanel viewPanel)
   {
-    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+    Map<Object, AtomSpecModel> map = buildColoursMap(viewPanel);
+
+    return JmolCommands.getColourBySequenceCommand(map);
   }
 
   /**
@@ -600,74 +608,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
-  // ////////////////////////////////
-  // /StructureListener
-  // @Override
-  public synchronized String[] getPdbFilex()
-  {
-    if (viewer == null)
-    {
-      return new String[0];
-    }
-    if (modelFileNames == null)
-    {
-      List<String> mset = new ArrayList<>();
-      _modelFileNameMap = new int[viewer.ms.mc];
-      String m = viewer.ms.getModelFileName(0);
-      if (m != null)
-      {
-        String filePath = m;
-        try
-        {
-          filePath = new File(m).getAbsolutePath();
-        } catch (AccessControlException x)
-        {
-          // usually not allowed to do this in applet
-          System.err.println(
-                  "jmolBinding: Using local file string from Jmol: " + m);
-        }
-        if (filePath.indexOf("/file:") != -1)
-        {
-          // applet path with docroot - discard as format won't match pdbfile
-          filePath = m;
-        }
-        mset.add(filePath);
-        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
-      }
-      int j = 1;
-      for (int i = 1; i < viewer.ms.mc; i++)
-      {
-        m = viewer.ms.getModelFileName(i);
-        String filePath = m;
-        if (m != null)
-        {
-          try
-          {
-            filePath = new File(m).getAbsolutePath();
-          } catch (AccessControlException x)
-          {
-            // usually not allowed to do this in applet, so keep raw handle
-            // System.err.println("jmolBinding: Using local file string from
-            // Jmol: "+m);
-          }
-        }
-
-        /*
-         * add this model unless it is read from a structure file we have
-         * already seen (example: 2MJW is an NMR structure with 10 models)
-         */
-        if (!mset.contains(filePath))
-        {
-          mset.add(filePath);
-          _modelFileNameMap[j] = i; // record the model index for the filename
-          j++;
-        }
-      }
-      modelFileNames = mset.toArray(new String[mset.size()]);
-    }
-    return modelFileNames;
-  }
-
   @Override
   public synchronized String[] getStructureFiles()
   {
@@ -862,7 +802,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int mnumber = new Integer(mdlId).intValue() - 1;
+        int mnumber = Integer.valueOf(mdlId).intValue() - 1;
         if (_modelFileNameMap != null)
         {
           int _mp = _modelFileNameMap.length - 1;
@@ -1240,7 +1180,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return chainNames;
   }
 
-  protected abstract IProgressIndicator getIProgressIndicator();
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return null;
+  }
 
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
@@ -1468,4 +1411,40 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     showConsole(false);
   }
+
+  @Override
+  public void showStructures(AlignViewportI av, boolean refocus)
+  {
+    StringBuilder cmd = new StringBuilder(128);
+
+    if (isShowAlignmentOnly())
+    {
+      cmd.append("hide *;");
+
+    AtomSpecModel model = getShownResidues(av);
+    String atomSpec = JmolCommands.getAtomSpec(model);
+
+    cmd.append("display ").append(atomSpec);
+    }
+    else
+    {
+      cmd.append("display *");
+    }
+    cmd.append("; cartoon");
+    if (refocus)
+    {
+      cmd.append("; zoom 100");
+    }
+    evalStateCommand(cmd.toString());
+  }
+
+  /**
+   * Answers a Jmol syntax style structure model specification. Model number 0, 1,
+   * 2... is formatted as "1.1", "2.1", "3.1" etc.
+   */
+  @Override
+  public String getModelSpec(int model)
+  {
+    return String.valueOf(model + 1) + ".1";
+  }
 }