X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=d82027313276531c367a03a03dabb5e138b0dc30;hb=a663c1c844de90b4c125dbbcf5c8b953b00a809d;hp=d3177228ff0cf05ca2b3e7c83231718856fbdf8c;hpb=e34c8452beda2cf80c2a3224f236d3096db69ae9;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index d317722..d820273 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -27,13 +27,13 @@ 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;
@@ -49,6 +49,7 @@ import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.StringTokenizer;
 import java.util.Vector;
 
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
@@ -64,6 +65,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
 {
+  private String lastMessage;
+
   boolean allChainsSelected = false;
 
   /*
@@ -88,8 +91,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   String lastCommand;
 
-  String lastMessage;
-
   boolean loadedInline;
 
   StringBuffer resetLastRes = new StringBuffer();
@@ -132,9 +133,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * prepare the view for a given set of models/chains. chainList contains
-   * strings of the form 'pdbfilename:Chaincode'
+   * prepare the view for a given set of models/chains. chainList contains strings
+   * of the form 'pdbfilename:Chaincode'
+   * 
+   * @deprecated now only used by applet code
    */
+  @Deprecated
   public void centerViewer()
   {
     StringBuilder cmd = new StringBuilder(128);
@@ -476,14 +480,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   Thread colourby = null;
+  
   /**
    * Sends a set of colour commands to the structure viewer
    * 
-   * @param colourBySequenceCommands
+   * @param commands
    */
   @Override
-  protected void colourBySequence(
-          final StructureMappingcommandSet[] colourBySequenceCommands)
+  protected void colourBySequence(final String[] commands)
   {
     if (colourby != null)
     {
@@ -495,12 +499,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       @Override
       public void run()
       {
-        for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+        for (String cmd : commands)
         {
-          for (String cbyseq : cpdbbyseq.commands)
-          {
-            executeWhenReady(cbyseq);
-          }
+          executeWhenReady(cmd);
         }
       }
     });
@@ -513,11 +514,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @return
    */
   @Override
-  protected StructureMappingcommandSet[] getColourBySequenceCommands(
+  protected String[] getColourBySequenceCommands(
           String[] files, AlignmentViewPanel viewPanel)
   {
-    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            this, viewPanel);
+    Map<Object, AtomSpecModel> map = buildColoursMap(viewPanel);
+
+    return JmolCommands.getColourBySequenceCommand(map);
   }
 
   /**
@@ -750,7 +752,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     viewer.openStringInline(string);
   }
 
-  public void mouseOverStructure(int atomIndex, String strInfo)
+  protected void mouseOverStructure(int atomIndex, final String strInfo)
   {
     int pdbResNum;
     int alocsep = strInfo.indexOf("^");
@@ -831,18 +833,36 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       } catch (Exception e)
       {
       }
-      ;
     }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
+
+    /*
+     * highlight position on alignment(s); if some text is returned, 
+     * show this as a second line on the structure hover tooltip
+     */
+    String label = getSsm().mouseOverStructure(pdbResNum, chainId,
+            pdbfilename);
+    if (label != null)
     {
-      getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+      // change comma to pipe separator (newline token for Jmol)
+      label = label.replace(',', '|');
+      StringTokenizer toks = new StringTokenizer(strInfo, " ");
+      StringBuilder sb = new StringBuilder();
+      sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
+              .append(chainId).append("/1");
+      sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
+              .append(toks.nextToken());
+      sb.append("|").append(label).append("\"");
+      evalStateCommand(sb.toString());
     }
-
-    lastMessage = strInfo;
   }
 
   public void notifyAtomHovered(int atomIndex, String strInfo, String data)
   {
+    if (strInfo.equals(lastMessage))
+    {
+      return;
+    }
+    lastMessage = strInfo;
     if (data != null)
     {
       System.err.println("Ignoring additional hover info: " + data
@@ -1417,7 +1437,36 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public void showStructures(AlignViewportI av, boolean refocus)
   {
-    // TODO show Jmol structure optionally restricted to visible alignment
-    // and/or selected chains
+    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 0");
+    }
+    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";
   }
 }