X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=82f5e5ce9c36544e91a4f7fc7f024c602c041792;hp=7033ba77e135c11865e340c31a3da979ed423ecd;hb=2273eba5668e5340354da60fed329c6c716cc439;hpb=497958b4e5217efaa3ddeece38f38c3a6e98cb96

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 7033ba7..82f5e5c 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -74,13 +74,14 @@ public abstract class JalviewChimeraBinding extends
   private boolean loadingFromArchive = false;
 
   /**
-   * second flag to indicate if the jmol viewer should ignore sequence colouring
-   * events from the structure manager because the GUI is still setting up
+   * second flag to indicate if the Chimera viewer should ignore sequence
+   * colouring events from the structure manager because the GUI is still
+   * setting up
    */
   private boolean loadingFinished = true;
 
   /**
-   * state flag used to check if the Jmol viewer's paint method can be called
+   * state flag used to check if the Chimera viewer's paint method can be called
    */
   private boolean finishedInit = false;
 
@@ -173,7 +174,7 @@ public abstract class JalviewChimeraBinding extends
         } catch (Error e)
         {
         }
-        // Explicitly map to the filename used by Jmol ;
+        // Explicitly map to the filename used by Chimera ;
         // pdbentry[pe].getFile(), protocol);
 
         if (ssm != null)
@@ -236,13 +237,6 @@ public abstract class JalviewChimeraBinding extends
     }
     viewer = new ChimeraManager(
             csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
-    /*
-     * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
-     * "jalviewJmol", ap.av.applet .getDocumentBase(),
-     * ap.av.applet.getCodeBase(), "", this);
-     * 
-     * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
-     */
   }
 
   public JalviewChimeraBinding(StructureSelectionManager ssm,
@@ -335,15 +329,13 @@ public abstract class JalviewChimeraBinding extends
     {
       viewer.exitChimera();
     }
-    // viewer.evalStringQuiet("zap");
-    // viewer.setJmolStatusListener(null);
     lastCommand = null;
     viewer = null;
     releaseUIResources();
   }
 
   /**
-   * called by JalviewJmolbinding after closeViewer is called - release any
+   * called by JalviewChimerabinding after closeViewer is called - release any
    * resources and references so they can be garbage collected.
    */
   protected abstract void releaseUIResources();
@@ -351,17 +343,15 @@ public abstract class JalviewChimeraBinding extends
   public void colourByChain()
   {
     colourBySequence = false;
-    // TODO: colour by chain should colour each chain distinctly across all
-    // visible models
-    // TODO: http://issues.jalview.org/browse/JAL-628
-    evalStateCommand("select *;color chain",false);
+    evalStateCommand("rainbow chain", false);
   }
 
   public void colourByCharge()
   {
     colourBySequence = false;
-    evalStateCommand("colour *;color white;select ASP,GLU;color red;"
-            + "select LYS,ARG;color blue;select CYS;color yellow", false);
+    evalStateCommand(
+            "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS",
+            false);
   }
 
   /**
@@ -411,7 +401,7 @@ public abstract class JalviewChimeraBinding extends
     assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
     StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd
     String[] files = getPdbFile();
-    // check to see if we are still waiting for Jmol files
+    // check to see if we are still waiting for Chimera files
     long starttime = System.currentTimeMillis();
     boolean waiting = true;
     do
@@ -792,7 +782,7 @@ public abstract class JalviewChimeraBinding extends
 
   private void waitForChimera()
   {
-    while (viewer.isBusy())
+    while (viewer != null && viewer.isBusy())
     {
       try {
         Thread.sleep(15);
@@ -964,7 +954,7 @@ public abstract class JalviewChimeraBinding extends
     }
   }
 
-  boolean debug = true;
+  boolean debug = false;
 
   private void log(String message)
   {
@@ -973,8 +963,8 @@ public abstract class JalviewChimeraBinding extends
 
   private void viewerCommandHistory(boolean enable)
   {
-    log("(Not yet implemented) History "
-            + ((debug || enable) ? "on" : "off"));
+    // log("(Not yet implemented) History "
+    // + ((debug || enable) ? "on" : "off"));
   }
 
   public void loadInline(String string)
@@ -1225,10 +1215,13 @@ public abstract class JalviewChimeraBinding extends
     String res;
     int index;
     Color col;
+    // Chimera expects RBG values in the range 0-1
+    final double normalise = 255D;
     viewerCommandHistory(false);
     // TODO: Switch between nucleotide or aa selection expressions
     Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
+    StringBuilder command = new StringBuilder(128);
+    command.append("color white;");
     while (en.hasMoreElements())
     {
       res = en.nextElement().toString();
@@ -1239,32 +1232,19 @@ public abstract class JalviewChimeraBinding extends
       }
 
       col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-      // TODO: need colour string function and res selection here
-      command.append("select " + res + ";color[" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
+      command.append("color " + col.getRed() / normalise + ","
+              + col.getGreen() / normalise + "," + col.getBlue()
+              / normalise + " ::" + res + ";");
     }
 
     evalStateCommand(command.toString(),false);
     viewerCommandHistory(true);
   }
 
-  public void showHelp()
-  {
-    // chimera help
-    showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
-  }
-
   /**
-   * open the URL somehow
-   * 
-   * @param target
-   */
-  public abstract void showUrl(String url, String target);
-
-  /**
-   * called when the binding thinks the UI needs to be refreshed after a Jmol
+   * called when the binding thinks the UI needs to be refreshed after a Chimera
    * state change. this could be because structures were loaded, or because an
-   * error has occured.
+   * error has occurred.
    */
   public abstract void refreshGUI();
 
@@ -1293,8 +1273,8 @@ public abstract class JalviewChimeraBinding extends
 
   /**
    * 
-   * @return true if Jmol is still restoring state or loading is still going on
-   *         (see setFinsihedLoadingFromArchive)
+   * @return true if Chimeral is still restoring state or loading is still going
+   *         on (see setFinsihedLoadingFromArchive)
    */
   public boolean isLoadingFromArchive()
   {
@@ -1312,13 +1292,22 @@ public abstract class JalviewChimeraBinding extends
     loadingFinished = finishedLoading;
   }
 
-  public void setBackgroundColour(java.awt.Color col)
+  /**
+   * Send the Chimera 'background solid <color>" command.
+   * 
+   * @see https
+   *      ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
+   *      .html
+   * @param col
+   */
+  public void setBackgroundColour(Color col)
   {
     viewerCommandHistory(false);
-    // todo set background colour
-    viewer.sendChimeraCommand(
-            "background [" + col.getRed() + "," + col.getGreen() + ","
-                    + col.getBlue() + "];", false);
+    double normalise = 255D;
+    final String command = "background solid " + col.getRed() / normalise + ","
+            + col.getGreen() / normalise + "," + col.getBlue()
+            / normalise + ";";
+    viewer.sendChimeraCommand(command, false);
     viewerCommandHistory(true);
   }