[Jmol-commits] SF.net SVN: jmol:[14800] branches/v12_0/Jmol

[<ha...@us...>]

Revision: 14800
          http://jmol.svn.sourceforge.net/jmol/?rev=14800&view=rev
Author:   hansonr
Date:     2010-12-17 14:50:14 +0000 (Fri, 17 Dec 2010)

Log Message:
-----------
version=12.0.25_dev

# code: JUnit test for file reading GenNBO and CIF files lacks viewer object

Modified Paths:
--------------
    branches/v12_0/Jmol/src/org/jmol/api/JmolAdapter.java
    branches/v12_0/Jmol/src/org/jmol/api/JmolViewer.java
    branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties
    branches/v12_0/Jmol/src/org/jmol/viewer/Viewer.java
    branches/v12_0/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java

Modified: branches/v12_0/Jmol/src/org/jmol/api/JmolAdapter.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/api/JmolAdapter.java	2010-12-17 14:49:24 UTC (rev 14799)
+++ branches/v12_0/Jmol/src/org/jmol/api/JmolAdapter.java	2010-12-17 14:50:14 UTC (rev 14800)
@@ -192,6 +192,7 @@
                                                Hashtable htParams) {
     if (htParams == null)
       htParams = new Hashtable();
+    htParams.put("viewer", JmolViewer.allocateViewer(null, this));
     Object a = getAtomSetCollectionReader(name, type, bufferedReader, htParams);
     if (a instanceof String)
       return a;

Modified: branches/v12_0/Jmol/src/org/jmol/api/JmolViewer.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/api/JmolViewer.java	2010-12-17 14:49:24 UTC (rev 14799)
+++ branches/v12_0/Jmol/src/org/jmol/api/JmolViewer.java	2010-12-17 14:50:14 UTC (rev 14800)
@@ -110,7 +110,6 @@
   /**
    * OK, but safer to assign htmlName, URL bases, comandOptions, and statusListener now.
    * 
-   * @deprecated
    * @param awtComponent
    * @param jmolAdapter
    * @return             a viewer

Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties	2010-12-17 14:49:24 UTC (rev 14799)
+++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties	2010-12-17 14:50:14 UTC (rev 14800)
@@ -4,6 +4,7 @@
 
 version=12.0.25_dev
 
+# code: JUnit test for file reading GenNBO and CIF files lacks viewer object
 # bug fix: GenNBO reader does not read MOs properly
 # bug fix: GenNBO reader does not read xxx.31 file P orbitals not in X Y Z order
 # bug fix: applying unit cell in LOAD command to XYZ file containing multiple models 

Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/viewer/Viewer.java	2010-12-17 14:49:24 UTC (rev 14799)
+++ branches/v12_0/Jmol/src/org/jmol/viewer/Viewer.java	2010-12-17 14:50:14 UTC (rev 14800)
@@ -253,6 +253,11 @@
     if (Logger.debugging) {
       Logger.debug("Viewer constructor " + this);
     }
+    isDataOnly = (display == null);
+    haveDisplay = (!isDataOnly && (commandOptions == null || commandOptions.indexOf("-n") < 0));
+    mustRender = haveDisplay;
+    if (!haveDisplay)
+      display = null;
     this.display = display;
     this.modelAdapter = modelAdapter;
     strJavaVendor = System.getProperty("java.vendor");
@@ -280,7 +285,7 @@
     scriptManager = new ScriptManager(this);
     transformManager = new TransformManager11(this);
     selectionManager = new SelectionManager(this);
-    if (display != null) {
+    if (haveDisplay) {
       if (multiTouch) {
         if (commandOptions.indexOf("-multitouch-sparshui-simulated") < 0) {
           int[] pixels = new int[1];
@@ -364,7 +369,7 @@
     return isPreviewOnly;
   }
 
-  public boolean haveDisplay = true;
+  public boolean haveDisplay = false;
   public boolean autoExit = false;
 
   private boolean mustRender = true;
@@ -432,11 +437,6 @@
       isCmdLine_C_Option = (str.indexOf("-C") >= 0);
       listCommands = (str.indexOf("-l") >= 0);
       autoExit = (str.indexOf("-x") >= 0);
-      isDataOnly = (display == null);
-      haveDisplay = (display != null && str.indexOf("-n") < 0);
-      if (!haveDisplay)
-        display = null;
-      mustRender = haveDisplay;
       cd(".");
     }
     isPreviewOnly = (str.indexOf("#previewOnly") >= 0);
@@ -4538,7 +4538,7 @@
   }
 
   public void setCursor(int cursor) {
-    if (multiTouch || currentCursor == cursor || display == null)
+    if (multiTouch || currentCursor == cursor || !haveDisplay)
       return;
     int c;
     switch (currentCursor = cursor) {
@@ -8537,9 +8537,8 @@
 
   void repaint() {
     // from RepaintManager
-    if (display == null)
-      return;
-    display.repaint();
+    if (haveDisplay)
+      display.repaint();
   }
 
   public OutputStream getOutputStream(String localName, String[] fullPath) {
@@ -8671,11 +8670,11 @@
   }
 
   public boolean hasFocus() {
-    return (display != null && (isKiosk || display.hasFocus()));
+    return (haveDisplay && (isKiosk || display.hasFocus()));
   }
 
   public void setFocus() {
-    if (display != null && !display.hasFocus())
+    if (haveDisplay && !display.hasFocus())
       display.requestFocusInWindow();
   }
 

Modified: branches/v12_0/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java
===================================================================
--- branches/v12_0/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java	2010-12-17 14:49:24 UTC (rev 14799)
+++ branches/v12_0/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java	2010-12-17 14:50:14 UTC (rev 14800)
@@ -13,6 +13,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.util.Hashtable;
 import java.util.zip.GZIPInputStream;
 
 import org.jmol.util.JUnitLogger;
@@ -84,6 +85,9 @@
     result.addDirectory(false, "gamess", "out", ";Gamess;GamessUS;GamessUK;");
     result.addDirectory(false, "gaussian", "log", "Gaussian");
     result.addDirectory(false, "gaussian", "out", "Gaussian");
+    result.addDirectory(false, "gennbo", "out", "GenNBO");
+    result.addDirectory(false, "gennbo", "36", "GenNBO");
+    result.addDirectory(false, "gennbo", "37", "GenNBO");
     result.addDirectory(false, "ghemical", "gpr", "GhemicalMM");
     result.addDirectory(false, "gpt2", "gpt2","MopacGraphf");
     result.addDirectory(false, "gromacs", "gro", "Gromacs");
@@ -220,7 +224,9 @@
         fail("Wrong type for " + file.getPath() + ": " + fileType + " instead of " + typeAllowed);
       }
     }
-    Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, null);
+    Hashtable htParams = new Hashtable();
+    htParams.put("fullPathName", file.getAbsolutePath());
+    Object result = adapter.getAtomSetCollectionFromReader(file.getName(), null, bReader, htParams);
     assertNotNull("Nothing read for " + file.getPath(), result);
     assertFalse("Error returned for " + file.getPath() + ": " + result, result instanceof String);
     assertTrue("Not an AtomSetCollection for " + file.getPath(), result instanceof AtomSetCollection);


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