Revert "Added a cdk.saveCML(List<? extends IMolecules>, String) to sa…

…ve lists of molecules as CML" Causes regressions. This reverts commit 00a8777.
bioclipse · Aug 28, 2011 · 9e8dd18 · 9e8dd18
1 parent 00a8777
commit 9e8dd18
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Showing 3 changed files with 5 additions and 41 deletions.
diff --git a/...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java b/...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java
@@ -1333,17 +1333,6 @@ public void testSaveMDLMolfile() throws Exception {
         ));
     }
 
-    @Test
-    public void testSaveCMLList() throws Exception {
-    	List<ICDKMolecule> molecules = cdk.createMoleculeList();
-        molecules.add(cdk.fromSMILES("CCC"));
-        molecules.add(cdk.fromSMILES("CCO"));
-        molecules.add(cdk.fromSMILES("COC"));
-        String path = "/Virtual/testSaveCMLfile" + molecules.hashCode() + ".cml";
-        cdk.saveCML(molecules, path);
-        // cannot read it yet, but for now, if it did not crash
-    }
-
     @Test
     public void testSaveCML() throws Exception {
         ICDKMolecule propane  = cdk.fromSMILES("CCC");

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java
@@ -50,6 +50,7 @@
 import net.bioclipse.core.domain.IMolecule;
 import net.bioclipse.core.domain.IMolecule.Property;
 import net.bioclipse.core.domain.RecordableList;
+import net.bioclipse.core.domain.SMILESMolecule;
 import net.bioclipse.core.util.LogUtils;
 import net.bioclipse.jobs.IReturner;
 import net.bioclipse.managers.business.IBioclipseManager;
@@ -910,24 +911,21 @@ public void saveMolecule( IMolecule mol,
        */
       public void saveMolecules( List<? extends IMolecule> molecules,
                                  String path,
-                               IChemFormat filetype, IProgressMonitor monitor )
+                               IChemFormat filetype )
                   throws BioclipseException, CoreException {
 
           saveMolecules( molecules,
                          ResourcePathTransformer.getInstance().transform(path),
-                         filetype,
-                         null) ;
+                         filetype) ;
       }
 
       /**
        * Save a list of molecules in SDF or CML
        */
       public void saveMolecules( List<? extends IMolecule> molecules,
                                  IFile target,
-                                 IChemFormat filetype,
-                                 IProgressMonitor monitor)
+                                 IChemFormat filetype )
                   throws BioclipseException, CoreException {
-    	  if (monitor == null) monitor = new NullProgressMonitor();
 
           if ( filetype == CMLFormat.getInstance() ||
                filetype == MDLV2000Format.getInstance() ||
@@ -2031,17 +2029,6 @@ public void saveCML(ICDKMolecule cml,  String filename)
           saveMolecule(cml, filename, (IChemFormat)CMLFormat.getInstance());
       }
 
-      public void saveCML(List<? extends IMolecule> molecules,
-    		  String filename, IProgressMonitor monitor)
-                  throws BioclipseException, InvocationTargetException,
-                         CoreException {
-    	  saveMolecules(
-    		  molecules, filename,
-    		  (IChemFormat)CMLFormat.getInstance(),
-    		  monitor
-    	  );
-      }
-
       public void saveMDLMolfile(ICDKMolecule mol, String filename)
                   throws InvocationTargetException,
                          BioclipseException,

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java
@@ -39,6 +39,7 @@
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.SubProgressMonitor;
 import org.eclipse.core.runtime.content.IContentType;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IChemModel;
@@ -777,19 +778,6 @@ public void saveCML(ICDKMolecule cml, String filename)
                        BioclipseException, 
                        CoreException;
 
-    @Recorded
-    @PublishedMethod(
-        params = "List<? extends IMolecule> molecules, String filename",
-        methodSummary = "Saves a list of molecules in the Chemical Markup Language " +
-        		            "format (filename must be relative to workspace " +
-        		            "root and folder must exist). Example of file " +
-        		            "String: \"/Virtual/bla.cml\"" )
-    @TestMethods("testSaveCMLList")
-    public void saveCML(List<? extends IMolecule> molecules, String filename) 
-                throws InvocationTargetException, 
-                       BioclipseException, 
-                       CoreException;
-
     /**
      * Loads molecules from a SMILES file.
      *