Exposed the JNI-InChI functionality for checking InChIs (not Standard…

… InChI it seems; try inchi.checkStrict("InChI=1S/CH4/h1H4"))
bioclipse · Nov 1, 2012 · 1f5cd00 · 1f5cd00
1 parent b558482
commit 1f5cd00
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diff --git a/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/IInChIManager.java b/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/IInChIManager.java
@@ -17,6 +17,7 @@
 import net.bioclipse.core.Recorded;
 import net.bioclipse.core.TestClasses;
 import net.bioclipse.core.TestMethods;
+import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.core.domain.IMolecule;
 import net.bioclipse.inchi.InChI;
 import net.bioclipse.jobs.BioclipseJob;
@@ -57,6 +58,27 @@ public BioclipseJob<InChI> generate(IMolecule molecule, String options,
     @TestMethods("testOptions")
     public List<String> options();
 
+    @Recorded
+    @PublishedMethod(
+        methodSummary = "Checks the validity of an InChIKey.",
+        params="String inchikey"
+    )
+    public boolean checkKey(String inchikey) throws BioclipseException;
+
+    @Recorded
+    @PublishedMethod(
+        methodSummary = "Checks the validity of an InChI (loose).",
+        params="String inchi"
+    )
+    public boolean check(String inchi) throws BioclipseException;
+
+    @Recorded
+    @PublishedMethod(
+        methodSummary = "Checks the validity of an InChI (strict).",
+        params="String inchi"
+    )
+    public boolean checkStrict(String inchi) throws BioclipseException;
+
     @Recorded
     @PublishedMethod(
         methodSummary = "Loads the InChI library.")

diff --git a/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/InChIManager.java b/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/InChIManager.java
@@ -17,12 +17,17 @@
 
 import net.bioclipse.core.PublishedMethod;
 import net.bioclipse.core.Recorded;
+import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.core.domain.IMolecule;
 import net.bioclipse.inchi.InChI;
 import net.bioclipse.jobs.IReturner;
 import net.bioclipse.managers.business.IBioclipseManager;
+import net.sf.jniinchi.INCHI_KEY_STATUS;
 import net.sf.jniinchi.INCHI_OPTION;
 import net.sf.jniinchi.INCHI_RET;
+import net.sf.jniinchi.INCHI_STATUS;
+import net.sf.jniinchi.JniInchiException;
+import net.sf.jniinchi.JniInchiWrapper;
 
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.OperationCanceledException;
@@ -165,6 +170,45 @@ public boolean isLoaded() {
     	return isLoaded;
     }
 
+    public boolean checkKey(String inchikey) throws BioclipseException {
+    	INCHI_KEY_STATUS status;
+		try {
+			status = JniInchiWrapper.checkInchiKey(inchikey);
+		} catch (JniInchiException exception) {
+			throw new BioclipseException("Error while validating the inchi: " + exception.getMessage(), exception);
+		}
+    	if (status == INCHI_KEY_STATUS.VALID_STANDARD || status == INCHI_KEY_STATUS.VALID_NON_STANDARD)
+    		return true;
+    	// everything else is false
+    	return false;
+    }
+
+    public boolean check(String inchi) throws BioclipseException {
+    	INCHI_STATUS status;
+		try {
+			status = JniInchiWrapper.checkInchi(inchi, false);
+		} catch (JniInchiException exception) {
+			throw new BioclipseException("Error while validating the inchi: " + exception.getMessage(), exception);
+		}
+    	if (status == INCHI_STATUS.VALID_STANDARD || status == INCHI_STATUS.VALID_NON_STANDARD)
+    		return true;
+    	// everything else is false
+    	return false;
+    }
+
+    public boolean checkStrict(String inchi) throws BioclipseException {
+    	INCHI_STATUS status;
+		try {
+			status = JniInchiWrapper.checkInchi(inchi, true);
+		} catch (JniInchiException exception) {
+			throw new BioclipseException("Error while validating the inchi: " + exception.getMessage(), exception);
+		}
+    	if (status == INCHI_STATUS.VALID_STANDARD || status == INCHI_STATUS.VALID_NON_STANDARD)
+    		return true;
+    	// everything else is false
+    	return false;
+    }
+
     public boolean isAvailable() {
     	if (!isLoaded && loadingFailed) return false;
     	if (!loadingFailed && isLoaded) return true;