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[Cdk-commits] SF.net SVN: cdk: [10437] cdk/trunk/src/main/org/openscience/cdk/tools/ manipulator/ReactionSetManipulator.java
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From: <mig...@us...> - 2008-03-18 12:04:53
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Revision: 10437
http://cdk.svn.sourceforge.net/cdk/?rev=10437&view=rev
Author: miguelrojasch
Date: 2008-03-18 05:04:14 -0700 (Tue, 18 Mar 2008)
Log Message:
-----------
added parameters to the List objects
Modified Paths:
--------------
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java
Modified: cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java 2008-03-18 11:02:44 UTC (rev 10436)
+++ cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java 2008-03-18 12:04:14 UTC (rev 10437)
@@ -29,9 +29,18 @@
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IElectronContainer;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IReaction;
+import org.openscience.cdk.interfaces.IReactionSet;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
/**
@@ -46,8 +55,8 @@
@TestMethod("testGetAtomCount_IReactionSet")
public static int getAtomCount(IReactionSet set) {
int count = 0;
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- count += ReactionManipulator.getAtomCount((IReaction)iter.next());
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ count += ReactionManipulator.getAtomCount(iter.next());
}
return count;
}
@@ -55,41 +64,58 @@
@TestMethod("testGetBondCount_IReactionSet")
public static int getBondCount(IReactionSet set) {
int count = 0;
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- count += ReactionManipulator.getBondCount((IReaction)iter.next());
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ count += ReactionManipulator.getBondCount(iter.next());
}
return count;
}
public static void removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
ReactionManipulator.removeAtomAndConnectedElectronContainers(reaction, atom);
}
}
public static void removeElectronContainer(IReactionSet set, IElectronContainer electrons) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
ReactionManipulator.removeElectronContainer(reaction, electrons);
}
}
-
+
+ /**
+ * get all Molecules object from a set of Reactions.
+ *
+ * @param set The set of reaction to inspect
+ * @return The IMoleculeSet
+ */
@TestMethod("testGetAllMolecules_IReactionSet")
public static IMoleculeSet getAllMolecules(IReactionSet set) {
IMoleculeSet moleculeSet = set.getBuilder().newMoleculeSet();
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
- moleculeSet.add(ReactionManipulator.getAllMolecules(reaction));
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
+ IMoleculeSet newMoleculeSet = ReactionManipulator.getAllMolecules(reaction);
+ for(Iterator<IAtomContainer> it = newMoleculeSet.molecules(); it.hasNext(); ){
+ IAtomContainer ac = it.next();
+ boolean contain = false;
+ for(Iterator<IAtomContainer> it2 = moleculeSet.molecules(); it2.hasNext(); )
+ if(it2.equals(ac)){
+ contain = true;
+ break;
+ }
+ if(!contain)
+ moleculeSet.addMolecule((IMolecule)(ac));
+ }
}
return moleculeSet;
}
-
- public static List getAllIDs(IReactionSet set) {
+
+ public static List<String> getAllIDs(IReactionSet set) {
List<String> IDlist = new ArrayList<String>();
if (set.getID() != null) IDlist.add(set.getID());
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
IDlist.addAll(ReactionManipulator.getAllIDs(reaction));
}
return IDlist;
@@ -101,7 +127,7 @@
* @return a List containing the IAtomContainer objects in the IReactionSet
*/
@TestMethod("testGetAllAtomContainers_IReactionSet")
- public static List getAllAtomContainers(IReactionSet set) {
+ public static List<IAtomContainer> getAllAtomContainers(IReactionSet set) {
return MoleculeSetManipulator.getAllAtomContainers(
getAllMolecules(set)
@@ -110,8 +136,8 @@
@TestMethod("testGetRelevantReaction_IReactionSet_IAtom")
public static IReaction getRelevantReaction(IReactionSet set, IAtom atom) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(reaction, atom);
if (container != null) { // a match!
return reaction;
@@ -122,8 +148,8 @@
@TestMethod("testGetRelevantReaction_IReactionSet_IBond")
public static IReaction getRelevantReaction(IReactionSet set, IBond bond) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(reaction, bond);
if (container != null) { // a match!
return reaction;
@@ -134,7 +160,7 @@
@TestMethod("testGetRelevantAtomContainer_IReactionSet_IAtom")
public static IAtomContainer getRelevantAtomContainer(IReactionSet set, IAtom atom) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
IReaction reaction = (IReaction)iter.next();
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(reaction, atom);
if (container != null) { // a match!
@@ -146,7 +172,7 @@
@TestMethod("testGetRelevantAtomContainer_IReactionSet_IBond")
public static IAtomContainer getRelevantAtomContainer(IReactionSet set, IBond bond) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
IReaction reaction = (IReaction)iter.next();
IAtomContainer container = ReactionManipulator.getRelevantAtomContainer(reaction, bond);
if (container != null) { // a match!
@@ -158,18 +184,18 @@
@TestMethod("testSetAtomProperties_IReactionSet_Object_Object")
public static void setAtomProperties(IReactionSet set, Object propKey, Object propVal) {
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
IReaction reaction = (IReaction)iter.next();
ReactionManipulator.setAtomProperties(reaction, propKey, propVal);
}
}
@TestMethod("testGetAllChemObjects_IReactionSet")
- public static List getAllChemObjects(IReactionSet set) {
+ public static List<IChemObject> getAllChemObjects(IReactionSet set) {
ArrayList<IChemObject> list = new ArrayList<IChemObject>();
list.add(set);
- for (java.util.Iterator iter = set.reactions(); iter.hasNext();) {
- IReaction reaction = (IReaction)iter.next();
+ for (Iterator<IReaction> iter = set.reactions(); iter.hasNext();) {
+ IReaction reaction = iter.next();
list.addAll(ReactionManipulator.getAllChemObjects(reaction));
}
return list;
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