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[Cdk-commits] SF.net SVN: cdk: [10558] cdk-taverna/trunk/src/main/java/org/openscience/ cdk/applications/taverna/reactionenumerator/ReactionEnumerator.java
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From: <tho...@us...> - 2008-03-27 14:11:39
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Revision: 10558
http://cdk.svn.sourceforge.net/cdk/?rev=10558&view=rev
Author: thomaskuhn
Date: 2008-03-27 07:11:36 -0700 (Thu, 27 Mar 2008)
Log Message:
-----------
Some clean up and upgrade to Java 5 standards
Modified Paths:
--------------
cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/reactionenumerator/ReactionEnumerator.java
Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/reactionenumerator/ReactionEnumerator.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/reactionenumerator/ReactionEnumerator.java 2008-03-27 14:11:27 UTC (rev 10557)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/reactionenumerator/ReactionEnumerator.java 2008-03-27 14:11:36 UTC (rev 10558)
@@ -76,13 +76,13 @@
*
*/
public class ReactionEnumerator implements LocalWorkerCDK {
- // Region: input and outpout definition
+ // Region: input and output definition
private IPseudoAtom[] reactantsPseudoAtoms = null;
private int reactantsPseudoAtomsCounter = 0;
private String[] inputNames = new String[] { "reactantOne", "reactantTwo", "reaction" };
private String[] outputNames = new String[] { "productStructures", "Comment"};
// private List<Integer> numberOfUsedPseudoAtomsPerReactant = new ArrayList<Integer>();
- // Region: input and outpout definition
+ // Region: input and output definition
public String[] inputNames() {
return inputNames;
@@ -102,7 +102,7 @@
// Region: local worker execution
- public Map execute(Map inputs) throws TaskExecutionException {
+ public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException {
try {
FileNameGenerator fileNameGenerator = new FileNameGenerator();
@@ -114,20 +114,17 @@
List<CMLChemFile> productStructuresList = new ArrayList<CMLChemFile>();
Reaction reaction = null;
if (inputs.get(inputNames[0]) != null) {
- reactantOneList = (List<CMLChemFile>) ((DataThing) inputs
- .get(inputNames[0])).getDataObject();
+ reactantOneList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0]));
} else {
comment += "No reactans available; ";
}
if (inputs.get(inputNames[1]) != null) {
- reactantTwoList = (List<CMLChemFile>) ((DataThing) inputs
- .get(inputNames[1])).getDataObject();
+ reactantTwoList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[1]));
} else {
comment += "No reactans available; ";
}
if (inputs.get(inputNames[2]) != null) {
- reactionList = (List<Reaction>) ((DataThing) (inputs.get(inputNames[2])))
- .getDataObject();
+ reactionList = CMLChemFileWrapper.getListOfReactionFromDataThing(inputs.get(inputNames[2]));
reaction = reactionList.get(0);
} else {
comment += "No reacion available; ";
@@ -141,8 +138,8 @@
IAtomContainer[] reactantTwo = CMLChemFileWrapper.convertCMLChemFileListToAtomContainerArray(reactantTwoList);
IAtomContainer[] reactantsFromReaction = new AtomContainer[reaction.getReactantCount()];
int acCounter = 0;
- for (Iterator iter = reaction.getReactants().atomContainers(); iter.hasNext();) {
- reactantsFromReaction[acCounter] = (IAtomContainer) iter.next();
+ for (Iterator<IAtomContainer> iter = reaction.getReactants().atomContainers(); iter.hasNext();) {
+ reactantsFromReaction[acCounter] = iter.next();
acCounter++;
}
this.reactantsPseudoAtoms = new PseudoAtom[reaction.getReactantCount()];
@@ -166,7 +163,7 @@
for (int i = 0; i < resultProducts.length; i++) {
file = CMLChemFileWrapper.wrapAtomContainerInChemModel(resultProducts[i]);
// FIXME This can cause problems because it will create everytime a new list for each molecule and will not take the old list from the reactants
- file.setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(fileName, (List<String>)file.getProperty(FileNameGenerator.FILENAME)));
+ file.setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(fileName, (List<String>)file.getProperty(FileNameGenerator.FILENAME)));
productStructuresList.add(file);
}
} catch (Exception e) {
@@ -176,7 +173,7 @@
}
// End of block
- Map outputs = new HashMap();
+ Map<String, DataThing> outputs = new HashMap<String, DataThing>();
outputs.put("Comment", new DataThing(comment));
outputs.put("productStructures", new DataThing(productStructuresList));
return outputs;
@@ -197,7 +194,7 @@
*/
private IAtomContainer[] eliminateSubstructureAndTagConnectedAtom(IAtomContainer[] atomContainerArray, IAtomContainer substructure) throws TaskExecutionException{
// FIXME Put this into a different class later
- List d = null;
+ List<ArrayList<RMap>> d = null;
Vector v = null;
RMap[] rmaps = null;
List<IAtom> connectedAtoms = null;
@@ -218,17 +215,17 @@
for (int i = 0; i < atomContainerArray.length; i++) {
d = UniversalIsomorphismTester.getSubgraphAtomsMaps(atomContainerArray[i], queryAC);
if (d.size() > 0) {
- ArrayList<RMap> rMapList = (ArrayList<RMap>)d.get(0);
+ ArrayList<RMap> rMapList = d.get(0);
rmaps = new RMap[rMapList.size()];
for (int j = 0; j < rMapList.size(); j++) {
rmaps[j] = rMapList.get(j);
if (!(queryAC.getAtom(rmaps[j].getId2()) instanceof AnyAtom)) {
atomContainerArray[i].getAtom(rmaps[j].getId1()).setFlag(0, true);
- // Marked this atoms as deletable
+ // Marked this atoms as delitable
atomContainerArray[i].getAtom(rmaps[j].getId1()).setFlag(1, true);
connectedAtoms = atomContainerArray[i].getConnectedAtomsList(atomContainerArray[i].getAtom(rmaps[j].getId1()));
- for (Iterator iter = connectedAtoms.iterator(); iter.hasNext();) {
- IAtom connectedAtom = (IAtom) iter.next();
+ for (Iterator<IAtom> iter = connectedAtoms.iterator(); iter.hasNext();) {
+ IAtom connectedAtom = iter.next();
connectedAtom.setFlag(0, true);
}
}
@@ -283,8 +280,8 @@
if (product.getAtom(j) instanceof PseudoAtom &&
((PseudoAtom) product.getAtom(j)).getLabel().equalsIgnoreCase(pseudoAtom.getLabel())) {
connectedAtoms = product.getConnectedAtomsList(product.getAtom(j));
- for (Iterator iter = connectedAtoms.iterator(); iter.hasNext();) {
- IAtom atom = (IAtom) iter.next();
+ for (Iterator<IAtom> iter = connectedAtoms.iterator(); iter.hasNext();) {
+ IAtom atom = iter.next();
atom.setFlag(0, true);
}
allConnectedBonds = product.getConnectedBondsList(product.getAtom(j));
@@ -326,66 +323,65 @@
}
}
} catch (Exception e) {
- String t = e.getMessage();
// TODO: handle exception
}
return resultAtomContainer;
}
- /**
- * This method removes a given substructure from a each molecule of the atomContainerArray using the UniversalIsomorphismTester
- * @param atomContainerArray AtomContainer array which contains molecules from which the substructure should be removed
- * @param substructure Substructure which should be removed from the molecules
- * @return AtomContainer which contains the molecules from the atomContainerArray without the substructure
- */
- private IAtomContainer[] eliminateSubstructureAndTagConnectedAtom_Old(IAtomContainer[] atomContainerArray, IAtomContainer substructure) {
- // FIXME Put this into a different class later
- List d = null;
- Vector v = null;
- RMap[] rmaps = null;
- List<IAtom> connectedAtoms = null;
- try {
- // Remove the pseudo atom from the substructure due to problem to find the this substructure within the molecules
- // FIXME Use the QueryAtom construction to define a better queryatom and to be more case sensitive
- for (int i = 0; i < substructure.getAtomCount(); i++) {
- if (substructure.getAtom(i) instanceof PseudoAtom) {
- connectedAtoms = substructure.getConnectedAtomsList(substructure.getAtom(i));
- this.reactantsPseudoAtoms[this.reactantsPseudoAtomsCounter] = (PseudoAtom) substructure.getAtom(i);
- // FIXME At this case the 0 could be a problem later
- substructure.removeBond(substructure.getAtom(i), connectedAtoms.get(0));
- substructure.removeAtom(substructure.getAtom(i));
- }
- }
- for (int i = 0; i < atomContainerArray.length; i++) {
- // FIXME Create an handling for molecules which don't contain the substructure
- d = UniversalIsomorphismTester.getSubgraphAtomsMaps(atomContainerArray[i], substructure);
- ArrayList<RMap> rMapList = (ArrayList<RMap>)d.get(0);
- rmaps = new RMap[rMapList.size()];
- for (int j = 0; j < rMapList.size(); j++) {
- rmaps[j] = rMapList.get(j);
+// /**
+// * This method removes a given substructure from a each molecule of the atomContainerArray using the UniversalIsomorphismTester
+// * @param atomContainerArray AtomContainer array which contains molecules from which the substructure should be removed
+// * @param substructure Substructure which should be removed from the molecules
+// * @return AtomContainer which contains the molecules from the atomContainerArray without the substructure
+// */
+// private IAtomContainer[] eliminateSubstructureAndTagConnectedAtom_Old(IAtomContainer[] atomContainerArray, IAtomContainer substructure) {
+// // FIXME Put this into a different class later
+// List d = null;
+// Vector v = null;
+// RMap[] rmaps = null;
+// List<IAtom> connectedAtoms = null;
+// try {
+// // Remove the pseudo atom from the substructure due to problem to find the this substructure within the molecules
+// // FIXME Use the QueryAtom construction to define a better queryatom and to be more case sensitive
+// for (int i = 0; i < substructure.getAtomCount(); i++) {
+// if (substructure.getAtom(i) instanceof PseudoAtom) {
+// connectedAtoms = substructure.getConnectedAtomsList(substructure.getAtom(i));
+// this.reactantsPseudoAtoms[this.reactantsPseudoAtomsCounter] = (PseudoAtom) substructure.getAtom(i);
+// // FIXME At this case the 0 could be a problem later
+// substructure.removeBond(substructure.getAtom(i), connectedAtoms.get(0));
+// substructure.removeAtom(substructure.getAtom(i));
+// }
+// }
+// for (int i = 0; i < atomContainerArray.length; i++) {
+// // FIXME Create an handling for molecules which don't contain the substructure
+// d = UniversalIsomorphismTester.getSubgraphAtomsMaps(atomContainerArray[i], substructure);
+// ArrayList<RMap> rMapList = (ArrayList<RMap>)d.get(0);
+// rmaps = new RMap[rMapList.size()];
+// for (int j = 0; j < rMapList.size(); j++) {
+// rmaps[j] = rMapList.get(j);
+//
+// atomContainerArray[i].getAtom(rmaps[j].getId1()).setFlag(0, true);
+// // Marked this atoms as deletable
+// atomContainerArray[i].getAtom(rmaps[j].getId1()).setFlag(1, true);
+// connectedAtoms = atomContainerArray[i].getConnectedAtomsList(atomContainerArray[i].getAtom(rmaps[j].getId1()));
+// for (Iterator iter = connectedAtoms.iterator(); iter.hasNext();) {
+// IAtom connectedAtom = (IAtom) iter.next();
+// connectedAtom.setFlag(0, true);
+// }
+// }
+// // Start deleting atoms at the end of the atom array
+// for (int j = atomContainerArray[i].getAtomCount() - 1; j > -1; j--) {
+// if (atomContainerArray[i].getAtom(j).getFlag(1)) {
+// atomContainerArray[i].removeAtomAndConnectedElectronContainers(atomContainerArray[i].getAtom(j));
+// }
+// }
+// }
+// }
+// catch (Exception e) {
+// boolean test = true;
+// // TODO: handle exception
+// }
+// return atomContainerArray;
+// }
- atomContainerArray[i].getAtom(rmaps[j].getId1()).setFlag(0, true);
- // Marked this atoms as deletable
- atomContainerArray[i].getAtom(rmaps[j].getId1()).setFlag(1, true);
- connectedAtoms = atomContainerArray[i].getConnectedAtomsList(atomContainerArray[i].getAtom(rmaps[j].getId1()));
- for (Iterator iter = connectedAtoms.iterator(); iter.hasNext();) {
- IAtom connectedAtom = (IAtom) iter.next();
- connectedAtom.setFlag(0, true);
- }
- }
- // Start deleting atoms at the end of the atom array
- for (int j = atomContainerArray[i].getAtomCount() - 1; j > -1; j--) {
- if (atomContainerArray[i].getAtom(j).getFlag(1)) {
- atomContainerArray[i].removeAtomAndConnectedElectronContainers(atomContainerArray[i].getAtom(j));
- }
- }
- }
- }
- catch (Exception e) {
- boolean test = true;
- // TODO: handle exception
- }
- return atomContainerArray;
- }
-
}
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