Typed Lists etc

Change-Id: If284e854566b2cf50c85c03741953acb1489dace Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · May 1, 2013 · e2d004f · e2d004f
1 parent 21d24ca
commit e2d004f
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Showing 27 changed files with 126 additions and 121 deletions.
diff --git a/src/main/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java b/src/main/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
@@ -182,7 +182,7 @@ public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer a
                 break out;
 
 //            bonds = ac.getBonds();
-            Iterator bonds = ac.bonds().iterator();
+            Iterator<IBond> bonds = ac.bonds().iterator();
             while (bonds.hasNext()) {
                 IBond bond = (IBond) bonds.next();
 

diff --git a/src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java b/src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java
@@ -21,6 +21,7 @@
  */
 package org.openscience.cdk.charges;
 
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -88,7 +89,7 @@ public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac) throws Excep
 		Object data = null;
 		Object bondData = null;
 		Object dataNeigh = null;
-		java.util.Iterator<IAtom> atoms = ac.atoms().iterator();
+		Iterator<IAtom> atoms = ac.atoms().iterator();
 		while(atoms.hasNext()) {
 			//logger.debug("ATOM "+i+ " " +atoms[i].getSymbol());
 			thisAtom = atoms.next();

diff --git a/src/main/org/openscience/cdk/formula/AdductFormula.java b/src/main/org/openscience/cdk/formula/AdductFormula.java
@@ -188,8 +188,8 @@ public int getIsotopeCount() {
 	 */
     @TestMethod("testIsotopes")
 	public Iterable<IIsotope> isotopes() {
-		return new Iterable() {
-            public Iterator iterator() {
+		return new Iterable<IIsotope>() {
+            public Iterator<IIsotope> iterator() {
                 return isotopesList().iterator();
             }
         };

diff --git a/src/main/org/openscience/cdk/geometry/AtomTools.java b/src/main/org/openscience/cdk/geometry/AtomTools.java
@@ -72,7 +72,7 @@ public static void add3DCoordinates1(AtomContainer atomContainer) {
         	IAtom atom = atomContainer.getAtom(i);
             // is this atom without 3D coords, and has only one ligand?
             if (atom.getPoint3d() == null) {
-            	java.util.List connectedAtoms = atomContainer.getConnectedAtomsList(atom);
+            	List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
                 if (connectedAtoms.size() == 1) {
                 	IAtom refAtom = (IAtom)connectedAtoms.get(0);;
                     if (refAtom.getPoint3d() != null) {
@@ -93,7 +93,7 @@ public static void add3DCoordinates1(AtomContainer atomContainer) {
         double angle = TETRAHEDRAL_ANGLE;
         for (int i = 0; i < refAtoms.getAtomCount(); i++) {
         	IAtom refAtom = refAtoms.getAtom(i);
-        	java.util.List noCoordLigands = noCoords.getConnectedAtomsList(refAtom);
+        	List<IAtom> noCoordLigands = noCoords.getConnectedAtomsList(refAtom);
             int nLigands = noCoordLigands.size();
             int nwanted = nLigands;
             String elementType = refAtom.getSymbol();
@@ -191,7 +191,7 @@ public static Point3d[] calculate3DCoordinatesForLigands(
         Point3d newPoints[] = new Point3d[0];
         Point3d aPoint = refAtom.getPoint3d();
         // get ligands
-	    List connectedAtoms = atomContainer.getConnectedAtomsList(refAtom);
+	    List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(refAtom);
         if (connectedAtoms == null) {
             return newPoints;
         }

diff --git a/src/main/org/openscience/cdk/geometry/CrystalGeometryTools.java b/src/main/org/openscience/cdk/geometry/CrystalGeometryTools.java
@@ -27,6 +27,8 @@
  *  */
 package org.openscience.cdk.geometry;
 
+import java.util.Iterator;
+
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
@@ -191,9 +193,9 @@ public static double[] cartesianToNotional(Vector3d aAxis, Vector3d bAxis, Vecto
 	 * @return  boolean indication that 3D coordinates are available 
 	 */
     public static boolean hasCrystalCoordinates(IAtomContainer container) {
-    	java.util.Iterator atoms = container.atoms().iterator();
+    	Iterator<IAtom> atoms = container.atoms().iterator();
         while (atoms.hasNext()) {
-            if (((IAtom)atoms.next()).getFractionalPoint3d() == null) {
+            if (atoms.next().getFractionalPoint3d() == null) {
                 return false;
             }
         }
@@ -204,12 +206,12 @@ public static boolean hasCrystalCoordinates(IAtomContainer container) {
      * Creates cartesian coordinates for all Atoms in the Crystal.
 	 */
     public static void fractionalToCartesian(ICrystal crystal) {
-    	java.util.Iterator atoms = crystal.atoms().iterator();
+    	Iterator<IAtom> atoms = crystal.atoms().iterator();
         Vector3d aAxis = crystal.getA();
         Vector3d bAxis = crystal.getB();
         Vector3d cAxis = crystal.getC();
         while (atoms.hasNext()) {
-        	IAtom atom = (IAtom)atoms.next();
+        	IAtom atom = atoms.next();
             Point3d fracPoint = atom.getFractionalPoint3d();
             if (fracPoint != null) {
                 atom.setPoint3d(fractionalToCartesian(aAxis,bAxis,cAxis, fracPoint));

diff --git a/src/main/org/openscience/cdk/geometry/Projector.java b/src/main/org/openscience/cdk/geometry/Projector.java
@@ -57,7 +57,7 @@ public static void project2D(IAtomContainer container) {
       }
     }
   }
-  public static void project2D(IAtomContainer container, HashMap renderingCoordinates) {
+  public static void project2D(IAtomContainer container, HashMap<IAtom,Point2d> renderingCoordinates) {
     for (int i = 0; i < container.getAtomCount(); i++) {
       IAtom atom = container.getAtom(i);
       if (atom.getPoint3d() != null) {

diff --git a/src/main/org/openscience/cdk/graph/invariant/CanonicalLabeler.java b/src/main/org/openscience/cdk/graph/invariant/CanonicalLabeler.java
@@ -83,22 +83,22 @@ public synchronized void canonLabel(IAtomContainer atomContainer) {
     	atomContainer.getAtom(0).setProperty(InvPair.CANONICAL_LABEL, 1);
     }
 
-    ArrayList vect = createInvarLabel(atomContainer);
+    List<InvPair> vect = createInvarLabel(atomContainer);
     step3(vect, atomContainer);
   }
 
   /**
    * @param v the invariance pair vector
    */
-  private void step2(ArrayList v, IAtomContainer atoms) {
+  private void step2(List<InvPair> v, IAtomContainer atoms) {
     primeProduct(v, atoms);
     step3(v, atoms);
   }
 
   /**
    * @param v the invariance pair vector
    */
-  private void step3(ArrayList v, IAtomContainer atoms) {
+  private void step3(List<InvPair> v, IAtomContainer atoms) {
     sortArrayList(v);
     rankArrayList(v);
     if (!isInvPart(v)) {
@@ -121,11 +121,11 @@ private void step3(ArrayList v, IAtomContainer atoms) {
    *
    * @return ArrayList containting the
    */
-  private ArrayList createInvarLabel(IAtomContainer atomContainer) {
-    java.util.Iterator atoms = atomContainer.atoms().iterator();
+  private List<InvPair> createInvarLabel(IAtomContainer atomContainer) {
+    Iterator<IAtom> atoms = atomContainer.atoms().iterator();
     IAtom a;
     StringBuffer inv;
-    ArrayList vect = new ArrayList();
+    List<InvPair> vect = new ArrayList<InvPair>();
     while(atoms.hasNext()) {
       a = (IAtom)atoms.next();
       inv = new StringBuffer();
@@ -152,19 +152,19 @@ private ArrayList createInvarLabel(IAtomContainer atomContainer) {
    *
    * @param v the invariance pair vector
    */
-  private void primeProduct(ArrayList v, IAtomContainer atomContainer) {
-    Iterator it = v.iterator();
-    Iterator n;
+  private void primeProduct(List<InvPair> v, IAtomContainer atomContainer) {
+    Iterator<InvPair> it = v.iterator();
+    Iterator<IAtom> n;
     InvPair inv;
     IAtom a;
     long summ;
     while (it.hasNext()) {
       inv = (InvPair) it.next();
-      List neighbour = atomContainer.getConnectedAtomsList(inv.getAtom());
+      List<IAtom> neighbour = atomContainer.getConnectedAtomsList(inv.getAtom());
       n = neighbour.iterator();
       summ = 1;
       while (n.hasNext()) {
-        a = (IAtom) n.next();
+        a = n.next();
         int next = ((InvPair)a.getProperty(InvPair.INVARIANCE_PAIR)).getPrime();
         summ = summ * next;
       }
@@ -206,11 +206,11 @@ public int compare(InvPair o1, InvPair o2) {
    *
    *  @param v the invariance pair vector
    */
-  private void rankArrayList(ArrayList v) {
+  private void rankArrayList(List<InvPair> v) {
     int num = 1;
     int[] temp = new int[v.size()];
     InvPair last = (InvPair) v.get(0);
-    Iterator it = v.iterator();
+    Iterator<InvPair> it = v.iterator();
     InvPair curr;
     for (int x = 0; it.hasNext(); x++) {
       curr = (InvPair) it.next();
@@ -234,10 +234,10 @@ private void rankArrayList(ArrayList v) {
    * @param v the invariance pair vector
    * @return true if the vector is invariantely partitioned, false otherwise
    */
-  private boolean isInvPart(ArrayList v) {
+  private boolean isInvPart(List<InvPair> v) {
     if (((InvPair) v.get(v.size()-1)).getCurr() == v.size())
       return true;
-    Iterator it = v.iterator();
+    Iterator<InvPair> it = v.iterator();
     InvPair curr;
     while (it.hasNext()) {
       curr = (InvPair) it.next();
@@ -252,14 +252,14 @@ private boolean isInvPart(ArrayList v) {
    *
    * @param v the invariance pair vector
    */
-  private void breakTies(ArrayList v) {
-    Iterator it = v.iterator();
+  private void breakTies(List<InvPair> v) {
+    Iterator<InvPair> it = v.iterator();
     InvPair curr;
     InvPair last = null;
     int tie = 0;
     boolean found = false;
     for (int x = 0; it.hasNext(); x++) {
-      curr = (InvPair) it.next();
+      curr = it.next();
       curr.setCurr(curr.getCurr() * 2);
       curr.setPrime();
       if (x != 0 && !found && curr.getCurr() == last.getCurr()) {

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java
@@ -35,13 +35,14 @@
 import java.util.Map;
 import java.util.Set;
 
-import org.openscience.cdk.Monomer;
 import org.openscience.cdk.Strand;
 import org.openscience.cdk.annotations.TestClass;
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBioPolymer;
+import org.openscience.cdk.interfaces.IMonomer;
+import org.openscience.cdk.interfaces.IStrand;
 import org.openscience.cdk.qsar.DescriptorSpecification;
 import org.openscience.cdk.qsar.DescriptorValue;
 import org.openscience.cdk.qsar.IMolecularDescriptor;
@@ -130,18 +131,18 @@ public class TaeAminoAcidDescriptor implements IMolecularDescriptor {
 
     private Map<String,String> nametrans = new HashMap<String,String>();
 
-    private List getMonomers(IBioPolymer iBioPolymer) {
-        List monomList = new ArrayList();
+    private List<IMonomer> getMonomers(IBioPolymer iBioPolymer) {
+        List<IMonomer> monomList = new ArrayList<IMonomer>();
 
-        Map strands = iBioPolymer.getStrands();
-        Set strandKeys = strands.keySet();
-        for (Iterator iterator = strandKeys.iterator(); iterator.hasNext();) {
-            Object key = iterator.next();
+        Map<String,IStrand> strands = iBioPolymer.getStrands();
+        Set<String> strandKeys = strands.keySet();
+        for (Iterator<String> iterator = strandKeys.iterator(); iterator.hasNext();) {
+            String key = iterator.next();
             Strand aStrand = (Strand) strands.get(key);
-            Map tmp = aStrand.getMonomers();
-            Set keys = tmp.keySet();
-            for (Iterator iterator1 = keys.iterator(); iterator1.hasNext();) {
-                Object o1 = iterator1.next();
+            Map<String,IMonomer> tmp = aStrand.getMonomers();
+            Set<String> keys = tmp.keySet();
+            for (Iterator<String> iterator1 = keys.iterator(); iterator1.hasNext();) {
+                String o1 = iterator1.next();
                 monomList.add(tmp.get(o1));
             }
         }
@@ -300,10 +301,10 @@ public DescriptorValue calculate(IAtomContainer container) {
         double[] desc = new double[ndesc];
         for (int i = 0; i < ndesc; i++) desc[i] = 0.0;
 
-        List monomers = getMonomers(peptide);
+        List<IMonomer> monomers = getMonomers(peptide);
 
-        for (Iterator iterator = monomers.iterator(); iterator.hasNext();) {
-            Monomer monomer = (Monomer) iterator.next();
+        for (Iterator<IMonomer> iterator = monomers.iterator(); iterator.hasNext();) {
+            IMonomer monomer = iterator.next();
 
             String o = monomer.getMonomerName();
 

diff --git a/src/main/org/openscience/cdk/renderer/JCPAction2D.java b/src/main/org/openscience/cdk/renderer/JCPAction2D.java
@@ -31,6 +31,7 @@
 import java.awt.Container;
 import java.awt.event.ActionEvent;
 import java.util.Hashtable;
+import java.util.Map;
 
 import javax.swing.AbstractAction;
 import javax.swing.JFrame;
@@ -73,8 +74,8 @@ public class JCPAction2D extends AbstractAction
 	protected static ILoggingTool logger =
 	    LoggingToolFactory.createLoggingTool(JCPAction2D.class);
 
-	private Hashtable actions = null;
-	private Hashtable popupActions = null;
+	private Map<String,JCPAction2D> actions = null;
+	private Map<String,JCPAction2D> popupActions = null;
 
 	/**
 	 *  Description of the Field
@@ -106,11 +107,11 @@ public JCPAction2D(JFrame jcpPanel, String type, boolean isPopupAction)
 		logger.debug("JCPAction->type: " + type);
 		if (this.actions == null)
 		{
-			this.actions = new Hashtable();
+			this.actions = new Hashtable<String,JCPAction2D>();
 		}
 		if (this.popupActions == null)
 		{
-			this.popupActions = new Hashtable();
+			this.popupActions = new Hashtable<String,JCPAction2D>();
 		}
 		this.type = "";
 		this.isPopupAction = isPopupAction;

diff --git a/src/main/org/openscience/cdk/ringsearch/RingPartitioner.java b/src/main/org/openscience/cdk/ringsearch/RingPartitioner.java
@@ -32,7 +32,6 @@
 import org.openscience.cdk.interfaces.IRingSet;
 
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 
 /**

diff --git a/src/main/org/openscience/cdk/ringsearch/cyclebasis/CycleBasis.java b/src/main/org/openscience/cdk/ringsearch/cyclebasis/CycleBasis.java
@@ -29,6 +29,16 @@
 
 package org.openscience.cdk.ringsearch.cyclebasis;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 import org._3pq.jgrapht.Edge;
 import org._3pq.jgrapht.UndirectedGraph;
 import org._3pq.jgrapht.alg.DijkstraShortestPath;
@@ -37,8 +47,6 @@
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.graph.BiconnectivityInspector;
 
-import java.util.*;
-
 /**
  * A minimum basis of all cycles in a graph.
  * All cycles in a graph G can be constructed from the basis cycles by binary
@@ -60,15 +68,15 @@
 public class CycleBasis {
 
 	//private List cycles = new Vector();
-	private List mulitEdgeCycles = new Vector();
-	private List multiEdgeList = new Vector();
+	private List<SimpleCycle> mulitEdgeCycles = new ArrayList<SimpleCycle>();
+	private List<Edge> multiEdgeList = new ArrayList<Edge>();
 
 	private SimpleCycleBasis cachedCycleBasis;
 
 	//private List edgeList = new Vector();
 	//private List multiEdgeList = new Vector();
 	private UndirectedGraph baseGraph;
-	private List subgraphBases = new Vector();
+	private List<SimpleCycleBasis> subgraphBases = new ArrayList<SimpleCycleBasis>();
 
 	/**
 	 * Constructs a minimum cycle basis of a graph.
@@ -236,8 +244,8 @@ public Map relevantCycles() {
 		Map result = new HashMap();
 		//minimize();
 
-        for (Object subgraphBase : subgraphBases) {
-            SimpleCycleBasis cycleBasis = (SimpleCycleBasis) subgraphBase;
+        for (SimpleCycleBasis subgraphBase : subgraphBases) {
+            SimpleCycleBasis cycleBasis = subgraphBase;
             result.putAll(cycleBasis.relevantCycles());
         }
 
@@ -258,8 +266,8 @@ public List equivalenceClasses() {
 		List result = new ArrayList();
 		//minimize();
 
-        for (Object subgraphBase : subgraphBases) {
-            SimpleCycleBasis cycleBasis = (SimpleCycleBasis) subgraphBase;
+        for (SimpleCycleBasis subgraphBase : subgraphBases) {
+            SimpleCycleBasis cycleBasis = subgraphBase;
             result.addAll(cycleBasis.equivalenceClasses());
         }