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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io/cml ChemFileCDO.java,1.31,1.32
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From: Egon W. <eg...@us...> - 2005-09-27 09:36:40
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io/cml In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14201/src/org/openscience/cdk/io/cml Modified Files: ChemFileCDO.java Log Message: CMLReader now reuses the passed ChemObject, so that one can have a CML file's content be read into a custom ChemObject Index: ChemFileCDO.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/cml/ChemFileCDO.java,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- ChemFileCDO.java 2 Sep 2005 08:03:39 -0000 1.31 +++ ChemFileCDO.java 27 Sep 2005 09:36:27 -0000 1.32 @@ -27,20 +27,22 @@ import javax.vecmath.Vector3d; -import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Bond; +import org.openscience.cdk.interfaces.Atom; +import org.openscience.cdk.interfaces.AtomContainer; +import org.openscience.cdk.interfaces.Bond; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.ChemFile; -import org.openscience.cdk.ChemModel; -import org.openscience.cdk.ChemSequence; -import org.openscience.cdk.Crystal; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.PseudoAtom; -import org.openscience.cdk.Reaction; -import org.openscience.cdk.SetOfMolecules; -import org.openscience.cdk.SetOfReactions; -import org.openscience.cdk.SingleElectron; +import org.openscience.cdk.interfaces.ChemFile; +import org.openscience.cdk.interfaces.ChemObjectBuilder; +import org.openscience.cdk.interfaces.ChemObjectChangeEvent; +import org.openscience.cdk.interfaces.ChemObjectListener; +import org.openscience.cdk.interfaces.ChemModel; +import org.openscience.cdk.interfaces.ChemSequence; +import org.openscience.cdk.interfaces.Crystal; +import org.openscience.cdk.interfaces.Molecule; +import org.openscience.cdk.interfaces.PseudoAtom; +import org.openscience.cdk.interfaces.Reaction; +import org.openscience.cdk.interfaces.SetOfMolecules; +import org.openscience.cdk.interfaces.SetOfReactions; import org.openscience.cdk.dict.DictRef; import org.openscience.cdk.io.cml.cdopi.CDOAcceptedObjects; import org.openscience.cdk.io.cml.cdopi.CDOInterface; @@ -54,8 +56,10 @@ * * @author Egon Willighagen <eg...@sc...> */ -public class ChemFileCDO extends ChemFile implements CDOInterface { +public class ChemFileCDO implements ChemFile, CDOInterface { + private ChemFile currentChemFile; + private AtomContainer currentMolecule; private SetOfMolecules currentSetOfMolecules; private ChemModel currentChemModel; @@ -77,19 +81,20 @@ private double crystal_axis_y; private double crystal_axis_z; - protected org.openscience.cdk.tools.LoggingTool logger; + protected LoggingTool logger; /** * Basic contructor */ - public ChemFileCDO() { + public ChemFileCDO(ChemFile file) { logger = new LoggingTool(this); - currentChemSequence = new ChemSequence(); - currentChemModel = new ChemModel(); - currentSetOfMolecules = new SetOfMolecules(); + currentChemFile = file; + currentChemSequence = file.getBuilder().newChemSequence(); + currentChemModel = file.getBuilder().newChemModel(); + currentSetOfMolecules = file.getBuilder().newSetOfMolecules(); currentSetOfReactions = null; currentReaction = null; - currentMolecule = new Molecule(); + currentMolecule = file.getBuilder().newMolecule(); atomEnumeration = new Hashtable(); } @@ -101,10 +106,10 @@ */ public void startDocument() { logger.info("New CDO Object"); - currentChemSequence = new ChemSequence(); - currentChemModel = new ChemModel(); - currentSetOfMolecules = new SetOfMolecules(); - currentMolecule = new Molecule(); + currentChemSequence = currentChemFile.getBuilder().newChemSequence(); + currentChemModel = currentChemFile.getBuilder().newChemModel(); + currentSetOfMolecules = currentChemFile.getBuilder().newSetOfMolecules(); + currentMolecule = currentChemFile.getBuilder().newMolecule(); atomEnumeration = new Hashtable(); } @@ -152,25 +157,25 @@ public void startObject(String objectType) { logger.debug("START:" + objectType); if (objectType.equals("Molecule")) { - if (currentChemModel == null) currentChemModel = new ChemModel(); - if (currentSetOfMolecules == null) currentSetOfMolecules = new SetOfMolecules(); - currentMolecule = new Molecule(); + if (currentChemModel == null) currentChemModel = currentChemFile.getBuilder().newChemModel(); + if (currentSetOfMolecules == null) currentSetOfMolecules = currentChemFile.getBuilder().newSetOfMolecules(); + currentMolecule = currentChemFile.getBuilder().newMolecule(); } else if (objectType.equals("Atom")) { - currentAtom = new Atom("H"); + currentAtom = currentChemFile.getBuilder().newAtom("H"); logger.debug("Atom # " + numberOfAtoms); numberOfAtoms++; } else if (objectType.equals("Bond")) { bond_id = null; bond_stereo = -99; } else if (objectType.equals("Animation")) { - currentChemSequence = new ChemSequence(); + currentChemSequence = currentChemFile.getBuilder().newChemSequence(); } else if (objectType.equals("Frame")) { - currentChemModel = new ChemModel(); + currentChemModel = currentChemFile.getBuilder().newChemModel(); } else if (objectType.equals("SetOfMolecules")) { - currentSetOfMolecules = new SetOfMolecules(); - currentMolecule = new Molecule(); + currentSetOfMolecules = currentChemFile.getBuilder().newSetOfMolecules(); + currentMolecule = currentChemFile.getBuilder().newMolecule(); } else if (objectType.equals("Crystal")) { - currentMolecule = new Crystal(currentMolecule); + currentMolecule = currentChemFile.getBuilder().newCrystal(currentMolecule); } else if (objectType.equals("a-axis") || objectType.equals("b-axis") || objectType.equals("c-axis")) { @@ -178,16 +183,16 @@ crystal_axis_y = 0.0; crystal_axis_z = 0.0; } else if (objectType.equals("SetOfReactions")) { - currentSetOfReactions = new SetOfReactions(); + currentSetOfReactions = currentChemFile.getBuilder().newSetOfReactions(); } else if (objectType.equals("Reaction")) { if (currentSetOfReactions == null) startObject("SetOfReactions"); - currentReaction = new Reaction(); + currentReaction = currentChemFile.getBuilder().newReaction(); } else if (objectType.equals("Reactant")) { if (currentReaction == null) startObject("Reaction"); - currentMolecule = new Molecule(); + currentMolecule = currentChemFile.getBuilder().newMolecule(); } else if (objectType.equals("Product")) { if (currentReaction == null) startObject("Reaction"); - currentMolecule = new Molecule(); + currentMolecule = currentChemFile.getBuilder().newMolecule(); } } @@ -226,7 +231,7 @@ } else { org.openscience.cdk.interfaces.Atom a1 = currentMolecule.getAtomAt(bond_a1); org.openscience.cdk.interfaces.Atom a2 = currentMolecule.getAtomAt(bond_a2); - Bond b = new Bond(a1, a2, bond_order); + Bond b = currentChemFile.getBuilder().newBond(a1, a2, bond_order); if (bond_id != null) b.setID(bond_id); if (bond_stereo != -99) { b.setStereo(bond_stereo); @@ -326,14 +331,14 @@ } else if (objectType.equals("PseudoAtom")) { if (propertyType.equals("label")) { if (!(currentAtom instanceof PseudoAtom)) { - currentAtom = new PseudoAtom(currentAtom); + currentAtom = currentChemFile.getBuilder().newPseudoAtom(currentAtom); } ((PseudoAtom)currentAtom).setLabel(propertyValue); } } else if (objectType.equals("Atom")) { if (propertyType.equals("type")) { if (propertyValue.equals("R") && !(currentAtom instanceof PseudoAtom)) { - currentAtom = new PseudoAtom(currentAtom); + currentAtom = currentChemFile.getBuilder().newPseudoAtom(currentAtom); } currentAtom.setSymbol(propertyValue); } else if (propertyType.equals("x2")) { @@ -368,7 +373,7 @@ } else if (propertyType.equals("spinMultiplicity")) { int unpairedElectrons = new Integer(propertyValue).intValue() -1; for (int i=0; i<unpairedElectrons; i++) { - currentMolecule.addElectronContainer(new SingleElectron(currentAtom)); + currentMolecule.addElectronContainer(currentChemFile.getBuilder().newSingleElectron(currentAtom)); } } else if (propertyType.equals("id")) { logger.debug("id: ", propertyValue); @@ -475,5 +480,93 @@ objects.add("Product"); return objects; } + + public void addChemSequence(org.openscience.cdk.interfaces.ChemSequence chemSequence) { + currentChemFile.addChemSequence(chemSequence); + } + + public org.openscience.cdk.interfaces.ChemSequence[] getChemSequences() { + return currentChemFile.getChemSequences(); + } + + public org.openscience.cdk.interfaces.ChemSequence getChemSequence(int number) { + return currentChemFile.getChemSequence(number); + } + + public int getChemSequenceCount() { + return currentChemFile.getChemSequenceCount(); + } + + public void addListener(ChemObjectListener col) { + currentChemFile.addListener(col); + } + + public int getListenerCount() { + return currentChemFile.getListenerCount(); + } + + public void removeListener(ChemObjectListener col) { + currentChemFile.removeListener(col); + } + + public void notifyChanged() { + currentChemFile.notifyChanged(); + } + + public void notifyChanged(ChemObjectChangeEvent evt) { + currentChemFile.notifyChanged(evt); + } + + public void setProperty(Object description, Object property) { + currentChemFile.setProperty(description, property); + } + + public void removeProperty(Object description) { + currentChemFile.removeProperty(description); + } + + public Object getProperty(Object description) { + return currentChemFile.getProperty(description); + } + + public Hashtable getProperties() { + return currentChemFile.getProperties(); + } + + public String getID() { + return currentChemFile.getID(); + } + + public void setID(String identifier) { + currentChemFile.setID(identifier); + } + + public void setFlag(int flag_type, boolean flag_value) { + currentChemFile.setFlag(flag_type, flag_value); + } + + public boolean getFlag(int flag_type) { + return currentChemFile.getFlag(flag_type); + } + + public void setProperties(Hashtable properties) { + currentChemFile.setProperties(properties); + } + + public void setFlags(boolean[] flagsNew) { + currentChemFile.setFlags(flagsNew); + } + + public boolean[] getFlags() { + return currentChemFile.getFlags(); + } + + public Object clone() { + return currentChemFile.clone(); + } + + public ChemObjectBuilder getBuilder() { + return currentChemFile.getBuilder(); + } } |