From: <raj...@us...> - 2006-09-19 16:13:51
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Revision: 6956 http://svn.sourceforge.net/cdk/?rev=6956&view=rev Author: rajarshi Date: 2006-09-19 09:13:34 -0700 (Tue, 19 Sep 2006) Log Message: ----------- Fixed PMD warnings Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java trunk/cdk/src/org/openscience/cdk/io/RssWriter.java Modified: trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java 2006-09-19 16:08:34 UTC (rev 6955) +++ trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java 2006-09-19 16:13:34 UTC (rev 6956) @@ -28,30 +28,12 @@ */ package org.openscience.cdk.io; -import java.io.IOException; -import java.io.OutputStream; -import java.io.OutputStreamWriter; -import java.io.StringWriter; -import java.io.Writer; - import nu.xom.Attribute; import nu.xom.Document; import nu.xom.Element; import nu.xom.Serializer; - import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.IAtom; -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.interfaces.IChemFile; -import org.openscience.cdk.interfaces.IChemModel; -import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.interfaces.ICrystal; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.interfaces.IReactionSet; +import org.openscience.cdk.interfaces.*; import org.openscience.cdk.io.formats.CMLFormat; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; @@ -60,6 +42,8 @@ import org.openscience.cdk.libio.cml.Convertor; import org.openscience.cdk.tools.LoggingTool; +import java.io.*; + /** * Serializes a SetOfMolecules or a Molecule object to CML 2 code. * Chemical Markup Language is an XML based file format {@cdk.cite PMR99}. @@ -124,8 +108,8 @@ public CMLWriter(Writer out) { this.writer = out; output = new OutputStream() { - public void write(int b) throws IOException { - writer.write(b); + public void write(int anInt) throws IOException { + writer.write(anInt); } }; logger = new LoggingTool(this); @@ -186,21 +170,25 @@ * @param object A Molecule of SetOfMolecules object */ public void write(IChemObject object) throws CDKException { - if (object instanceof IMolecule) { - } else if (object instanceof IAtomContainer) { - } else if (object instanceof IReaction) { - } else if (object instanceof IReactionSet) { - } else if (object instanceof IMoleculeSet) { - } else if (object instanceof IChemSequence) { - } else if (object instanceof IChemModel) { - } else if (object instanceof IChemFile) { - } else if (object instanceof ICrystal) { - } else if (object instanceof IAtom) { - } else if (object instanceof IBond) { - } else { - throw new CDKException("Cannot write this unsupported IChemObject: " + object.getClass().getName()); + + if (!(object instanceof IMolecule) && + !(object instanceof IAtomContainer) && + !(object instanceof IReaction) && + !(object instanceof IReactionSet) && + !(object instanceof IMoleculeSet) && + !(object instanceof IChemSequence) && + !(object instanceof IChemModel) && + !(object instanceof IChemFile) && + !(object instanceof ICrystal) && + !(object instanceof IAtom) && + !(object instanceof IBond)) { + throw new CDKException("Cannot write this unsupported IChemObject: " + object.getClass().getName()); } + + + + logger.debug("Writing object in CML of type: ", object.getClass().getName()); customizeJob(); Modified: trunk/cdk/src/org/openscience/cdk/io/RssWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/RssWriter.java 2006-09-19 16:08:34 UTC (rev 6955) +++ trunk/cdk/src/org/openscience/cdk/io/RssWriter.java 2006-09-19 16:13:34 UTC (rev 6956) @@ -1,47 +1,19 @@ package org.openscience.cdk.io; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStream; -import java.io.OutputStreamWriter; -import java.io.Writer; -import java.text.SimpleDateFormat; -import java.util.Collection; -import java.util.Date; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Locale; -import java.util.Map; -import java.util.Vector; - -import nu.xom.Attribute; -import nu.xom.Document; -import nu.xom.Element; -import nu.xom.ProcessingInstruction; -import nu.xom.Text; - +import nu.xom.*; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.ChemObject; import org.openscience.cdk.SetOfAtomContainers; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.IAtom; -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.interfaces.IChemFile; -import org.openscience.cdk.interfaces.IChemModel; -import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.interfaces.ICrystal; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.interfaces.IAtomContainerSet; -import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.interfaces.IReactionSet; +import org.openscience.cdk.interfaces.*; import org.openscience.cdk.io.formats.CMLRSSFormat; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.libio.cml.Convertor; +import java.io.*; +import java.text.SimpleDateFormat; +import java.util.*; + /** * Generatas an rss feed. It the object is a SetOfMolecules, the molecules * are put in separtly. All other objects a made cml and put in. @@ -113,14 +85,14 @@ */ public void write(IChemObject object) throws CDKException { try{ - ProcessingInstruction pi=new ProcessingInstruction("xml-stylesheet", "href=\"http://www.w3.org/2000/08/w3c-synd/style.css\" type=\"text/css\""); + ProcessingInstruction processingInstruction =new ProcessingInstruction("xml-stylesheet", "href=\"http://www.w3.org/2000/08/w3c-synd/style.css\" type=\"text/css\""); Element rdfElement = new Element("rdf:RDF",NS_RDF); rdfElement.addNamespaceDeclaration("",NS_RSS10); rdfElement.addNamespaceDeclaration("mn","http://usefulinc.com/rss/manifest/"); rdfElement.addNamespaceDeclaration("dc",NS_DCELEMENTS); rdfElement.addNamespaceDeclaration("cml",Convertor.NS_CML); Document doc = new Document(rdfElement); - doc.insertChild(pi,0); + doc.insertChild(processingInstruction,0); Element channelElement = new Element("channel",NS_RSS10); Element titleElement = new Element("title",NS_RSS10); titleElement.appendChild(new Text(title)); @@ -146,27 +118,27 @@ channelElement.appendChild(itemsElement); channelElement.addAttribute(new Attribute("rdf:about",NS_RDF,about)); rdfElement.appendChild(channelElement); - List l=new Vector(); + List list =new Vector(); if(object instanceof IAtomContainerSet){ for(int i=0;i<((SetOfAtomContainers)object).getAtomContainerCount();i++){ - l.add(((SetOfAtomContainers)object).getAtomContainer(i)); + list.add(((SetOfAtomContainers)object).getAtomContainer(i)); } }else{ - l.add(object); + list.add(object); } - for(int i=0;i<l.size();i++){ - ChemObject co=(ChemObject)l.get(i); + for(int i=0;i<list.size();i++){ + ChemObject chemObject =(ChemObject)list.get(i); Element itemElement = new Element("item",NS_RSS10); - String easylink=(String)linkmap.get(co); + String easylink=(String)linkmap.get(chemObject); if(easylink!=null) itemElement.addAttribute(new Attribute("rdf:about",NS_RDF,easylink)); Element link2Element = new Element("link",NS_RSS10); link2Element.appendChild(new Text(easylink)); itemElement.appendChild(link2Element); - String title=(String)co.getProperties().get(CDKConstants.TITLE); - if(titlemap.get(co)!=null){ + String title=(String)chemObject.getProperties().get(CDKConstants.TITLE); + if(titlemap.get(chemObject)!=null){ Element title2Element = new Element("title",NS_RSS10); - title2Element.appendChild(new Text((String)titlemap.get(co))); + title2Element.appendChild(new Text((String)titlemap.get(chemObject))); itemElement.appendChild(title2Element); } if(title!=null){ @@ -177,18 +149,18 @@ subjectElement.appendChild(new Text(title)); itemElement.appendChild(subjectElement); } - if(datemap.get(co)!=null){ + if(datemap.get(chemObject)!=null){ Element dateElement = new Element("dc:date",NS_DCELEMENTS); SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss", Locale.US); - dateElement.appendChild(new Text(formatter.format((Date)datemap.get(co))+timezone)); + dateElement.appendChild(new Text(formatter.format((Date)datemap.get(chemObject))+timezone)); itemElement.appendChild(dateElement); } Element creator2Element =new Element("dc:creator",NS_DCELEMENTS); - creator2Element.appendChild(new Text((String)creatormap.get(co))); + creator2Element.appendChild(new Text((String)creatormap.get(chemObject))); itemElement.appendChild(creator2Element); Element root=null; Convertor convertor=new Convertor(true,null); - object=(IChemObject)l.get(i); + object=(IChemObject)list.get(i); if (object instanceof IMolecule) { root = convertor.cdkMoleculeToCMLMolecule((IMolecule)object); }else if (object instanceof IAtomContainer) { @@ -215,16 +187,16 @@ throw new CDKException("Unsupported chemObject: " + object.getClass().getName()); } itemElement.appendChild(root); - if(multiMap.get(co)!=null){ - Collection coll=(Collection)multiMap.get(co); - Iterator it=coll.iterator(); - while(it.hasNext()){ - itemElement.appendChild((Element)it.next()); + if(multiMap.get(chemObject)!=null){ + Collection coll=(Collection)multiMap.get(chemObject); + Iterator iterator =coll.iterator(); + while(iterator.hasNext()){ + itemElement.appendChild((Element)iterator.next()); } } rdfElement.appendChild(itemElement); Element imageElement2 = new Element("rdf:li",NS_RDF); - imageElement2.addAttribute(new Attribute("rdf:resource",NS_RDF,(String)linkmap.get(co))); + imageElement2.addAttribute(new Attribute("rdf:resource",NS_RDF,(String)linkmap.get(chemObject))); seqElement.appendChild(imageElement2); } writer.write(doc.toXML()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |