ref #6369 adapt existing occurrences of interface to removed generics

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / taxonx2013 / TaxonXTreatmentExtractor.java

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java
index 6c5a9b5b8b372af4671b34d78127104e72298487..ca1ab2210de597b5ad4b59e866d312d1d473aa14 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java
@@ -51,6 +51,8 @@ import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
 import eu.etaxonomy.cdm.model.description.TextData;
 import eu.etaxonomy.cdm.model.name.BacterialName;
 import eu.etaxonomy.cdm.model.name.BotanicalName;
 import eu.etaxonomy.cdm.model.description.TextData;
 import eu.etaxonomy.cdm.model.name.BacterialName;
 import eu.etaxonomy.cdm.model.name.BotanicalName;

+import eu.etaxonomy.cdm.model.name.INonViralName;
+import eu.etaxonomy.cdm.model.name.ITaxonNameBase;

 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;


@@ -2439,14 +2441,14 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
 
         boolean parseNameManually=false;
         INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();
 
         boolean parseNameManually=false;
         INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();

-        TaxonNameBase<?,?>  nameToBeFilledTest ;
+        ITaxonNameBase  nameToBeFilledTest ;

 
         //if selected the atomised version
         if(newName==atomisedNameStr){
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
                 addProblemNameToFile("ato",atomisedNameStr,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
 
         //if selected the atomised version
         if(newName==atomisedNameStr){
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
                 addProblemNameToFile("ato",atomisedNameStr,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());

-                nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode,rank);
+                nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode, rank);

                 if (nameToBeFilledTest.hasProblem()){
                     addProblemNameToFile("full",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
                     parseNameManually=true;
                 if (nameToBeFilledTest.hasProblem()){
                     addProblemNameToFile("full",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
                     parseNameManually=true;


@@ -2455,7 +2457,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
         }else{
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
         }else{
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){

-                addProblemNameToFile("fullversion",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
+                addProblemNameToFile("fullversion",fullName, nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());

                 nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode,rank);
                 parseNameManually=true;
                 if(!originalName.equalsIgnoreCase(atomisedNameStr)) {
                 nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode,rank);
                 parseNameManually=true;
                 if(!originalName.equalsIgnoreCase(atomisedNameStr)) {


@@ -2581,7 +2583,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
 
         boolean parseNameManually=false;
         INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
 
         boolean parseNameManually=false;
         INonViralNameParser parser = NonViralNameParserImpl.NewInstance();

-        TaxonNameBase  nameToBeFilledTest = null;
+        ITaxonNameBase  nameToBeFilledTest = null;

 
         //if selected the atomised version
         if(newName==atomisedNameStr){
 
         //if selected the atomised version
         if(newName==atomisedNameStr){


@@ -2620,13 +2622,13 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
 
     }
 
 
     }
 

-    private TaxonNameBase<?,?> parseWithExtension(INonViralNameParser parser, String atomisedNameStr, Rank rank, String followingText, HashMap<String, String> atomisedMap) {
+    private ITaxonNameBase parseWithExtension(INonViralNameParser parser, String atomisedNameStr, Rank rank, String followingText, HashMap<String, String> atomisedMap) {

        Object[] nameExtensionResult = getPossibleExtension(followingText, atomisedMap, nomenclaturalCode);
 
        Object[] nameExtensionResult = getPossibleExtension(followingText, atomisedMap, nomenclaturalCode);
 

-       TaxonNameBase<?,?> name = parser.parseFullName(atomisedNameStr, nomenclaturalCode, rank);
+       ITaxonNameBase name = parser.parseFullName(atomisedNameStr, nomenclaturalCode, rank);

        if (nameExtensionResult != null && nameExtensionResult[0] != null){
                String ext = (String)nameExtensionResult[0];
        if (nameExtensionResult != null && nameExtensionResult[0] != null){
                String ext = (String)nameExtensionResult[0];

-               TaxonNameBase<?,?> extName =parser.parseFullName(atomisedNameStr + " " + ext, nomenclaturalCode, rank);
+               ITaxonNameBase extName =parser.parseFullName(atomisedNameStr + " " + ext, nomenclaturalCode, rank);

                if (! extName.hasProblem()){
                        name = extName;
                        this.usedFollowingTextPrefix = ext;
                if (! extName.hasProblem()){
                        name = extName;
                        this.usedFollowingTextPrefix = ext;


@@ -3510,7 +3512,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
                     logger.warn("Problem with status");
                 }
             }
                     logger.warn("Problem with status");
                 }
             }

-            List<TaxonBase> tmpList = new ArrayList<TaxonBase>();
+            List<TaxonBase> tmpList = new ArrayList<>();

 
             Pager<TaxonBase> taxontest = importer.getTaxonService().findByTitle(TaxonBase.class, newName2, MatchMode.BEGINNING, null, null, null, null, null);
             tmpList.addAll(taxontest.getRecords());
 
             Pager<TaxonBase> taxontest = importer.getTaxonService().findByTitle(TaxonBase.class, newName2, MatchMode.BEGINNING, null, null, null, null, null);
             tmpList.addAll(taxontest.getRecords());


@@ -3518,7 +3520,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
             //logger.info("tmpList returned: "+tmpList.size());
 
 
             //logger.info("tmpList returned: "+tmpList.size());
 
 

-            NonViralName<?> identicName = null;
+            INonViralName identicName = null;

             boolean foundIdentic=false;
             TaxonBase<?> tmpTaxonBase=null;
             //            Taxon tmpPartial=null;
             boolean foundIdentic=false;
             TaxonBase<?> tmpTaxonBase=null;
             //            Taxon tmpPartial=null;


@@ -3531,7 +3533,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
                             crank =tnb.getRank();
                             if (crank !=null && rank !=null){
                                 if (crank.equals(rank)){
                             crank =tnb.getRank();
                             if (crank !=null && rank !=null){
                                 if (crank.equals(rank)){

-                                       identicName = CdmBase.deproxy(tnb, NonViralName.class);
+                                       identicName = tnb;

                                        if (isSynonym && tmpb.isInstanceOf(Synonym.class) || !isSynonym && tmpb.isInstanceOf(Taxon.class)){
                                                foundIdentic=true;
                                                tmpTaxonBase=tmpb;
                                        if (isSynonym && tmpb.isInstanceOf(Synonym.class) || !isSynonym && tmpb.isInstanceOf(Taxon.class)){
                                                foundIdentic=true;
                                                tmpTaxonBase=tmpb;


@@ -3557,7 +3559,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
             }
             if ((tmpTaxonBase == null || !foundIdentic) ||  (tmpTaxonBase != null && !statusMatch) ||  (tmpTaxonBase != null && !appendedMatch && !statusMatch)){
 
             }
             if ((tmpTaxonBase == null || !foundIdentic) ||  (tmpTaxonBase != null && !statusMatch) ||  (tmpTaxonBase != null && !appendedMatch && !statusMatch)){
 

-               NonViralName<?> tnb;
+               INonViralName tnb;

                if (identicName == null){
                        tnb = getNonViralNameAccNomenclature();
                        tnb.setRank(rank);
                if (identicName == null){
                        tnb = getNonViralNameAccNomenclature();
                        tnb.setRank(rank);


@@ -3897,7 +3899,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
          * @param nameToBeFilledTest
          */
         @SuppressWarnings("rawtypes")
          * @param nameToBeFilledTest
          */
         @SuppressWarnings("rawtypes")

-        public void setParsedName(TaxonNameBase nameToBeFilledTest) {
+        public void setParsedName(ITaxonNameBase nameToBeFilledTest) {

             this.taxonNameBase = (NonViralName<?>) nameToBeFilledTest;
 
         }
             this.taxonNameBase = (NonViralName<?>) nameToBeFilledTest;
 
         }


@@ -4804,7 +4806,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
      * @param tnb
      * @return
      */
      * @param tnb
      * @return
      */

-    private Taxon findMatchingTaxon(NonViralName<?> tnb, Reference refMods) {
+    private Taxon findMatchingTaxon(INonViralName tnb, Reference refMods) {

         logger.info("findMatchingTaxon");
         Taxon tmp=null;
 
         logger.info("findMatchingTaxon");
         Taxon tmp=null;
 


@@ -4886,7 +4888,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
      * @param similarityAuthor
      * @return
      */
      * @param similarityAuthor
      * @return
      */

-    private boolean compareAndCheckTaxon(NonViralName<?> tnb, Reference refMods, double similarityScore,
+    private boolean compareAndCheckTaxon(INonViralName tnb, Reference refMods, double similarityScore,

             Taxon bestMatchingTaxon, double similarityAuthor) {
         //logger.info("compareAndCheckTaxon");
         boolean insertAsExisting;
             Taxon bestMatchingTaxon, double similarityAuthor) {
         //logger.info("compareAndCheckTaxon");
         boolean insertAsExisting;


@@ -4902,7 +4904,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
         }
         //        }
 
         }
         //        }
 

-        logDecision(tnb,bestMatchingTaxon,insertAsExisting, refMods);
+        logDecision(tnb, bestMatchingTaxon, insertAsExisting, refMods);

         return insertAsExisting;
     }
 
         return insertAsExisting;
     }
 


@@ -4910,7 +4912,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
      * @return
      */
     @SuppressWarnings("rawtypes")
      * @return
      */
     @SuppressWarnings("rawtypes")

-    private List<Taxon> getMatchingTaxa(TaxonNameBase tnb) {
+    private List<Taxon> getMatchingTaxa(ITaxonNameBase tnb) {

         //logger.info("getMatchingTaxon");
        if (tnb.getTitleCache() == null){
                tnb.setTitleCache(tnb.toString(), tnb.isProtectedTitleCache());
         //logger.info("getMatchingTaxon");
        if (tnb.getTitleCache() == null){
                tnb.setTitleCache(tnb.toString(), tnb.isProtectedTitleCache());


@@ -5569,11 +5571,11 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
      * @param insertAsExisting
      * @param refMods
      */
      * @param insertAsExisting
      * @param refMods
      */

-    private void logDecision(NonViralName<?> tnb, Taxon bestMatchingTaxon, boolean insertAsExisting, Reference refMods) {
+    private void logDecision(INonViralName tnb, Taxon bestMatchingTaxon, boolean insertAsExisting, Reference refMods) {

         try{
         try{

-            FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "Decisions_"+classification.toString()+".txt",true);
+            FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "Decisions_"+classification.toString()+".txt", true);

             BufferedWriter out = new BufferedWriter(fstream);
             BufferedWriter out = new BufferedWriter(fstream);

-            out.write(tnb.getTitleCache()+" sec. "+refMods+"\t"+bestMatchingTaxon.getTitleCache()+"\t"+insertAsExisting+"\n");
+            out.write(tnb.getTitleCache() + " sec. " + refMods + "\t" + bestMatchingTaxon.getTitleCache() + "\t" + insertAsExisting + "\n");

             //Close the output stream
             out.close();
         }catch (Exception e){//Catch exception if any
             //Close the output stream
             out.close();
         }catch (Exception e){//Catch exception if any