Fixed bugs in the CrossValidate and Reprocess

Author: wangqion

src/edu/msu/cme/rdp/classifier/train/validation/crossvalidate/CrossValidate.java

@@ -69,7 +69,7 @@ public ArrayList<HashMap> runTest(File tax_file, File source_file, File out_file
         DecisionMaker dm = new DecisionMaker(factory);
          // get all the genus node list
         HashMap<String, HierarchyTree> genusNodeMap = new HashMap<String, HierarchyTree>();
-        factory.getRoot().getNodeMap(Taxonomy.GENUS, genusNodeMap);
+        factory.getRoot().getNodeMap(factory.getLowestRank(), genusNodeMap);
         if (genusNodeMap.isEmpty()) {
           throw new IllegalArgumentException("\nThere is no node in GENUS level!");
         }
@@ -115,7 +115,7 @@ public ArrayList<HashMap> runTest(File tax_file, File source_file, File out_file
           }
 
           List result = dm.getBestClasspath( wordIterator, genusNodeMap, useSeed, min_bootstrap_words);
-
+          
           //xxx
           ValidClassificationResultFacade resultFacade = new ValidClassificationResultFacade(pSeq, result);
 

src/edu/msu/cme/rdp/classifier/utils/ClassifierSequence.java

@@ -36,9 +36,12 @@ public ClassifierSequence(String seqName, String desc, String seqString) throws
         * Fetches every overlapping word from the sequence string, changes each
         * word to integer format and saves in an array.
         */
-        GoodWordIterator iterator = new GoodWordIterator(this.getSeqString());
-        this.wordIndexArr = iterator.getWordArr();        
-        this.goodWordCount = wordIndexArr.length;
+        // Note when user provide the classification result, we don't get the sequence string
+        if ( !this.getSeqString().isEmpty()){
+            GoodWordIterator iterator = new GoodWordIterator(this.getSeqString());
+            this.wordIndexArr = iterator.getWordArr();        
+            this.goodWordCount = wordIndexArr.length;
+        }
     }
 
     /**

src/edu/msu/cme/rdp/multicompare/Reprocess.java

@@ -140,7 +140,8 @@ public static void main(String [] args) throws Exception {
                 }
                 gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();
 
-                if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)) {
+                if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)
+                    && !gene.equals(ClassifierFactory.FUNGALITS_warcup_GENE) && !gene.equals(ClassifierFactory.FUNGALITS_unite_GENE) ) {
                     throw new IllegalArgumentException(gene + " is NOT valid, only allows " + ClassifierFactory.RRNA_16S_GENE
                      + ", " + ClassifierFactory.FUNGALLSU_GENE + ", " + ClassifierFactory.FUNGALITS_warcup_GENE + " and " + ClassifierFactory.FUNGALITS_unite_GENE);
                 }