Removed deprecated parameter 'description_score_relative_description_…

…frequency_weight' from all example and test input files (YMLs).
groupschoof · Jan 5, 2015 · e415359 · e415359
1 parent 1db29f3
commit e415359
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Showing 8 changed files with 5 additions and 16 deletions.
diff --git a/batcher_input_example.yml b/batcher_input_example.yml
@@ -7,7 +7,6 @@ batch_ymls_dir: ./test/resources/batch_ymls
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 
 blast_dbs:
   swissprot:

diff --git a/src/ahrd/view/OutputWriter.java b/src/ahrd/view/OutputWriter.java
@@ -30,12 +30,10 @@ public void writeOutput() throws IOException {
 		// Column-Names:
 		bw.write("# AHRD-Version " + AHRD.VERSION + "\n");
 		bw.write("\n");
-		bw
-				.write("Protein-Accession\tBlast-Hit-Accession\tAHRD-Quality-Code\tHuman-Readable-Description\tInterpro-ID (Description)\tGene-Ontology-ID (Name)");
+		bw.write("Protein-Accession\tBlast-Hit-Accession\tAHRD-Quality-Code\tHuman-Readable-Description\tInterpro-ID (Description)\tGene-Ontology-ID (Name)");
 
 		if (getSettings().isInTrainingMode()) {
-			bw
-					.write("\tHRD-Length\tReference-Description\tRef-Lenght\tEvaluation-Score\tDiff-to-bestCompetitor\tTPR\tFPR");
+			bw.write("\tHRD-Length\tReference-Description\tRef-Lenght\tEvaluation-Score\tDiff-to-bestCompetitor\tTPR\tFPR");
 		}
 		if (getSettings().getWriteBestBlastHitsToOutput()) {
 			bw.write(buildBestBlastHitsHeader());
@@ -44,13 +42,11 @@ public void writeOutput() throws IOException {
 			bw.write("\t\"Tokens (tkn->score)\"");
 		}
 		if (getSettings().getWriteScoresToOutput()) {
-			bw
-					.write("\tSum(Token-Scores)\tTokenHighScore\tCorrection-Factor\tGO-Score\tLexical-Score\tRelativeBitScore");
+			bw.write("\tSum(Token-Scores)\tTokenHighScore\tCorrection-Factor\tGO-Score\tLexical-Score\tRelativeBitScore");
 		}
 		if (getSettings().getPathToBlast2GoAnnotations() != null
 				&& !getSettings().getPathToBlast2GoAnnotations().equals("")) {
-			bw
-					.write("\tBlast2GO-Annotation\tBlast2GO-Length\tBlast2GO-Evaluation-Score");
+			bw.write("\tBlast2GO-Annotation\tBlast2GO-Length\tBlast2GO-Evaluation-Score");
 		}
 		if (getSettings().doFindHighestPossibleEvaluationScore()) {
 			bw.write("\tHighest-Blast-Hit-Evaluation-Score");
@@ -207,7 +203,7 @@ public String buildTrainerColumns(Protein prot) {
 	 * Append the following columns to the current CSV-Row:
 	 * sum_of_all_token_scores, token_high_score, correction_factor, go_score,
 	 * lexical_score, rel_bit_score, desc_line_frequency,
-	 * max_desc_line_frequency, pattern_factor
+	 * max_desc_line_frequency
 	 * 
 	 * @note: Printing out these values may slow down the running-time, as these
 	 *        values are not necessarily stored in memory.

diff --git a/test/resources/ahrd_input.yml b/test/resources/ahrd_input.yml
@@ -31,7 +31,6 @@ gene_ontology_result: ./test/resources/go_results.csv
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 write_token_set_to_output: false
 write_best_blast_hits_to_output: true
 write_scores_to_output: false

diff --git a/test/resources/ahrd_input_test_run.yml b/test/resources/ahrd_input_test_run.yml
@@ -30,5 +30,4 @@ gene_ontology_result: ./test/resources/go_results.csv
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 output: ./test/ahrd_output.csv
diff --git a/test/resources/batcher_input.yml b/test/resources/batcher_input.yml
@@ -7,7 +7,6 @@ batch_ymls_dir: ./solyc_test_run/batch_ymls/
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 
 blast_dbs:
   swissprot:

diff --git a/test/resources/batcher_input_test.yml b/test/resources/batcher_input_test.yml
@@ -7,7 +7,6 @@ batch_ymls_dir: ./test/resources/batch_ymls
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 no_start_positions_in_parameter_space: 10
 
 blast_dbs:

diff --git a/test/resources/scores_test/ahrd_input.yml b/test/resources/scores_test/ahrd_input.yml
@@ -31,7 +31,6 @@ gene_ontology_result: ./test/resources/empty_file.txt
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 write_token_set_to_output: false
 write_best_blast_hits_to_output: false
 write_scores_to_output: true

diff --git a/test/resources/trainer_input.yml b/test/resources/trainer_input.yml
@@ -32,7 +32,6 @@ gene_ontology_result: ./test/resources/go_results.csv
 token_score_bit_score_weight: 0.5
 token_score_database_score_weight: 0.3
 token_score_overlap_score_weight: 0.2
-description_score_relative_description_frequency_weight: 0.6
 output: ./test/ahrd_output.csv
 path_log: ./test/sim_anneal_path_log.csv
 remember_simulated_annealing_path: true