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Removed deprecated parameter 'description_score_relative_description_…

…frequency_weight' from all example and test input files (YMLs).
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asishallab committed Jan 5, 2015
1 parent 1db29f3 commit e415359e73a4427833c6d5c7b05c271bd9538183
@@ -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:
@@ -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.
@@ -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
@@ -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
@@ -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:
@@ -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:
@@ -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
@@ -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

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