if ( ForesterUtil.isEmpty( line ) || line.startsWith( "#" ) ) {
continue;
}
- // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
+ // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
// # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
// # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target
// #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
if ( !isAllowProteinsWithSameName() ) {
if ( query.equals( prev_query ) ) {
throw new IOException( "more than one protein named [" + query + "]" + " lengths: " + qlen
- + ", " + prev_qlen );
+ + ", " + prev_qlen );
}
if ( prev_queries.contains( query ) ) {
throw new IOException( "more than one protein named [" + query + "]" );
}
else {
throw new IOException( "could not find a score cutoff value for domain id \"" + target_id
- + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
}
final String uc_id = target_id.toUpperCase();
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse \" +label + \" from \"" + double_str + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
return d;
}
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse \"" + label + "\" from \"" + double_str + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
return i;
}
/**
* To ignore domains which are completely engulfed by domains (individual
* ones or stretches of overlapping ones) with better support values.
- *
- *
+ *
+ *
* @param ignored_engulfed_domains
*/
public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) {
/**
* Sets the individual score cutoff values (for example, gathering
* thresholds from Pfam). Domain ids are the keys, cutoffs the values.
- *
+ *
* @param individual_score_cutoffs
*/
public void setIndividualScoreCutoffs( final Map<String, Double> individual_score_cutoffs ) {