}
else if ( isVerbose() ) {
ForesterUtil.printWarningMessage( getClass().getName(), "query \"" + query
- + "\" is not unique [line " + line_number + "] in ["
- + getInputFile().getCanonicalPath() + "]" );
+ + "\" is not unique [line " + line_number + "] in ["
+ + getInputFile().getCanonicalPath() + "]" );
}
}
else {
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse seq-f from \"" + line + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
try {
to = Integer.valueOf( to_str ).intValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse seq-t from \"" + line + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
try {
score = Double.valueOf( score_str ).doubleValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse score from \"" + line + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
try {
e_value = Double.valueOf( e_value_str ).doubleValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse E-value from \"" + line + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
if ( hmm_match_str.equals( "[]" ) ) {
//is_complete_hmm_match = true;
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse domain number from \"" + line + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
try {
total = Integer.valueOf( ( total_str ) ).intValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "could not parse domain count from \"" + line + "\" [line " + line_number
- + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
++_domains_encountered;
boolean failed_cutoff = false;
}
else {
throw new IOException( "could not find a score cutoff value for domain id \"" + id
- + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
+ + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
}
final String uc_id = id.toUpperCase();
/**
* 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 domain score cutoff values (for example, gathering
* thresholds from Pfam). Domain ids are the keys, cutoffs the values.
- *
+ *
* @param individual_domain_score_cutoffs
*/
public void setIndividualDomainScoreCutoffs( final Map<String, String> individual_domain_score_cutoffs ) {