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cleanup
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
io
/
parsers
/
HmmPfamOutputParser.java
diff --git
a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
index
2fae940
..
534eadc
100644
(file)
--- a/
forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
+++ b/
forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
@@
-44,7
+44,6
@@
import org.forester.protein.BasicDomain;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
-import org.forester.surfacing.SurfacingUtil;
import org.forester.util.ForesterUtil;
public final class HmmPfamOutputParser {
import org.forester.util.ForesterUtil;
public final class HmmPfamOutputParser {
@@
-65,7
+64,6
@@
public final class HmmPfamOutputParser {
private final FilterType _filter_type;
private final File _input_file;
private final String _species;
private final FilterType _filter_type;
private final File _input_file;
private final String _species;
- private final String _model_type;
private double _e_value_maximum;
private Map<String, String> _individual_domain_score_cutoffs;
private boolean _ignore_dufs;
private double _e_value_maximum;
private Map<String, String> _individual_domain_score_cutoffs;
private boolean _ignore_dufs;
@@
-94,7
+92,6
@@
public final class HmmPfamOutputParser {
public HmmPfamOutputParser( final File input_file, final String species, final String model_type ) {
_input_file = input_file;
_species = species;
public HmmPfamOutputParser( final File input_file, final String species, final String model_type ) {
_input_file = input_file;
_species = species;
- _model_type = model_type;
_filter = null;
_filter_type = FilterType.NONE;
init();
_filter = null;
_filter_type = FilterType.NONE;
init();
@@
-102,12
+99,10
@@
public final class HmmPfamOutputParser {
public HmmPfamOutputParser( final File input_file,
final String species,
public HmmPfamOutputParser( final File input_file,
final String species,
- final String model_type,
final Set<String> filter,
final FilterType filter_type ) {
_input_file = input_file;
_species = species;
final Set<String> filter,
final FilterType filter_type ) {
_input_file = input_file;
_species = species;
- _model_type = model_type;
_filter = filter;
_filter_type = filter_type;
init();
_filter = filter;
_filter_type = filter_type;
init();
@@
-219,10
+214,6
@@
public final class HmmPfamOutputParser {
return _max_allowed_overlap;
}
return _max_allowed_overlap;
}
- private String getModelType() {
- return _model_type;
- }
-
public int getProteinsEncountered() {
return _proteins_encountered;
}
public int getProteinsEncountered() {
return _proteins_encountered;
}
@@
-408,9
+399,9
@@
public final class HmmPfamOutputParser {
if ( ( getMaxAllowedOverlap() != HmmPfamOutputParser.MAX_ALLOWED_OVERLAP_DEFAULT )
|| isIgnoreEngulfedDomains() ) {
final int domains_count = current_protein.getNumberOfProteinDomains();
if ( ( getMaxAllowedOverlap() != HmmPfamOutputParser.MAX_ALLOWED_OVERLAP_DEFAULT )
|| isIgnoreEngulfedDomains() ) {
final int domains_count = current_protein.getNumberOfProteinDomains();
- current_protein = SurfacingUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
- isIgnoreEngulfedDomains(),
- current_protein );
+ current_protein = ForesterUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
+ isIgnoreEngulfedDomains(),
+ current_protein );
final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
_domains_stored -= domains_removed;
_domains_ignored_due_to_overlap += domains_removed;
final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
_domains_stored -= domains_removed;
_domains_ignored_due_to_overlap += domains_removed;
@@
-437,8
+428,6
@@
public final class HmmPfamOutputParser {
int to = -1;
double e_value = -1;
double score = -1;
int to = -1;
double e_value = -1;
double score = -1;
- boolean is_complete_hmm_match = false;
- boolean is_complete_query_match = false;
try {
from = Integer.valueOf( from_str ).intValue();
}
try {
from = Integer.valueOf( from_str ).intValue();
}
@@
-468,7
+457,7
@@
public final class HmmPfamOutputParser {
+ "] in [" + getInputFile().getCanonicalPath() + "]" );
}
if ( hmm_match_str.equals( "[]" ) ) {
+ "] in [" + getInputFile().getCanonicalPath() + "]" );
}
if ( hmm_match_str.equals( "[]" ) ) {
- is_complete_hmm_match = true;
+ //is_complete_hmm_match = true;
}
else if ( !( hmm_match_str.equals( ".]" ) || hmm_match_str.equals( "[." ) || hmm_match_str
.equals( ".." ) ) ) {
}
else if ( !( hmm_match_str.equals( ".]" ) || hmm_match_str.equals( "[." ) || hmm_match_str
.equals( ".." ) ) ) {
@@
-476,7
+465,7
@@
public final class HmmPfamOutputParser {
+ line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
if ( query_match_str.equals( ".." ) ) {
+ line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
}
if ( query_match_str.equals( ".." ) ) {
- is_complete_query_match = true;
+ // is_complete_query_match = true;
}
else if ( !( query_match_str.equals( ".]" ) || query_match_str.equals( "[." ) || query_match_str
.equals( "[]" ) ) ) {
}
else if ( !( query_match_str.equals( ".]" ) || query_match_str.equals( "[." ) || query_match_str
.equals( "[]" ) ) ) {