git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
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
eda7e55
..
534eadc
100644
(file)
--- a/
forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
+++ b/
forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
@@
-64,7
+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;
@@
-93,7
+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();
@@
-101,12
+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();
@@
-218,10
+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;
}
@@
-436,8
+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();
}
@@
-467,7
+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( ".." ) ) ) {
@@
-475,7
+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( "[]" ) ) ) {