git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (from parent 1:
64f76d5
)
JAL-2629 can now choose number of jackhmmer iterations
merge/JAL-3285_mchmmer_with_211_develop
author
Thomas
<170013569@dundee.ac.uk>
Fri, 12 Jul 2019 14:46:32 +0000
(15:46 +0100)
committer
Thomas
<170013569@dundee.ac.uk>
Fri, 12 Jul 2019 14:46:32 +0000
(15:46 +0100)
resources/lang/Messages.properties
patch
|
blob
|
history
src/jalview/hmmer/HMMERParamStore.java
patch
|
blob
|
history
src/jalview/hmmer/HmmerCommand.java
patch
|
blob
|
history
src/jalview/hmmer/Search.java
patch
|
blob
|
history
diff --git
a/resources/lang/Messages.properties
b/resources/lang/Messages.properties
index
2c0fbb9
..
b627ac8
100644
(file)
--- a/
resources/lang/Messages.properties
+++ b/
resources/lang/Messages.properties
@@
-1380,6
+1380,7
@@
label.executable_not_found = The ''{0}'' executable file was not found
warn.command_failed = {0} failed
label.invalid_folder = Invalid Folder
label.number_of_results = Number of Results to Return
warn.command_failed = {0} failed
label.invalid_folder = Invalid Folder
label.number_of_results = Number of Results to Return
+label.number_of_iterations = Number of jackhmmer Iterations
label.auto_align_seqs = Automatically Align Fetched Sequences
label.new_returned = new sequences returned
label.use_accessions = Return Accessions
label.auto_align_seqs = Automatically Align Fetched Sequences
label.new_returned = new sequences returned
label.use_accessions = Return Accessions
@@
-1394,6
+1395,7
@@
label.inclusion_seq_score = Inclusion Sequence Score Threshold
label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off
label.inclusion_dom_score = Inclusion Domain Score Threshold
label.number_of_results_desc = The maximum number of hmmsearch results to display
label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off
label.inclusion_dom_score = Inclusion Domain Score Threshold
label.number_of_results_desc = The maximum number of hmmsearch results to display
+label.number_of_iterations_desc = The number of iterations jackhmmer will complete when searching for new sequences
label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment
label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment
label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
diff --git
a/src/jalview/hmmer/HMMERParamStore.java
b/src/jalview/hmmer/HMMERParamStore.java
index
be03ec5
..
df9ab55
100644
(file)
--- a/
src/jalview/hmmer/HMMERParamStore.java
+++ b/
src/jalview/hmmer/HMMERParamStore.java
@@
-221,6
+221,10
@@
public final class HMMERParamStore implements ParamDatastoreI
String database = MessageManager.getString("label.database");
args.add(new FileParameter(database, "", false, "", ""));
String database = MessageManager.getString("label.database");
args.add(new FileParameter(database, "", false, "", ""));
+ args.add(new IntegerParameter(
+ MessageManager.getString(HMMSearch.NUMBER_OF_ITERATIONS),
+ MessageManager.getString("label.number_of_iterations_desc"),
+ true, 5, 1, 20));
args.add(new RadioChoiceParameter(
MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
args.add(new RadioChoiceParameter(
MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
f38be02
..
b311b76
100644
(file)
--- a/
src/jalview/hmmer/HmmerCommand.java
+++ b/
src/jalview/hmmer/HmmerCommand.java
@@
-60,6
+60,8
@@
public abstract class HmmerCommand implements Runnable
static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+ static final String NUMBER_OF_ITERATIONS = "label.number_of_iterations";
+
static final String TRIM_TERMINI_KEY = "label.trim_termini";
static final String RETURN_N_NEW_SEQ = "label.check_for_new_sequences";
static final String TRIM_TERMINI_KEY = "label.trim_termini";
static final String RETURN_N_NEW_SEQ = "label.check_for_new_sequences";
diff --git
a/src/jalview/hmmer/Search.java
b/src/jalview/hmmer/Search.java
index
5c7da7c
..
ceb79e5
100644
(file)
--- a/
src/jalview/hmmer/Search.java
+++ b/
src/jalview/hmmer/Search.java
@@
-329,6
+329,15
@@
public abstract class Search extends HmmerCommand
searchAlignment = false;
}
}
searchAlignment = false;
}
}
+ else if (MessageManager.getString(NUMBER_OF_ITERATIONS)
+ .equals(name))
+ {
+ if (!arg.getValue().isEmpty())
+ {
+ args.add("-N");
+ args.add(arg.getValue());
+ }
+ }
}
}
}
}