label.structure_chooser_no_of_structures = Structure Chooser - {0} Found ({1})
info.no_pdb_entry_found_for = No PDB entry found for {0}
exception.unable_to_detect_internet_connection = Jalview is unable to detect an internet connection
-exception.fts_rest_service_no_longer_available = {0} rest services no longer available!
-exception.resource_not_be_found = The requested resource could not be found
-exception.fts_server_error = There seems to be an error from the {0} server
exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \nPlease ensure that you are connected to the internet and try again.
label.nw_mapping = Needleman & Wunsch Alignment
label.sifts_mapping = SIFTs Mapping
action.prev_page= <<
label.next_page_tooltip=Next Page
label.prev_page_tooltip=Previous Page
-exception.bad_request=Bad request. There is a problem with your input.
-exception.service_not_available=Service not available. The server is being updated, try again later.
status.launching_3d_structure_viewer = Launching 3D Structure viewer...
status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
label.no_of_sequences = Number of sequences returned
label.reporting_cutoff = Reporting Cut-off
+ label.inclusion_threshold = Inlcusion Threshold
label.freq_alignment = Use alignment background frequencies
label.freq_uniprot = Use Uniprot background frequencies
label.hmmalign_options = hmmalign options
label.invalid_folder = Invalid Folder
label.number_of_results = Number of Results to Return
label.auto_align_seqs = Automatically Align Fetched Sequences
+ label.new_returned = new sequences returned
label.use_accessions = Return Accessions
- label.seq_evalue = Sequence E-value Cut-off
- label.seq_score = Sequence Score Threshold
- label.dom_evalue = Domain E-value Cut-off
- label.dom_score = Domain Score Threshold
+ label.check_for_new_sequences = Return Number of New Sequences
+ label.evalue = E-Value
+ label.reporting_seq_evalue = Reporting Sequence E-value Cut-off
+ label.reporting_seq_score = Reporting Sequence Score Threshold
+ label.reporting_dom_evalue = Reporting Domain E-value Cut-off
+ label.reporting_dom_score = Reporting Domain Score Threshold
+ label.inclusion_seq_evalue = Inclusion Sequence E-value Cut-off
+ 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.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.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E)
- label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T)
- label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch --domE)
- label.dom_score_desc = The score threshold for returned domains (hmmsearch --domT)
+ label.reporting_seq_e_value_desc = The E-value cutoff for returned sequences
+ label.reporting_seq_score_desc = The score threshold for returned sequences
+ label.reporting_dom_e_value_desc = The E-value cutoff for returned domains
+ label.reporting_dom_score_desc = The score threshold for returned domains
+ label.inclusion_seq_e_value_desc = Sequences with an E-value less than this cut-off are classed as significant
+ label.inclusion_seq_score_desc = Sequences with a bit score greater than this threshold are classed as significant
+ label.inclusion_dom_e_value_desc = Domains with an E-value less than this cut-off are classed as significant
+ label.inclusion_dom_score_desc = Domains with a bit score greater than this threshold are classed as significant
label.add_database = Add Database
label.this_alignment = This alignment
warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
*/
public boolean alignmentIsSufficient(int required)
{
- if (getViewport().getAlignment().getSequences().size() < required)
- {
- JOptionPane.showMessageDialog(this,
- MessageManager.getString("label.not_enough_sequences"));
- return false;
- }
- return true;
+ if (getViewport().getSequenceSelection().length < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("label.not_enough_sequences"));
+ return false;
+ }
+ return true;
}
/**
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.getName().toLowerCase().contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
}
}
build_urlServiceMenu(me.webService);
+
+ // TODO Mateusz - follow pattern for adding web service
+ // JMenuItems for slivka-based services
+
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
{
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
git://source.jalview.org / jalview.git / commitdiff