final boolean forceEnabled = line.hasOption( "force" ); CommandLineOptions myOptions = CommandLineOptions.getInstance(); myOptions.setDefaultInteractorTaxid( defaultTaxid ); myOptions.setDefaultInteractionType( defaultInteractionType ); myOptions.setReuseExistingProtein( reuseProtein ); myOptions.setDebugEnabled( debugEnabled ); myOptions.setGuiEnabled( guiEnabled );
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; if ( guiEnabled ) {
} else { if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) { final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid(); hostOrganism = new OrganismTag( defaultTaxid );
if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) { final String defaultInteractionType = CommandLineOptions.getInstance().getDefaultInteractionType(); if ( DEBUG ) { System.err.println( "Give a default interactionType: " + defaultInteractionType );
if ( CommandLineOptions.getInstance().reuseProtein() && taxId != null ) {
} else { if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) { final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid(); hostOrganism = new OrganismTag( defaultTaxid );
if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) { final String defaultInteractionType = CommandLineOptions.getInstance().getDefaultInteractionType(); if ( DEBUG ) { System.err.println( "Give a default interactionType: " + defaultInteractionType );
if ( CommandLineOptions.getInstance().reuseProtein() && taxId != null ) {
final boolean forceEnabled = line.hasOption( "force" ); CommandLineOptions myOptions = CommandLineOptions.getInstance(); myOptions.setDefaultInteractorTaxid( defaultTaxid ); myOptions.setDefaultInteractionType( defaultInteractionType ); myOptions.setReuseExistingProtein( reuseProtein ); myOptions.setDebugEnabled( debugEnabled ); myOptions.setGuiEnabled( guiEnabled );
} else { if ( CommandLineOptions.getInstance().hasDefaultInteractorTaxid() ) { final String defaultTaxid = CommandLineOptions.getInstance().getDefaultInteractorTaxid(); hostOrganism = new OrganismTag( defaultTaxid );
if ( CommandLineOptions.getInstance().hasDefaultInteractionType() ) { final String defaultInteractionType = CommandLineOptions.getInstance().getDefaultInteractionType(); if ( DEBUG ) { System.err.println( "Give a default interactionType: " + defaultInteractionType );
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; if ( guiEnabled ) {
if ( CommandLineOptions.getInstance().reuseProtein() && taxId != null ) {
final boolean forceEnabled = line.hasOption( "force" ); CommandLineOptions myOptions = CommandLineOptions.getInstance(); myOptions.setDefaultInteractorTaxid( defaultTaxid ); myOptions.setDefaultInteractionType( defaultInteractionType ); myOptions.setReuseExistingProtein( reuseProtein ); myOptions.setDebugEnabled( debugEnabled ); myOptions.setGuiEnabled( guiEnabled );
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; if ( guiEnabled ) {
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; boolean displayProgressBar = guiEnabled && keys.size() > 0;
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; boolean displayProgressBar = guiEnabled && keys.size() > 0;
boolean guiEnabled = CommandLineOptions.getInstance().isGuiEnabled(); Monitor monitor = null; boolean displayProgressBar = guiEnabled && keys.size() > 0;