import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import java.util.TreeSet;
import org.forester.io.parsers.FastaParser;
import org.forester.msa.Msa;
final List<Sequence> found_seqs = new ArrayList<Sequence>();
for( final Sequence orig_seq : orig ) {
final String orig_seq_id = orig_seq.getIdentifier();
- if ( orig_seq_id.indexOf( id_ ) >= 0 && orig_seq_id.indexOf( "[" + range + "]" ) >= 0 ) {
+ if ( ( orig_seq_id.indexOf( id_ ) >= 0 ) && ( orig_seq_id.indexOf( "[" + range + "]" ) >= 0 ) ) {
found++;
found_seqs.add( orig_seq );
}
if ( found > 0 ) {
for( final Sequence found_seq : found_seqs ) {
if ( found_seq.getLength() >= 85 ) {
-
- all_found_seqs.add( BasicSequence.createAaSequence( id, found_seq.getMolecularSequenceAsString() ) );
+ all_found_seqs.add( BasicSequence.createAaSequence( id, found_seq
+ .getMolecularSequenceAsString() ) );
}
}
if ( found > 1 ) {
System.exit( -1 );
}
}
- String fasta_ary[] = new String[ all_found_seqs.size() ];
+ final String fasta_ary[] = new String[ all_found_seqs.size() ];
int i = 0;
- for( Sequence sequence : all_found_seqs ) {
+ for( final Sequence sequence : all_found_seqs ) {
fasta_ary[ i ] = ">" + sequence.getIdentifier() + "\n" + sequence.getMolecularSequenceAsString();
System.out.println( sequence );
i++;
}
Arrays.sort( fasta_ary );
-
for( int j = 0; j < fasta_ary.length; ++j ) {
- System.out.println( fasta_ary[ j ] );
+ System.out.println( fasta_ary[ j ] );
}
-
System.out.println( "DONE." );
}
catch ( final Exception e ) {
package org.forester.application;
import java.io.FileInputStream;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import org.forester.io.parsers.FastaParser;
import org.forester.sequence.Sequence;
+import org.forester.util.EasyWriter;
+import org.forester.util.ForesterUtil;
public class aaa {
public final static Pattern GN_PATTERN = Pattern.compile( "GN=(\\S+)\\s" ); //use w+ instead of S+ for more stringent setting.
public final static Pattern RANGE_PATTERN = Pattern.compile( "\\[(\\d+-\\d+)\\]" ); //use w+ instead of S+ for more stringent setting.
+ public final static int MIN_LENGTH = 85;
public static void main( final String args[] ) {
try {
+ final EasyWriter out = ( EasyWriter ) ForesterUtil.createEasyWriter( "aaa_out" );
System.out.println( "STARTING..." );
+ final List<Sequence> too_short = new ArrayList<Sequence>();
final List<Sequence> orig = FastaParser
.parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20_2.fasta" ) );
+ final int initial_number = orig.size();
final List<String> new_seqs = new ArrayList<String>();
for( final Sequence seq : orig ) {
+ if ( seq.getLength() < MIN_LENGTH ) {
+ too_short.add( seq );
+ continue;
+ }
final Matcher matcher = GN_PATTERN.matcher( seq.getIdentifier() );
String gn = "";
if ( matcher.find() ) {
final Set<String> mol_seq_set = new HashSet<String>();
Collections.sort( new_seqs );
int unique_counter = 0;
- int duplicate_counter_gn_ra = 0;
- int duplicate_counter_mol_seq = 0;
+ final List<String> duplicate_gn_ra = new ArrayList<String>();
+ final List<String> duplicate_mol_seq = new ArrayList<String>();
final List<String> new_seqs_unique = new ArrayList<String>();
for( final String seq : new_seqs ) {
final Matcher matcher_ra = RANGE_PATTERN.matcher( seq );
unique_counter++;
}
else {
- duplicate_counter_mol_seq++;
+ duplicate_mol_seq.add( seq );
}
}
else {
- duplicate_counter_gn_ra++;
+ duplicate_gn_ra.add( seq );
}
}
String prev_gn = "___";
boolean is_first = true;
- List<String> same_protein_seqs = new ArrayList<String>();
+ List<String> seqs_from_same_protein = new ArrayList<String>();
for( final String seq : new_seqs_unique ) {
-
final Matcher matcher_gn = GN_PATTERN.matcher( seq );
matcher_gn.find();
final String gn = matcher_gn.group( 1 );
if ( !prev_gn.equals( gn ) && !is_first ) {
- doit( same_protein_seqs );
- same_protein_seqs = new ArrayList<String>();
+ doit( seqs_from_same_protein, out );
+ seqs_from_same_protein = new ArrayList<String>();
}
prev_gn = gn;
is_first = false;
- same_protein_seqs.add( seq );
+ seqs_from_same_protein.add( seq );
+ }
+ doit( seqs_from_same_protein, out );
+ out.println( "" );
+ out.println( "" );
+ out.println( "Removed because same GN and region:" );
+ for( final String s : duplicate_gn_ra ) {
+ out.println( s );
+ }
+ out.println( "" );
+ out.println( "" );
+ out.println( "Removed because identical mol sequence:" );
+ for( final String s : duplicate_mol_seq ) {
+ out.println( s );
+ }
+ out.println( "" );
+ out.println( "" );
+ out.println( "Removed because too short:" );
+ for( final Sequence s : too_short ) {
+ out.println( s.toString() );
}
- doit( same_protein_seqs );
- System.out.println( "unique : " + unique_counter );
- System.out.println( "duplicate because gn and range same: " + duplicate_counter_gn_ra );
- System.out.println( "duplicate because mol seq same : " + duplicate_counter_mol_seq );
+ out.println( "" );
+ out.println( "" );
+ out.println( "initial:" + initial_number );
+ out.println( "ignored because shorter than " + MIN_LENGTH + "aa: " + too_short.size() );
+ out.println( "unique : " + unique_counter );
+ out.println( "unique : " + new_seqs_unique.size() );
+ out.println( "duplicate because gn and range same: " + duplicate_gn_ra.size() );
+ out.println( "duplicate because mol seq same : " + duplicate_mol_seq.size() );
+ out.flush();
+ out.close();
+ System.out.println( "DONE " );
}
catch ( final Exception e ) {
e.printStackTrace();
}
}
- private static void doit( List<String> same_protein_seqs ) {
+ private static void doit( final List<String> same_protein_seqs, final EasyWriter out ) throws IOException {
final int count = same_protein_seqs.size();
if ( count == 1 ) {
- System.out.println( same_protein_seqs.get( 0 ) );
+ out.println( same_protein_seqs.get( 0 ) );
}
else {
int c = 1;
for( final String s : same_protein_seqs ) {
- System.out.println( new StringBuffer( s ).insert( s.indexOf( "|" ),
- "__" + c + "_OF_" + count ).toString() );
+ out.println( new StringBuffer( s ).insert( s.indexOf( "|" ), "__" + c + "_OF_" + count ).toString() );
c++;
}
}
ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
}
catch ( final Exception e ) {
- ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
+ ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() );
}
try {
final PhylogenyWriter w = new PhylogenyWriter();
import java.util.TreeMap;
import java.util.TreeSet;
-
import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
import org.forester.go.GoId;
import org.forester.go.GoNameSpace;
final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
//final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference";
- final static private String FILTER_POSITIVE_OPTION = "pos_filter";
+ final static private String FILTER_POSITIVE_OPTION = "pos_filter";
final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
final static private String INPUT_FILES_FROM_FILE_OPTION = "input";
private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
- final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e";
-
-
+ final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e";
private static final boolean VERBOSE = false;
private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
return intrees;
}
-
-
private static void log( final String msg, final Writer w ) {
try {
w.write( msg );
//
if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) {
try {
- output_list_of_all_proteins_per_domain_e_value_max = cla.getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
+ output_list_of_all_proteins_per_domain_e_value_max = cla
+ .getOptionValueAsDouble( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" );
+ "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
}
query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
-
}
DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
System.out.println( "E-value maximum (inclusive) : " + e_value_max );
html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
}
- if ( output_protein_lists_for_all_domains ) {
+ if ( output_protein_lists_for_all_domains ) {
System.out.println( "Domain E-value max : " + output_list_of_all_proteins_per_domain_e_value_max );
- html_desc.append( "<tr><td>Protein lists: E-value maximum per domain (inclusive):</td><td>" + output_list_of_all_proteins_per_domain_e_value_max + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Protein lists: E-value maximum per domain (inclusive):</td><td>"
+ + output_list_of_all_proteins_per_domain_e_value_max + "</td></tr>" + nl );
}
System.out.println( "Ignore DUFs : " + ignore_dufs );
if ( ignore_virus_like_ids ) {
protein_lists_per_species,
domain_id_to_go_ids_map,
go_id_to_term_map,
- plus_minus_analysis_numbers
- );
+ plus_minus_analysis_numbers );
}
if ( output_protein_lists_for_all_domains ) {
- writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list, output_list_of_all_proteins_per_domain_e_value_max );
+ writeProteinListsForAllSpecies( out_dir,
+ protein_lists_per_species,
+ gwcd_list,
+ output_list_of_all_proteins_per_domain_e_value_max );
}
-
if ( all_bin_domain_combinations_gained_fitch != null ) {
try {
executeFitchGainsAnalysis( new File( output_file
}
}
-
private static void printHelp() {
System.out.println();
System.out.println( "Usage:" );
System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
+ ": to output binary domain combinations for (downstream) graph analysis" );
System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
- System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION + ": e value max per domain for output of all proteins per domain" );
-
+ System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION
+ + ": e value max per domain for output of all proteins per domain" );
System.out.println();
System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
+ " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
proteins_file_writer,
"\t",
LIMIT_SPEC_FOR_PROT_EX,
- domain_e_cutoff );
+ domain_e_cutoff );
proteins_file_writer.close();
}
catch ( final IOException e ) {
return _path_to_local_mafft;
}
-
-
public File getPathToLocalFastme() {
return _path_to_local_fastme;
}
_path_to_local_mafft = path_to_local_mafft;
}
-
-
private void setPathToLocalFastme( final File path_to_local_fastme ) {
_path_to_local_fastme = path_to_local_fastme;
}
setPathToLocalMafft( new File( str ) );
}
}
-
else if ( key.equals( "fastme_local" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
if ( !ForesterUtil.isEmpty( str ) ) {
}
public boolean canDoMsa() {
- return ( getPathToLocalMafft() != null )
- || ( getPathToLocalClustalo() != null );
+ return ( getPathToLocalMafft() != null ) || ( getPathToLocalClustalo() != null );
}
public File getPathToLocalMafft() {
return _path_to_local_mafft;
}
-
-
public File getPathToLocalFastme() {
return _path_to_local_fastme;
}
final File path_to_local_raxml,
final File path_to_local_clustalo ) {
_path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
-
_path_to_local_fastme = createLocalPath( path_to_local_fastme, "fastme" );
_path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );
_path_to_local_clustalo = createLocalPath( path_to_local_clustalo, "clustalo" );
private JTextField _input_seqs_min_length_tf;
private JTextField _input_seqs_max_length_tf;
private JTextField _input_seqs_type_tf;
-
private JTextField _mafft_paramenters_tf;
private JTextField _clustalo_paramenters_tf;
private JTextField _msa_processing_max_allowed_gap_ratio_tf;
inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
inputfile_pnl_2.add( new JLabel( "Type:" ) );
inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
-
-
- inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT") );
+ inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT" ) );
inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
-
- inputfile_pnl_4.add( _clustalo_cb = new JCheckBox( "ClustalO") );
+ inputfile_pnl_4.add( _clustalo_cb = new JCheckBox( "ClustalO" ) );
inputfile_pnl_4.add( new JLabel( "Parameters: " ) );
inputfile_pnl_4.add( _clustalo_paramenters_tf = new JTextField() );
_input_seqs_median_length_tf.setColumns( 4 );
_input_seqs_max_length_tf.setEditable( false );
_input_seqs_number_tf.setEditable( false );
_input_seqs_type_tf.setEditable( false );
-
_mafft_paramenters_tf.setColumns( 26 );
_mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
_clustalo_paramenters_tf.setColumns( 26 );
_value = JOptionPane.CANCEL_OPTION;
if ( from_unaligned_seqs ) {
updateSeqsItems();
- }
+ }
else {
updateMsaItems();
}
package org.forester.archaeopteryx.tools;
import java.io.BufferedWriter;
-import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
// SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
// writer.close();
switch ( msa_prg ) {
- case MAFFT:
+ case MAFFT:
return runMAFFT( _seqs, processMafftOptions() );
-
case CLUSTAL_O:
return runClustalOmega( _seqs, processMafftOptions() );
default:
return null;
}
-
-
}
private List<String> processMafftOptions() {
}
}
}
-
+
public enum MSA_PRG {
MAFFT, CLUSTAL_O;
}
return _exit_code;
}
-
+ @Override
public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
final File file = File.createTempFile( "__clustalo_input_", ".fasta" );
file.deleteOnExit();
file.delete();
return msa;
}
-
-
+
@Override
public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
init();
_error = null;
_exit_code = -100;
}
-
-
}
public class PhylogenyMethods {
- private static PhylogenyMethods _instance = null;
-
- private PhylogenyNode _farthest_1 = null;
- private PhylogenyNode _farthest_2 = null;
+ private static PhylogenyMethods _instance = null;
+ private PhylogenyNode _farthest_1 = null;
+ private PhylogenyNode _farthest_2 = null;
private PhylogenyMethods() {
// Hidden constructor.
}
-
-
-
-
/**
* Calculates the distance between PhylogenyNodes node1 and node2.
*
return farthest_d;
}
- final public static Event getEventAtLCA( PhylogenyNode n1,
- PhylogenyNode n2 ) {
+ final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
return obtainLCA( n1, n2 ).getNodeData().getEvent();
}
-
-
-
+
@Override
public Object clone() throws CloneNotSupportedException {
throw new CloneNotSupportedException();
return _farthest_2;
}
- final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy,
- final PhylogenyNode n) {
+ final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
if ( n.isInternal() ) {
throw new IllegalArgumentException( "node is not external" );
}
-
final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
- for ( PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode i = it.next();
if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
- to_delete.add( i );
+ to_delete.add( i );
}
}
- for( PhylogenyNode d : to_delete ) {
+ for( final PhylogenyNode d : to_delete ) {
phy.deleteSubtree( d, true );
}
phy.clearHashIdToNodeMap();
phy.externalNodesHaveChanged();
-
}
-
-
-
+
/**
* Returns the LCA of PhylogenyNodes node1 and node2.
*
private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
if ( ForesterUtil.isEmpty( identifier ) ) {
- throw new IllegalArgumentException( "identifier of sequence cannot be empty");
+ throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
}
if ( ForesterUtil.isEmpty( mol_sequence ) ) {
- throw new IllegalArgumentException( "molecular sequence cannot be empty");
+ throw new IllegalArgumentException( "molecular sequence cannot be empty" );
}
_mol_sequence = mol_sequence.toCharArray();
_identifier = identifier;
// Only use if you know what you are doing!
public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) {
if ( ForesterUtil.isEmpty( identifier ) ) {
- throw new IllegalArgumentException( "identifier of sequence cannot be empty");
+ throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
}
- if ( mol_sequence == null || mol_sequence.length < 1 ) {
- throw new IllegalArgumentException( "molecular sequence cannot be empty");
+ if ( ( mol_sequence == null ) || ( mol_sequence.length < 1 ) ) {
+ throw new IllegalArgumentException( "molecular sequence cannot be empty" );
}
_mol_sequence = mol_sequence;
_identifier = identifier;
}
@Override
- public boolean equals(Object obj) {
- if (obj == null) {
+ public boolean equals( final Object obj ) {
+ if ( obj == null ) {
return false;
}
- if (obj.getClass() != getClass()) {
+ if ( obj.getClass() != getClass() ) {
return false;
}
- Sequence other = ( Sequence) obj;
- if ( getMolecularSequenceAsString() .equals( other.getMolecularSequenceAsString() )) {
+ final Sequence other = ( Sequence ) obj;
+ if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
return true;
}
return false;
}
-
+
@Override
public int hashCode() {
return getMolecularSequenceAsString().hashCode();
}
-
-
+
@Override
public String toString() {
final StringBuffer sb = new StringBuffer();
@Override
public String getMolecularSequenceAsString() {
-
return new String( getMolecularSequence() );
}
}
public abstract int getNumberOfGapResidues();
public abstract char[] getMolecularSequence();
-
+
public abstract String getMolecularSequenceAsString();
public abstract char getResidueAt( final int position );
import org.forester.go.PfamToGoMapping;
import org.forester.io.parsers.nexus.NexusConstants;
import org.forester.io.writers.PhylogenyWriter;
-import org.forester.msa.MsaCompactor.SORT_BY;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
}
for( int i = 0; i < nodes.size() - 1; ++i ) {
for( int j = i + 1; j < nodes.size(); ++j ) {
- final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ),
- nodes.get( j ) );
+ final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ), nodes.get( j ) );
String rank = "unknown";
if ( lca.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
final String limit_to_species,
final double domain_e_cutoff ) throws IOException {
System.out.println( "Per domain E-value: " + domain_e_cutoff );
-
for( final Species species : protein_lists_per_species.keySet() ) {
System.out.println( species + ":" );
for( final Protein protein : protein_lists_per_species.get( species ) ) {
if ( ForesterUtil.isEmpty( limit_to_species )
|| protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
final List<Domain> domains = protein.getProteinDomains( domain_id );
-
if ( domains.size() > 0 ) {
out.write( protein.getSpecies().getSpeciesId() );
out.write( separator );
out.write( domain_id.toString() );
out.write( separator );
int prev_to = -1;
-
for( final Domain domain : domains ) {
-
- if ( domain_e_cutoff < 0 || domain.getPerDomainEvalue() <= domain_e_cutoff ) {
- out.write( "/" );
- out.write( domain.getFrom() + "-" + domain.getTo() );
- if ( prev_to >= 0) {
- final int l = domain.getFrom() - prev_to;
- System.out.println( l );
- }
- prev_to = domain.getTo();
+ if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
+ out.write( "/" );
+ out.write( domain.getFrom() + "-" + domain.getTo() );
+ if ( prev_to >= 0 ) {
+ final int l = domain.getFrom() - prev_to;
+ System.out.println( l );
+ }
+ prev_to = domain.getTo();
}
}
-
out.write( "/" );
out.write( separator );
-
-
final List<Domain> domain_list = new ArrayList<Domain>();
-
for( final Domain domain : protein.getProteinDomains() ) {
- if ( domain_e_cutoff < 0 || domain.getPerDomainEvalue() <= domain_e_cutoff ) {
+ if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
domain_list.add( domain );
}
}
-
- Domain domain_ary[] = new Domain[ domain_list.size() ];
-
+ final Domain domain_ary[] = new Domain[ domain_list.size() ];
for( int i = 0; i < domain_list.size(); ++i ) {
domain_ary[ i ] = domain_list.get( i );
}
-
Arrays.sort( domain_ary, new DomainComparator( true ) );
-
out.write( "{" );
boolean first = true;
-
for( final Domain domain : domain_ary ) {
if ( first ) {
first = false;
out.write( "," );
}
out.write( domain.getDomainId().toString() );
- out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
+ out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
out.write( ":" + domain.getPerDomainEvalue() );
}
out.write( "}" );
}
out.write( SurfacingConstants.NL );
}
-
}
}
}
@Override
public final int compare( final Domain d0, final Domain d1 ) {
-
if ( d0.getFrom() < d1.getFrom() ) {
return _ascending ? -1 : 1;
}
return _ascending ? 1 : -1;
}
return 0;
-
}
-
}
}
-
-
-
-
-
final boolean use_start_of_comment_line = !( ForesterUtil.isEmpty( start_of_comment_line ) );
while ( ( line = reader.readLine() ) != null ) {
line = line.trim();
- if ( !ForesterUtil.isEmpty( line) &&
-
-
- (( line.charAt( 0 ) == '"' && line.charAt( line.length() -1 ) == '"' && ForesterUtil.countChars( line, '"' ) == 2 )
-
- ||
-
-
- ( line.charAt( 0 ) == '\'' && line.charAt( line.length() -1 ) == '\'' && ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) {
- line = line.substring( 1, line.length() -1 ).trim();
+ if ( !ForesterUtil.isEmpty( line )
+ && ( ( ( line.charAt( 0 ) == '"' ) && ( line.charAt( line.length() - 1 ) == '"' ) && ( ForesterUtil
+ .countChars( line, '"' ) == 2 ) ) || ( ( line.charAt( 0 ) == '\'' )
+ && ( line.charAt( line.length() - 1 ) == '\'' ) && ( ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) ) {
+ line = line.substring( 1, line.length() - 1 ).trim();
}
-
if ( saw_first_table
&& ( ForesterUtil.isEmpty( line ) || ( tables_separated_by_single_string_line && ( line
.indexOf( column_delimiter ) < 0 ) ) ) ) {
git://source.jalview.org / jalview.git / commitdiff