// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.util;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
+import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.forester.archaeopteryx.Constants;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
+import org.forester.protein.BasicProtein;
+import org.forester.protein.Domain;
+import org.forester.protein.Protein;
+import org.forester.surfacing.SurfacingUtil;
public final class ForesterUtil {
public static final NumberFormat FORMATTER_6;
public static final NumberFormat FORMATTER_06;
public static final NumberFormat FORMATTER_3;
+ public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/";
+ public static final String NCBI_NUCCORE = "http://www.ncbi.nlm.nih.gov/nuccore/";
+ public final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/";
+ public static final String NCBI_GI = "http://www.ncbi.nlm.nih.gov/protein/gi:";
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
private ForesterUtil() {
}
+ public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
+ int overlap_count = 0;
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
+ ++overlap_count;
+ }
+ }
+ return overlap_count;
+ }
+
final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
if ( sb.length() > 0 ) {
sb.append( separator );
}
/**
+ *
+ * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
+ * domain with 0.3 is ignored
+ *
+ * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
+ *
+ *
+ * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
+ * ignored
+ *
+ * @param max_allowed_overlap
+ * maximal allowed overlap (inclusive) to be still considered not
+ * overlapping (zero or negative value to allow any overlap)
+ * @param remove_engulfed_domains
+ * to remove domains which are completely engulfed by coverage of
+ * domains with better support
+ * @param protein
+ * @return
+ */
+ public static Protein removeOverlappingDomains( final int max_allowed_overlap,
+ final boolean remove_engulfed_domains,
+ final Protein protein ) {
+ final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
+ .getSpeciesId(), protein.getLength() );
+ final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
+ final List<Boolean> covered_positions = new ArrayList<Boolean>();
+ for( final Domain domain : sorted ) {
+ if ( ( ( max_allowed_overlap < 0 ) || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
+ && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
+ final int covered_positions_size = covered_positions.size();
+ for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
+ covered_positions.add( false );
+ }
+ final int new_covered_positions_size = covered_positions.size();
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( i < new_covered_positions_size ) {
+ covered_positions.set( i, true );
+ }
+ else {
+ covered_positions.add( true );
+ }
+ }
+ pruned_protein.addProteinDomain( domain );
+ }
+ }
+ return pruned_protein;
+ }
+
+ /**
+ * Returns true is Domain domain falls in an uninterrupted stretch of
+ * covered positions.
+ *
+ * @param domain
+ * @param covered_positions
+ * @return
+ */
+ public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
* This calculates a color. If value is equal to min the returned color is
* minColor, if value is equal to max the returned color is maxColor,
* otherwise a color 'proportional' to value is returned.
}
}
+ public static void fatalError( final String message ) {
+ System.err.println();
+ System.err.println( "error: " + message );
+ System.err.println();
+ System.exit( -1 );
+ }
+
public static void fatalError( final String prg_name, final String message ) {
System.err.println();
System.err.println( "[" + prg_name + "] > " + message );
System.exit( -1 );
}
+ public static void fatalErrorIfFileNotReadable( final File file ) {
+ final String error = isReadableFile( file );
+ if ( !isEmpty( error ) ) {
+ System.err.println();
+ System.err.println( "error: " + error );
+ System.err.println();
+ System.exit( -1 );
+ }
+ }
+
public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) {
final String error = isReadableFile( file );
if ( !isEmpty( error ) ) {
return ary;
}
+ public static String[][] file22dArray( final File file ) throws IOException {
+ final List<String> list = new ArrayList<String>();
+ final BufferedReader in = new BufferedReader( new FileReader( file ) );
+ String str;
+ while ( ( str = in.readLine() ) != null ) {
+ str = str.trim();
+ if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
+ list.add( str );
+ }
+ }
+ in.close();
+ final String[][] ary = new String[ list.size() ][ 2 ];
+ final Pattern pa = Pattern.compile( "(\\S+)\\s+(\\S+)" );
+ int i = 0;
+ for( final String s : list ) {
+ final Matcher m = pa.matcher( s );
+ if ( m.matches() ) {
+ ary[ i ][ 0 ] = m.group( 1 );
+ ary[ i ][ 1 ] = m.group( 2 );
+ ++i;
+ }
+ else {
+ throw new IOException( "unexpcted format: " + s );
+ }
+ }
+ return ary;
+ }
+
final public static List<String> file2list( final File file ) throws IOException {
final List<String> list = new ArrayList<String>();
final BufferedReader in = new BufferedReader( new FileReader( file ) );
return isReadableFile( new File( s ) );
}
- public static boolean isWindowns() {
- return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+ public final static boolean isWindows() {
+ try {
+ return OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
+ return false;
+ }
+ }
+
+ public final static boolean isMac() {
+ try {
+ return OS_NAME.toLowerCase().startsWith( "mac" );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
+ return false;
+ }
}
final public static String isWritableFile( final File f ) {
return i;
}
- final public static SortedMap<Object, Integer> listToSortedCountsMap( final List list ) {
+ final public static SortedMap<Object, Integer> listToSortedCountsMap( final List<?> list ) {
final SortedMap<Object, Integer> map = new TreeMap<Object, Integer>();
for( final Object key : list ) {
if ( !map.containsKey( key ) ) {
}
}
- final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) {
+ final public static StringBuffer mapToStringBuffer( final Map<Object, Object> map, final String key_value_separator ) {
final StringBuffer sb = new StringBuffer();
- for( final Iterator iter = map.keySet().iterator(); iter.hasNext(); ) {
- final Object key = iter.next();
+ for( final Object key : map.keySet() ) {
sb.append( key.toString() );
sb.append( key_value_separator );
sb.append( map.get( key ).toString() );
return str_array;
}
+ final public static void unexpectedFatalError( final Exception e ) {
+ System.err.println();
+ System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." );
+ e.printStackTrace( System.err );
+ System.err.println();
+ System.exit( -1 );
+ }
+
+ final public static void unexpectedFatalError( final Error e ) {
+ System.err.println();
+ System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
+ e.printStackTrace( System.err );
+ System.err.println();
+ System.exit( -1 );
+ }
+
+ final public static void unexpectedFatalError( final String message ) {
+ System.err.println();
+ System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
+ System.err.println( message );
+ System.err.println();
+ System.exit( -1 );
+ }
+
final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
System.err.println();
System.err.println( "[" + prg_name
- + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
+ + "] > unexpected error; should not have occured! Please contact program author(s)." );
e.printStackTrace( System.err );
System.err.println();
System.exit( -1 );
final public static void unexpectedFatalError( final String prg_name, final String message ) {
System.err.println();
System.err.println( "[" + prg_name
- + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
+ + "] > unexpected error: should not have occured! Please contact program author(s)." );
System.err.println( message );
System.err.println();
System.exit( -1 );
final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) {
System.err.println();
System.err.println( "[" + prg_name
- + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
+ + "] > unexpected error: should not have occured! Please contact program author(s)." );
System.err.println( message );
e.printStackTrace( System.err );
System.err.println();
final int width = 50;
System.out.print( "\r[" );
int i = 0;
- for( ; i <= ( int ) ( progress_percentage * width ); i++ ) {
+ for( ; i <= ForesterUtil.roundToInt( progress_percentage * width ); i++ ) {
System.out.print( "." );
}
for( ; i < width; i++ ) {
System.out.print( "]" );
}
+ public final static void updateProgress( final int i, final DecimalFormat f ) {
+ System.out.print( "\r[" + f.format( i ) + "]" );
+ }
+
public final static String wordWrap( final String str, final int width ) {
final StringBuilder sb = new StringBuilder( str );
int start = 0;
final String regex = "[\\s;,]+";
return str.split( regex );
}
+
+ public final static void outOfMemoryError( final OutOfMemoryError e ) {
+ System.err.println();
+ System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+ System.err.println();
+ e.printStackTrace( System.err );
+ System.err.println();
+ System.exit( -1 );
+ }
+
+ public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) {
+ if ( !ForesterUtil.isEmpty( tax_group ) ) {
+ if ( tax_group.equals( "deuterostomia" ) ) {
+ return TaxonomyColors.DEUTEROSTOMIA_COLOR;
+ }
+ else if ( tax_group.equals( "protostomia" ) ) {
+ return TaxonomyColors.PROTOSTOMIA_COLOR;
+ }
+ else if ( tax_group.equals( "cnidaria" ) ) {
+ return TaxonomyColors.CNIDARIA_COLOR;
+ }
+ else if ( tax_group.equals( "placozoa" ) ) {
+ return TaxonomyColors.PLACOZOA_COLOR;
+ }
+ else if ( tax_group.equals( "ctenophora" ) ) {
+ return TaxonomyColors.CTENOPHORA_COLOR;
+ }
+ else if ( tax_group.equals( "porifera" ) ) {
+ return TaxonomyColors.PORIFERA_COLOR;
+ }
+ else if ( tax_group.equals( "choanoflagellida" ) ) {
+ return TaxonomyColors.CHOANOFLAGELLIDA;
+ }
+ else if ( tax_group.equals( "ichthyophonida & filasterea" ) ) {
+ return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
+ }
+ else if ( tax_group.equals( "dikarya" ) ) {
+ return TaxonomyColors.DIKARYA_COLOR;
+ }
+ else if ( tax_group.equalsIgnoreCase( "fungi" ) || tax_group.equalsIgnoreCase( "other fungi" ) ) {
+ return TaxonomyColors.OTHER_FUNGI_COLOR;
+ }
+ else if ( tax_group.equals( "nucleariidae and fonticula" ) ) {
+ return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
+ }
+ else if ( tax_group.equals( "amoebozoa" ) ) {
+ return TaxonomyColors.AMOEBOZOA_COLOR;
+ }
+ else if ( tax_group.equals( "embryophyta" ) ) {
+ return TaxonomyColors.EMBRYOPHYTA_COLOR;
+ }
+ else if ( tax_group.equals( "chlorophyta" ) ) {
+ return TaxonomyColors.CHLOROPHYTA_COLOR;
+ }
+ else if ( tax_group.equals( "rhodophyta" ) ) {
+ return TaxonomyColors.RHODOPHYTA_COLOR;
+ }
+ else if ( tax_group.equals( "hacrobia" ) ) {
+ return TaxonomyColors.HACROBIA_COLOR;
+ }
+ else if ( tax_group.equals( "glaucocystophyceae" ) ) {
+ return TaxonomyColors.GLAUCOPHYTA_COLOR;
+ }
+ else if ( tax_group.equals( "stramenopiles" ) ) {
+ return TaxonomyColors.STRAMENOPILES_COLOR;
+ }
+ else if ( tax_group.equals( "alveolata" ) ) {
+ return TaxonomyColors.ALVEOLATA_COLOR;
+ }
+ else if ( tax_group.equals( "rhizaria" ) ) {
+ return TaxonomyColors.RHIZARIA_COLOR;
+ }
+ else if ( tax_group.equals( "excavata" ) ) {
+ return TaxonomyColors.EXCAVATA_COLOR;
+ }
+ else if ( tax_group.equals( "apusozoa" ) ) {
+ return TaxonomyColors.APUSOZOA_COLOR;
+ }
+ else if ( tax_group.equals( "archaea" ) ) {
+ return TaxonomyColors.ARCHAEA_COLOR;
+ }
+ else if ( tax_group.equals( "bacteria" ) ) {
+ return TaxonomyColors.BACTERIA_COLOR;
+ }
+ }
+ return null;
+ }
+
+ public final static String obtainNormalizedTaxonomyGroup( final String tax ) {
+ if ( tax.equalsIgnoreCase( "deuterostomia" ) ) {
+ return "deuterostomia";
+ }
+ else if ( tax.equalsIgnoreCase( "protostomia" ) ) {
+ return "protostomia";
+ }
+ else if ( tax.equalsIgnoreCase( "cnidaria" ) ) {
+ return "cnidaria";
+ }
+ else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( "placozoa" ) ) {
+ return "placozoa";
+ }
+ else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( "ctenophora" ) ) {
+ return "ctenophora";
+ }
+ else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( "porifera" ) ) {
+ return "porifera";
+ }
+ else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( "choanoflagellida" ) ) {
+ return "choanoflagellida";
+ }
+ else if ( tax.toLowerCase().startsWith( "ichthyophonida & filasterea" )
+ || tax.toLowerCase().startsWith( "ichthyophonida and filasterea" )
+ || tax.toLowerCase().startsWith( "ichthyosporea & filasterea" )
+ || tax.toLowerCase().startsWith( "ichthyosporea and filasterea" ) ) {
+ return "ichthyophonida & filasterea";
+ }
+ else if ( tax.equalsIgnoreCase( "dikarya" ) ) {
+ return "dikarya";
+ }
+ else if ( tax.equalsIgnoreCase( "other fungi" ) ) {
+ return "other fungi";
+ }
+ else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
+ return "nucleariidae and fonticula group";
+ }
+ else if ( tax.equalsIgnoreCase( "amoebozoa" ) ) {
+ return "amoebozoa";
+ }
+ else if ( tax.equalsIgnoreCase( "embryophyta" ) ) {
+ return "embryophyta";
+ }
+ else if ( tax.equalsIgnoreCase( "chlorophyta" ) ) {
+ return "chlorophyta";
+ }
+ else if ( tax.equalsIgnoreCase( "rhodophyta" ) ) {
+ return "rhodophyta";
+ }
+ else if ( tax.toLowerCase().startsWith( "hacrobia" ) ) {
+ return "hacrobia";
+ }
+ else if ( tax.equalsIgnoreCase( "glaucocystophyceae" ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
+ return "glaucocystophyceae";
+ }
+ else if ( tax.equalsIgnoreCase( "stramenopiles" ) ) {
+ return "stramenopiles";
+ }
+ else if ( tax.equalsIgnoreCase( "alveolata" ) ) {
+ return "alveolata";
+ }
+ else if ( tax.equalsIgnoreCase( "rhizaria" ) ) {
+ return "rhizaria";
+ }
+ else if ( tax.equalsIgnoreCase( "excavata" ) ) {
+ return "excavata";
+ }
+ else if ( tax.equalsIgnoreCase( "apusozoa" ) ) {
+ return "apusozoa";
+ }
+ else if ( tax.equalsIgnoreCase( "archaea" ) ) {
+ return "archaea";
+ }
+ else if ( tax.equalsIgnoreCase( "bacteria" ) ) {
+ return "bacteria";
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff