import java.net.URL;
import java.net.URLEncoder;
import java.text.ParseException;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedMap;
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.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
public final class AptxUtil {
+ private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
+ .getAvailableFontFamilyNames();
private final static Pattern seq_identifier_pattern_1 = Pattern
.compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
private final static Pattern seq_identifier_pattern_2 = Pattern
.compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
- private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
+ public static MaskFormatter createMaskFormatter( final String s ) {
+ MaskFormatter formatter = null;
+ try {
+ formatter = new MaskFormatter( s );
+ }
+ catch ( final ParseException e ) {
+ throw new IllegalArgumentException( e );
+ }
+ return formatter;
+ }
+
public final static String createUriForSeqWeb( final PhylogenyNode node,
final Configuration conf,
final TreePanel tp ) {
return uri_str;
}
- public static MaskFormatter createMaskFormatter( final String s ) {
- MaskFormatter formatter = null;
- try {
- formatter = new MaskFormatter( s );
- }
- catch ( final ParseException e ) {
- throw new IllegalArgumentException( e );
- }
- return formatter;
- }
-
final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb );
}
+ if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
+ }
if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
&& node.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
}
- final static Color calculateColorFromString( final String str ) {
- final String species_uc = str.toUpperCase();
- char first = species_uc.charAt( 0 );
+ final static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
+ final String my_str = str.toUpperCase();
+ char first = my_str.charAt( 0 );
char second = ' ';
char third = ' ';
- if ( species_uc.length() > 1 ) {
- second = species_uc.charAt( 1 );
- if ( species_uc.length() > 2 ) {
- if ( species_uc.indexOf( " " ) > 0 ) {
- third = species_uc.charAt( species_uc.indexOf( " " ) + 1 );
- }
- else {
- third = species_uc.charAt( 2 );
+ if ( my_str.length() > 1 ) {
+ if ( is_taxonomy ) {
+ second = my_str.charAt( 1 );
+ }
+ else {
+ second = my_str.charAt( my_str.length() - 1 );
+ }
+ if ( is_taxonomy ) {
+ if ( my_str.length() > 2 ) {
+ if ( my_str.indexOf( " " ) > 0 ) {
+ third = my_str.charAt( my_str.indexOf( " " ) + 1 );
+ }
+ else {
+ third = my_str.charAt( 2 );
+ }
}
}
+ else if ( my_str.length() > 2 ) {
+ third = ( char ) ( Math.abs( str.hashCode() / 16909320 ) );
+ System.out.println( str.hashCode() );
+ }
}
first = AptxUtil.normalizeCharForRGB( first );
second = AptxUtil.normalizeCharForRGB( second );
- third = AptxUtil.normalizeCharForRGB( third );
+ if ( is_taxonomy ) {
+ third = AptxUtil.normalizeCharForRGB( third );
+ }
+ else {
+ third = third > 255 ? 255 : third;
+ }
if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
first = 0;
}
return colorizations;
}
+ final static String createAnnotationString( final SortedSet<Annotation> annotations ) {
+ final SortedMap<String, List<Annotation>> m = new TreeMap<String, List<Annotation>>();
+ for( final Annotation an : annotations ) {
+ final String ref_source = ForesterUtil.isEmpty( an.getRefSource() ) ? "?" : an.getRefSource();
+ if ( !m.containsKey( ref_source ) ) {
+ m.put( ref_source, new ArrayList<Annotation>() );
+ }
+ m.get( ref_source ).add( an );
+ }
+ final StringBuilder sb = new StringBuilder();
+ for( final Entry<String, List<Annotation>> e : m.entrySet() ) {
+ final String ref_source = e.getKey();
+ final List<Annotation> ans = e.getValue();
+ if ( m.size() > 1 ) {
+ sb.append( "[" );
+ }
+ if ( !ref_source.equals( "?" ) ) {
+ sb.append( ref_source );
+ sb.append( ": " );
+ }
+ for( int i = 0; i < ans.size(); ++i ) {
+ final Annotation an = ans.get( i );
+ if ( !ForesterUtil.isEmpty( an.getRefValue() ) ) {
+ sb.append( an.getRefValue() );
+ sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( an.getDesc() ) ) {
+ sb.append( an.getDesc() );
+ }
+ if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
+ sb.deleteCharAt( sb.length() - 1 );
+ }
+ if ( i < ans.size() - 1 ) {
+ sb.append( ", " );
+ }
+ }
+ if ( m.size() > 1 ) {
+ sb.append( "] " );
+ }
+ }
+ return sb.toString();
+ }
+
final static String createBasicInformation( final Phylogeny phy ) {
final StringBuilder desc = new StringBuilder();
if ( ( phy != null ) && !phy.isEmpty() ) {
desc.append( "Distinct external taxonomies: " );
desc.append( taxs.size() );
}
+ for( final Taxonomy t : taxs ) {
+ System.out.println( t.toString() );
+ }
desc.append( "\n" );
final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
if ( bs.getN() > 3 ) {
desc.append( "\n" );
desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+ desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
+ + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
desc.append( "\n" );
desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
desc.append( "\n" );
desc.append( "\n" );
desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+ desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (stdev: "
+ + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) + ")" );
desc.append( "\n" );
desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
desc.append( "\n" );
desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
desc.append( "\n" );
desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
- desc.append( "\n" );
if ( cs.getN() > 2 ) {
- desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
- desc.append( "\n" );
+ desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
}
+ desc.append( "\n" );
desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
desc.append( "\n" );
desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
return true;
}
- final static boolean isMac() {
- try {
- final String s = ForesterUtil.OS_NAME.toLowerCase();
- return s.startsWith( "mac" );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
final static boolean isUsOrCanada() {
try {
if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
return false;
}
- final static boolean isWindows() {
- try {
- final String s = ForesterUtil.OS_NAME.toLowerCase();
- return s.indexOf( "win" ) > -1;
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
final ControlPanel atv_control,
final Configuration configuration ) {
if ( midpoint_reroot ) {
for( final Phylogeny phy : phys ) {
PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
}
}
return phys;
if ( os.toLowerCase().startsWith( "win" ) ) {
Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
}
- else if ( isMac() ) {
+ else if ( ForesterUtil.isMac() ) {
final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
open_url.invoke( null, new Object[] { url } );
// br.close();
// }
public static enum GraphicsExportType {
- GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" );
+ BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
private final String _suffix;
git://source.jalview.org / jalview.git / blobdiff