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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
phylogeny
/
data
/
DomainArchitecture.java
diff --git
a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
index
e93e742
..
0f09c55
100644
(file)
--- a/
forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
+++ b/
forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java
@@
-21,12
+21,13
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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.phylogeny.data;
import java.io.IOException;
import java.io.Writer;
package org.forester.phylogeny.data;
import java.io.IOException;
import java.io.Writer;
+import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.List;
import java.util.SortedMap;
import java.util.ArrayList;
import java.util.List;
import java.util.SortedMap;
@@
-40,10
+41,10
@@
import org.forester.util.ForesterUtil;
public class DomainArchitecture implements PhylogenyData {
public class DomainArchitecture implements PhylogenyData {
- public final static String NHX_SEPARATOR = ">";
- private static final double INCREASE_KEY = 0.0001;
- private SortedMap<Double, ProteinDomain> _domains;
- private int _total_length;
+ public final static String NHX_SEPARATOR = ">";
+ private static final BigDecimal INCREASE_KEY = new BigDecimal( "0.00001" );
+ private SortedMap<BigDecimal, ProteinDomain> _domains;
+ private int _total_length;
public DomainArchitecture() {
init();
public DomainArchitecture() {
init();
@@
-79,7
+80,7
@@
public class DomainArchitecture implements PhylogenyData {
}
}
catch ( final Exception e ) {
}
}
catch ( final Exception e ) {
- throw new IllegalArgumentException( "Malformed format for domain structure \"" + da_str + "\": "
+ throw new IllegalArgumentException( "malformed format for domain structure \"" + da_str + "\": "
+ e.getMessage() );
}
if ( to > total_length ) {
+ e.getMessage() );
}
if ( to > total_length ) {
@@
-89,9
+90,9
@@
public class DomainArchitecture implements PhylogenyData {
}
public void addDomain( final ProteinDomain pd ) {
}
public void addDomain( final ProteinDomain pd ) {
- Double key = new Double( pd.getFrom() );
+ BigDecimal key = new BigDecimal( "" + pd.getFrom() );
while ( _domains.containsKey( key ) ) {
while ( _domains.containsKey( key ) ) {
- key = new Double( key.doubleValue() + DomainArchitecture.INCREASE_KEY );
+ key = new BigDecimal( "" + ( key.doubleValue() + DomainArchitecture.INCREASE_KEY.doubleValue() ) );
}
_domains.put( key, pd );
}
}
_domains.put( key, pd );
}
@@
-133,7
+134,7
@@
public class DomainArchitecture implements PhylogenyData {
return ( ProteinDomain ) _domains.values().toArray()[ i ];
}
return ( ProteinDomain ) _domains.values().toArray()[ i ];
}
- public SortedMap<Double, ProteinDomain> getDomains() {
+ public SortedMap<BigDecimal, ProteinDomain> getDomains() {
return _domains;
}
return _domains;
}
@@
-146,7
+147,7
@@
public class DomainArchitecture implements PhylogenyData {
}
private void init() {
}
private void init() {
- _domains = new TreeMap<Double, ProteinDomain>();
+ _domains = new TreeMap<BigDecimal, ProteinDomain>();
_total_length = 0;
}
_total_length = 0;
}