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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
DomainLengthsTable.java
diff --git
a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
index
cbd14b0
..
44b6247
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/DomainLengthsTable.java
+++ b/
forester/java/src/org/forester/surfacing/DomainLengthsTable.java
@@
-22,7
+22,7
@@
// 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.surfacing;
package org.forester.surfacing;
@@
-33,7
+33,6
@@
import java.util.SortedMap;
import java.util.TreeMap;
import org.forester.protein.Domain;
import java.util.TreeMap;
import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
import org.forester.protein.Protein;
import org.forester.species.Species;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.protein.Protein;
import org.forester.species.Species;
import org.forester.util.BasicDescriptiveStatistics;
@@
-42,12
+41,12
@@
import org.forester.util.ForesterUtil;
public class DomainLengthsTable {
public class DomainLengthsTable {
- private final static DecimalFormat DF = new DecimalFormat( "#.0" );
- final SortedMap<DomainId, DomainLengths> _domain_lengths;
- final List<Species> _species;
+ private final static DecimalFormat DF = new DecimalFormat( "#.0" );
+ final SortedMap<String, DomainLengths> _domain_lengths;
+ final List<Species> _species;
public DomainLengthsTable() {
public DomainLengthsTable() {
- _domain_lengths = new TreeMap<DomainId, DomainLengths>();
+ _domain_lengths = new TreeMap<String, DomainLengths>();
_species = new ArrayList<Species>();
}
_species = new ArrayList<Species>();
}
@@
-59,7
+58,7
@@
public class DomainLengthsTable {
getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
}
getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
}
- private void addLength( final DomainId domain_id, final Species species, final int domain_length ) {
+ private void addLength( final String domain_id, final Species species, final int domain_length ) {
if ( !getDomainLengths().containsKey( domain_id ) ) {
addDomainLengths( new DomainLengths( domain_id ) );
}
if ( !getDomainLengths().containsKey( domain_id ) ) {
addDomainLengths( new DomainLengths( domain_id ) );
}
@@
-87,7
+86,7
@@
public class DomainLengthsTable {
return stats;
}
return stats;
}
- public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final DomainId domain_id ) {
+ public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final String domain_id ) {
return getDomainLengths( domain_id ).calculateMeanBasedStatistics();
}
return getDomainLengths( domain_id ).calculateMeanBasedStatistics();
}
@@
-143,11
+142,11
@@
public class DomainLengthsTable {
return sb;
}
return sb;
}
- private SortedMap<DomainId, DomainLengths> getDomainLengths() {
+ private SortedMap<String, DomainLengths> getDomainLengths() {
return _domain_lengths;
}
return _domain_lengths;
}
- public DomainLengths getDomainLengths( final DomainId domain_id ) {
+ public DomainLengths getDomainLengths( final String domain_id ) {
return getDomainLengths().get( domain_id );
}
return getDomainLengths().get( domain_id );
}
@@
-159,7
+158,7
@@
public class DomainLengthsTable {
return list;
}
return list;
}
- public DescriptiveStatistics getLengthStatistic( final DomainId domain_id, final Species species ) {
+ public DescriptiveStatistics getLengthStatistic( final String domain_id, final Species species ) {
return getDomainLengths( domain_id ).getLengthStatistic( species );
}
return getDomainLengths( domain_id ).getLengthStatistic( species );
}