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JAL-2844 colouring subtree method made public
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
SimpleDomain.java
diff --git
a/forester/java/src/org/forester/surfacing/SimpleDomain.java
b/forester/java/src/org/forester/surfacing/SimpleDomain.java
index
5182865
..
2520e6c
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/SimpleDomain.java
+++ b/
forester/java/src/org/forester/surfacing/SimpleDomain.java
@@
-26,9
+26,8
@@
package org.forester.surfacing;
package org.forester.surfacing;
-import org.forester.go.GoId;
+import org.forester.protein.BasicDomain;
import org.forester.protein.Domain;
import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
import org.forester.util.ForesterUtil;
/*
import org.forester.util.ForesterUtil;
/*
@@
-37,18
+36,13
@@
import org.forester.util.ForesterUtil;
*/
public class SimpleDomain implements Domain {
*/
public class SimpleDomain implements Domain {
- final private DomainId _id;
+ final private short _id;
- public SimpleDomain( final String id_str ) {
- if ( ForesterUtil.isEmpty( id_str ) ) {
+ public SimpleDomain( final String id ) {
+ if ( ForesterUtil.isEmpty( id ) ) {
throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
}
throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
}
- _id = new DomainId( id_str );
- }
-
- @Override
- public void addGoId( final GoId go_id ) {
- throw new RuntimeException( "method not implemented" );
+ _id = BasicDomain.obtainIdAsShort( id );
}
@Override
}
@Override
@@
-60,8
+54,8
@@
public class SimpleDomain implements Domain {
}
@Override
}
@Override
- public DomainId getDomainId() {
- return _id;
+ public String getDomainId() {
+ return BasicDomain.obtainIdFromShort( _id );
}
@Override
}
@Override
@@
-70,11
+64,6
@@
public class SimpleDomain implements Domain {
}
@Override
}
@Override
- public GoId getGoId( final int i ) {
- throw new RuntimeException( "method not implemented" );
- }
-
- @Override
public int getLength() {
throw new RuntimeException( "method not implemented" );
}
public int getLength() {
throw new RuntimeException( "method not implemented" );
}
@@
-85,11
+74,6
@@
public class SimpleDomain implements Domain {
}
@Override
}
@Override
- public int getNumberOfGoIds() {
- throw new RuntimeException( "method not implemented" );
- }
-
- @Override
public double getPerDomainEvalue() {
throw new RuntimeException( "method not implemented" );
}
public double getPerDomainEvalue() {
throw new RuntimeException( "method not implemented" );
}
@@
-100,34
+84,27
@@
public class SimpleDomain implements Domain {
}
@Override
}
@Override
- public double getPerSequenceEvalue() {
+ public int getTo() {
throw new RuntimeException( "method not implemented" );
}
@Override
throw new RuntimeException( "method not implemented" );
}
@Override
- public double getPerSequenceScore() {
- throw new RuntimeException( "method not implemented" );
- }
-
- public String getSearchParameter() {
+ public short getTotalCount() {
throw new RuntimeException( "method not implemented" );
}
@Override
throw new RuntimeException( "method not implemented" );
}
@Override
- public int getTo() {
+ public short getHmmLen() {
throw new RuntimeException( "method not implemented" );
}
@Override
throw new RuntimeException( "method not implemented" );
}
@Override
- public short getTotalCount() {
+ public short getHmmFrom() {
throw new RuntimeException( "method not implemented" );
}
throw new RuntimeException( "method not implemented" );
}
- public boolean isCompleteQueryMatch() {
- throw new RuntimeException( "method not implemented" );
- }
-
- public boolean isCompleteTargetMatch() {
+ @Override
+ public short getHmmTo() {
throw new RuntimeException( "method not implemented" );
}
}
throw new RuntimeException( "method not implemented" );
}
}