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JAL-4134 JAL-3855 store/restore groups, tree and threshold used to cluster a PAE...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
7c3eb41
..
c789857
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-20,17
+20,16
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
-import jalview.datamodel.Sequence.DBModList;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.datamodel.Sequence.DBModList;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
/**
* Methods for manipulating a sequence, its metadata and related annotation in
/**
* Methods for manipulating a sequence, its metadata and related annotation in
@@
-39,7
+38,7
@@
import fr.orsay.lri.varna.models.rna.RNA;
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public interface SequenceI extends ASequenceI
+public interface SequenceI extends ASequenceI, ContactMapHolderI
{
/**
* Set the display name for the sequence
{
/**
* Set the display name for the sequence
@@
-357,12
+356,13
@@
public interface SequenceI extends ASequenceI
/**
* set the array of Database references for the sequence.
*
/**
* set the array of Database references for the sequence.
*
- * BH 2019.02.04 changes param to DBModlist
+ * BH 2019.02.04 changes param to DBModlist
*
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
*
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
- * @throws InvalidArgumentException if the is not one created by Sequence itself
+ * @throws InvalidArgumentException
+ * if the is not one created by Sequence itself
*/
@Deprecated
public void setDBRefs(DBModList<DBRefEntry> dbs);
*/
@Deprecated
public void setDBRefs(DBModList<DBRefEntry> dbs);
@@
-447,8
+447,8
@@
public interface SequenceI extends ASequenceI
/**
* Returns a (possibly empty) list of any annotations that match on given
/**
* Returns a (possibly empty) list of any annotations that match on given
- * calcId (source), label (type) and description (observation instance).
- * Null values do not match.
+ * calcId (source), label (type) and description (observation instance). Null
+ * values do not match.
*
* @param calcId
* @param label
*
* @param calcId
* @param label
@@
-456,6
+456,7
@@
public interface SequenceI extends ASequenceI
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label, String description);
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label, String description);
+
/**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
/**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
@@
-530,7
+531,8
@@
public interface SequenceI extends ASequenceI
* optional feature types to restrict results to
* @return
*/
* optional feature types to restrict results to
* @return
*/
- List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+ List<SequenceFeature> findFeatures(int fromCol, int toCol,
+ String... types);
/**
* Method to call to indicate that the sequence (characters or alignment/gaps)
/**
* Method to call to indicate that the sequence (characters or alignment/gaps)
@@
-538,7
+540,7
@@
public interface SequenceI extends ASequenceI
* positions to be invalidated.
*/
void sequenceChanged();
* positions to be invalidated.
*/
void sequenceChanged();
-
+
/**
*
* @return BitSet corresponding to index [0,length) where Comparison.isGap()
/**
*
* @return BitSet corresponding to index [0,length) where Comparison.isGap()
@@
-570,9
+572,8
@@
public interface SequenceI extends ASequenceI
* @param chromosomeId
* @param map
*/
* @param chromosomeId
* @param map
*/
- void setGeneLoci(String speciesId, String assemblyId,
- String chromosomeId, MapList map);
-
+ void setGeneLoci(String speciesId, String assemblyId, String chromosomeId,
+ MapList map);
/**
* Returns the sequence string constructed from the substrings of a sequence
/**
* Returns the sequence string constructed from the substrings of a sequence
@@
-595,6
+596,7
@@
public interface SequenceI extends ASequenceI
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm);
}
}
-