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JAL-3878 update branch from 2.12 merge from 2.11.2
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
a1b2683
..
8f1d160
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-51,7
+51,6
@@
public interface SequenceI extends ASequenceI
public HiddenMarkovModel getHMM();
public void setHMM(HiddenMarkovModel hmm);
public HiddenMarkovModel getHMM();
public void setHMM(HiddenMarkovModel hmm);
-
/**
* Get the display name
*/
/**
* Get the display name
*/
@@
-519,7
+518,6
@@
public interface SequenceI extends ASequenceI
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
-
/**
* Answers true if the sequence has annotation for Hidden Markov Model
* information content, else false
/**
* Answers true if the sequence has annotation for Hidden Markov Model
* information content, else false
@@
-563,7
+561,7
@@
public interface SequenceI extends ASequenceI
* @param c1
* @param c2
*/
* @param c1
* @param c2
*/
- int replace(char c1, char c2);
+ public int replace(char c1, char c2);
/**
* Answers the GeneLociI, or null if not known
/**
* Answers the GeneLociI, or null if not known
@@
-593,7
+591,7
@@
public interface SequenceI extends ASequenceI
* the iterator to use
* @return a String corresponding to the sequence
*/
* the iterator to use
* @return a String corresponding to the sequence
*/
- String getSequenceStringFromIterator(Iterator<int[]> it);
+ public String getSequenceStringFromIterator(Iterator<int[]> it);
/**
* Locate the first position in this sequence which is not contained in an
/**
* Locate the first position in this sequence which is not contained in an
@@
-603,7
+601,6
@@
public interface SequenceI extends ASequenceI
* iterator over regions
* @return first residue not contained in regions
*/
* iterator over regions
* @return first residue not contained in regions
*/
-
public int firstResidueOutsideIterator(Iterator<int[]> it);
public int firstResidueOutsideIterator(Iterator<int[]> it);