git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
total annotation score is a double for maximum precision.
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
3e9e265
..
96b1972
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-157,7
+157,6
@@
public interface AlignmentI
*/
public Vector getGroups();
*/
public Vector getGroups();
- public void destroyAlignment();
/**
* Deletes all groups from this alignment.
/**
* Deletes all groups from this alignment.
@@
-166,55
+165,69
@@
public interface AlignmentI
/**
* Adds a new AlignmentAnnotation to this alignment
/**
* Adds a new AlignmentAnnotation to this alignment
+ * @note Care should be taken to ensure that annotation is at
+ * least as wide as the longest sequence in the alignment
+ * for rendering purposes.
*/
public void addAnnotation(AlignmentAnnotation aa);
*/
public void addAnnotation(AlignmentAnnotation aa);
-
+ /**
+ * moves annotation to a specified index in alignment annotation display stack
+ * @param aa the annotation object to be moved
+ * @param index the destination position
+ */
public void setAnnotationIndex(AlignmentAnnotation aa, int index);
/**
* Deletes a specific AlignmentAnnotation from the alignment.
*
public void setAnnotationIndex(AlignmentAnnotation aa, int index);
/**
* Deletes a specific AlignmentAnnotation from the alignment.
*
- * @param aa DOCUMENT ME!
+ * @param aa the annotation to delete
*/
public void deleteAnnotation(AlignmentAnnotation aa);
/**
*/
public void deleteAnnotation(AlignmentAnnotation aa);
/**
- * DOCUMENT ME!
+ * Get the annotation associated with this alignment
*
*
- * @return DOCUMENT ME!
+ * @return array of AlignmentAnnotation objects
*/
public AlignmentAnnotation[] getAlignmentAnnotation();
/**
*/
public AlignmentAnnotation[] getAlignmentAnnotation();
/**
- * DOCUMENT ME!
+ * Change the gap character used in this alignment to 'gc'
*
*
- * @param gc DOCUMENT ME!
+ * @param gc the new gap character.
*/
public void setGapCharacter(char gc);
/**
*/
public void setGapCharacter(char gc);
/**
- * DOCUMENT ME!
+ * Get the gap character used in this alignment
*
*
- * @return DOCUMENT ME!
+ * @return gap character
*/
public char getGapCharacter();
/**
*/
public char getGapCharacter();
/**
- * Returns true if alignment is nucleotide sequence
+ * Test for all nucleotide alignment
*
*
- * @return DOCUMENT ME!
+ * @return true if alignment is nucleotide sequence
*/
public boolean isNucleotide();
/**
*/
public boolean isNucleotide();
/**
- * Set true if the alignment is a nucleotide sequence
+ * Set alignment to be a nucleotide sequence
*
*
- * @return
*/
public void setNucleotide(boolean b);
*/
public void setNucleotide(boolean b);
+ /**
+ * Get the associated dataset for the alignment.
+ * @return Alignment containing dataset sequences or null of this is a dataset.
+ */
public Alignment getDataset();
public Alignment getDataset();
+ /**
+ * Set the associated dataset for the alignment, or create one.
+ * @param dataset The dataset alignment or null to construct one.
+ */
public void setDataset(Alignment dataset);
/**
public void setDataset(Alignment dataset);
/**
@@
-230,4
+243,8
@@
public interface AlignmentI
* @return CigarArray
*/
public CigarArray getCompactAlignment();
* @return CigarArray
*/
public CigarArray getCompactAlignment();
+
+ public void setProperty(Object key, Object value);
+
+ public Object getProperty(Object key);
}
}