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JAL-1807 Bob's first commit -- Applet loaded; needs image
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
fc67efd
..
55215a6
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,18
+20,21
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.jsdev.api.VarnaRNA;
+
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
-import fr.orsay.lri.varna.models.rna.RNA;
+//import fr.orsay.lri.varna.models.rna.RNA;
/**
/**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
*
* @author $author$
* @version $Revision$
*/
*
* @author $author$
* @version $Revision$
*/
-public interface SequenceI
+public interface SequenceI extends ASequenceI
{
/**
* Set the display name for the sequence
{
/**
* Set the display name for the sequence
@@
-134,12
+137,13
@@
public interface SequenceI
public char[] getSequence(int start, int end);
/**
public char[] getSequence(int start, int end);
/**
- * create a new sequence object from start to end of this sequence
+ * create a new sequence object with a subsequence of this one but sharing the
+ * same dataset sequence
*
* @param start
*
* @param start
- * int index for start position
+ * int index for start position (base 0, inclusive)
* @param end
* @param end
- * int index for end position
+ * int index for end position (base 0, exclusive)
*
* @return SequenceI
* @note implementations may use getSequence to get the sequence data
*
* @return SequenceI
* @note implementations may use getSequence to get the sequence data
@@
-147,12
+151,12
@@
public interface SequenceI
public SequenceI getSubSequence(int start, int end);
/**
public SequenceI getSubSequence(int start, int end);
/**
- * DOCUMENT ME!
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
*
* @param i
*
* @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * index
+ * @return character or ' '
*/
public char getCharAt(int i);
*/
public char getCharAt(int i);
@@
-172,8
+176,7
@@
public interface SequenceI
public String getDescription();
/**
public String getDescription();
/**
- * Return the alignment column for a sequence position * Return the alignment
- * position for a sequence position
+ * Return the alignment column for a sequence position
*
* @param pos
* lying from start to end
*
* @param pos
* lying from start to end
@@
-220,9
+223,9
@@
public interface SequenceI
* if necessary and adjusting start and end positions accordingly.
*
* @param i
* if necessary and adjusting start and end positions accordingly.
*
* @param i
- * first column in range to delete
+ * first column in range to delete (inclusive)
* @param j
* @param j
- * last column in range to delete
+ * last column in range to delete (exclusive)
*/
public void deleteChars(int i, int j);
*/
public void deleteChars(int i, int j);
@@
-238,13
+241,12
@@
public interface SequenceI
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
- * @param i
+ * @param position
* DOCUMENT ME!
* DOCUMENT ME!
- * @param c
+ * @param ch
* DOCUMENT ME!
*/
* DOCUMENT ME!
*/
- public void insertCharAt(int i, int length, char c);
+ public void insertCharAt(int position, int count, char ch);
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-267,14
+269,14
@@
public interface SequenceI
* @param id
* DOCUMENT ME!
*/
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector ids);
+ public void setPDBId(Vector<PDBEntry> ids);
/**
/**
- * DOCUMENT ME!
+ * Returns a list
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId();
+ public Vector<PDBEntry> getPDBId();
/**
* add entry to the vector of PDBIds, if it isn't in the list already
/**
* add entry to the vector of PDBIds, if it isn't in the list already
@@
-315,10
+317,22
@@
public interface SequenceI
public SequenceI getDatasetSequence();
public SequenceI getDatasetSequence();
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
public AlignmentAnnotation[] getAnnotation();
public AlignmentAnnotation[] getAnnotation();
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
public boolean hasAnnotation(AlignmentAnnotation ann);
public boolean hasAnnotation(AlignmentAnnotation ann);
+ /**
+ * Add the given annotation, if not already added, and set its sequence ref to
+ * be this sequence. Does nothing if this sequence's annotations already
+ * include this annotation (by identical object reference).
+ */
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
@@
-347,12
+361,11
@@
public interface SequenceI
public AlignmentAnnotation[] getAnnotation(String label);
/**
public AlignmentAnnotation[] getAnnotation(String label);
/**
- * Return a list of any annotations which match the given calcId (source) and
- * label (type). Null values do not match.
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source) and label (type). Null values do not match.
*
* @param calcId
* @param label
*
* @param calcId
* @param label
- * @return
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label);
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label);
@@
-395,12
+408,18
@@
public interface SequenceI
* @return The RNA of the sequence in the alignment
*/
* @return The RNA of the sequence in the alignment
*/
- public RNA getRNA();
+ public VarnaRNA getRNA();
/**
* @param rna
* The RNA.
*/
/**
* @param rna
* The RNA.
*/
- public void setRNA(RNA rna);
+ public void setRNA(VarnaRNA rna);
+
+ /**
+ *
+ * @return list of insertions (gap characters) in sequence
+ */
+ public List<int[]> getInsertions();
}
}