X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=2ff619bc37788f34251bf28202850b7f2e166148;hb=06e3a52df5af8243cdb67c023c8ddd834711ad36;hp=10bee55bf5be6e3d3833a4378ee97e3768c2e397;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 10bee55..2ff619b 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,32 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.List;
+import java.util.Vector;
+
+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 $Revision$
*/
-public interface SequenceI
+public interface SequenceI extends ASequenceI
{
/**
* Set the display name for the sequence
@@ -44,7 +50,7 @@ public interface SequenceI
* Set start position of first non-gapped symbol in sequence
*
* @param start
- * new start position
+ * new start position
*/
public void setStart(int start);
@@ -88,7 +94,7 @@ public interface SequenceI
* Replace the sequence with the given string
*
* @param sequence
- * new sequence string
+ * new sequence string
*/
public void setSequence(String sequence);
@@ -98,21 +104,21 @@ public interface SequenceI
public String getSequenceAsString();
/**
- * get a range on the seuqence as a string
+ * get a range on the sequence as a string
*
* @param start
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
* @param end
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
*
- * @return DOCUMENT ME!
+ * @return String containing all gap and symbols in specified range
*/
public String getSequenceAsString(int start, int end);
/**
- * DOCUMENT ME!
+ * Get the sequence as a character array
*
- * @return DOCUMENT ME!
+ * @return seqeunce and any gaps
*/
public char[] getSequence();
@@ -120,32 +126,35 @@ public interface SequenceI
* get stretch of sequence characters in an array
*
* @param start
- * absolute index into getSequence()
+ * absolute index into getSequence()
* @param end
- * exclusive index of last position in segment to be returned.
+ * exclusive index of last position in segment to be returned.
*
* @return char[max(0,end-start)];
*/
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
- * int
+ * int index for start position (base 0, inclusive)
* @param end
- * int
+ * int index for end position (base 0, exclusive)
+ *
* @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
*/
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
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * index
+ * @return character or ' '
*/
public char getCharAt(int i);
@@ -153,7 +162,7 @@ public interface SequenceI
* DOCUMENT ME!
*
* @param desc
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setDescription(String desc);
@@ -165,12 +174,17 @@ public interface SequenceI
public String getDescription();
/**
- * DOCUMENT ME!
+ * Return the alignment column for a sequence position
*
* @param pos
- * DOCUMENT ME!
+ * lying from start to end
+ *
+ * @return aligned column for residue (0 if residue is upstream from
+ * alignment, -1 if residue is downstream from alignment) note.
+ * Sequence object returns sequence.getEnd() for positions upstream
+ * currently. TODO: change sequence for
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
*
- * @return DOCUMENT ME!
*/
public int findIndex(int pos);
@@ -178,7 +192,7 @@ public interface SequenceI
* Returns the sequence position for an alignment position
*
* @param i
- * column index in alignment (from 1)
+ * column index in alignment (from 0.. ids);
/**
- * DOCUMENT ME!
+ * Returns a list
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId();
+ public Vector getAllPDBEntries();
/**
* add entry to the vector of PDBIds, if it isn't in the list already
@@ -302,8 +315,22 @@ public interface SequenceI
public SequenceI getDatasetSequence();
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
public AlignmentAnnotation[] getAnnotation();
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
+ 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);
@@ -326,15 +353,27 @@ public interface SequenceI
* Get one or more alignment annotations with a particular label.
*
* @param label
- * string which each returned annotation must have as a label.
+ * string which each returned annotation must have as a label.
* @return null or array of annotations.
*/
public AlignmentAnnotation[] getAnnotation(String label);
/**
+ * 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
+ */
+ public List getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
* 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
- * references on the sequence onto the dataset.
+ * references on the sequence onto the dataset. It will also make a duplicate
+ * of existing annotation rows for the dataset sequence, rather than relocate
+ * them in order to preserve external references (since 2.8.2).
*
* @return dataset sequence for this sequence
*/
@@ -342,12 +381,51 @@ public interface SequenceI
/**
* Transfer any database references or annotation from entry under a sequence
- * mapping.
+ * mapping.
+ * Note: DOES NOT transfer sequence associated alignment
+ * annotation
*
* @param entry
* @param mp
- * null or mapping from entry's numbering to local start/end
+ * null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
+ /**
+ * @param index
+ * The sequence index in the MSA
+ */
+ public void setIndex(int index);
+
+ /**
+ * @return The index of the sequence in the alignment
+ */
+ public int getIndex();
+
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna
+ * The RNA.
+ */
+ public void setRNA(RNA rna);
+
+ /**
+ *
+ * @return list of insertions (gap characters) in sequence
+ */
+ public List getInsertions();
+
+ /**
+ * Given a pdbId String, return the equivalent PDBEntry if available in the
+ * given sequence
+ *
+ * @param pdbId
+ * @return
+ */
+ public PDBEntry getPDBEntry(String pdbId);
}