/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
import java.util.*;
-import java.awt.*;
-
-
/**
* DOCUMENT ME!
*
*/
public interface SequenceI
{
- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- */
- public void setName(String name);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName();
-
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- */
- public void setStart(int start);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStart();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDisplayId(boolean jvsuffix);
-
- /**
- * DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
- */
- public void setEnd(int end);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEnd();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getLength();
-
- /**
- * DOCUMENT ME!
- *
- * @param sequence DOCUMENT ME!
- */
- public void setSequence(String sequence);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence();
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence(int start, int end);
- /**
- * create a new sequence object from start to end of this sequence
- * @param start int
- * @param end int
- * @return SequenceI
- */
- public SequenceI getSubSequence(int start, int end);
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
- */
- public void setDescription(String desc);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDescription();
-
- /**
- * DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int findIndex(int pos);
-
- /**
- * Returns the sequence position for an alignment position
- *
- * @param i column index in alignment (from 1)
- *
- * @return residue number for residue (left of and) nearest ith column
- */
- public int findPosition(int i);
-
- /**
- * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
- *
- * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
- */
- public int[] gapMap();
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void deleteChars(int i, int j);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- public void insertCharAt(int i, char c);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- public void insertCharAt(int i, int length, char c);
-
-
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceFeature[] getSequenceFeatures();
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature [] features);
-
- /**
- * DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
- */
- public void setPDBId(Vector ids);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getPDBId();
-
- public void addPDBId(PDBEntry entry);
-
- public String getVamsasId();
-
- public void setVamsasId(String id);
-
- public void setDBRef(DBRefEntry[] dbs);
-
- public DBRefEntry [] getDBRef();
-
- public void addDBRef(DBRefEntry entry);
-
- public void addSequenceFeature(SequenceFeature sf);
-
- public void deleteFeature(SequenceFeature sf);
-
- public void setDatasetSequence(SequenceI seq);
-
- public SequenceI getDatasetSequence();
-
- public AlignmentAnnotation [] getAnnotation();
-
- public void addAlignmentAnnotation(AlignmentAnnotation annotation);
-
- public SequenceGroup getHiddenSequences();
-
- public void addHiddenSequence(SequenceI seq);
-
- public void showHiddenSequence(SequenceI seq);
+ /**
+ * Set the display name for the sequence
+ *
+ * @param name
+ */
+ public void setName(String name);
+
+ /**
+ * Get the display name
+ */
+ public String getName();
+
+ /**
+ * Set start position of first non-gapped symbol in sequence
+ *
+ * @param start new start position
+ */
+ public void setStart(int start);
+
+ /**
+ * get start position of first non-gapped residue in sequence
+ * @return
+ */
+ public int getStart();
+
+ /**
+ * get the displayed id of the sequence
+ * @return true means the id will be returned in the form DisplayName/Start-End
+ */
+ public String getDisplayId(boolean jvsuffix);
+
+ /**
+ * set end position for last residue in sequence
+ * @param end
+ */
+ public void setEnd(int end);
+
+ /**
+ * get end position for last residue in sequence
+ * getEnd()>getStart() unless sequence only consists of gap characters
+ *
+ * @return
+ */
+ public int getEnd();
+
+ /**
+ * @return length of sequence including gaps
+
+ */
+ public int getLength();
+
+ /**
+ * Replace the sequence with the given string
+ *
+ * @param sequence new sequence string
+ */
+ public void setSequence(String sequence);
+
+ /**
+ * @return sequence as string
+ */
+ public String getSequenceAsString();
+
+ /**
+ * get a range on the seuqence as a string
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getSequenceAsString(int start, int end);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char[] getSequence();
+
+ /**
+ * get stretch of sequence characters in an array
+ *
+ * @param start absolute index into getSequence()
+ * @param end 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
+ * @param start int
+ * @param end int
+ * @return SequenceI
+ */
+ public SequenceI getSubSequence(int start, int end);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getCharAt(int i);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc DOCUMENT ME!
+ */
+ public void setDescription(String desc);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pos DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int findIndex(int pos);
+
+ /**
+ * Returns the sequence position for an alignment position
+ *
+ * @param i column index in alignment (from 1)
+ *
+ * @return residue number for residue (left of and) nearest ith column
+ */
+ public int findPosition(int i);
+
+ /**
+ * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+ */
+ public int[] gapMap();
+
+ /**
+ * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
+ * and adjusting start and end positions accordingly.
+ *
+ * @param i first column in range to delete
+ * @param j last column in range to delete
+ */
+ public void deleteChars(int i, int j);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ */
+ public void insertCharAt(int i, char c);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ * @param c DOCUMENT ME!
+ */
+ public void insertCharAt(int i, int length, char c);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceFeature[] getSequenceFeatures();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v DOCUMENT ME!
+ */
+ public void setSequenceFeatures(SequenceFeature[] features);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ */
+ public void setPDBId(Vector ids);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getPDBId();
+
+ /**
+ * add entry to the vector of PDBIds, if it isn't in the list already
+ * @param entry
+ */
+ public void addPDBId(PDBEntry entry);
+ /**
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural databases
+ * @return true if PDBEntry list was modified
+ */
+ public boolean updatePDBIds();
+
+ public String getVamsasId();
+
+ public void setVamsasId(String id);
+
+ public void setDBRef(DBRefEntry[] dbs);
+
+ public DBRefEntry[] getDBRef();
+
+ /**
+ * add the given entry to the list of DBRefs for this sequence,
+ * or replace a similar one if entry contains a map object
+ * and the existing one doesnt.
+ * @param entry
+ */
+ public void addDBRef(DBRefEntry entry);
+
+ public void addSequenceFeature(SequenceFeature sf);
+
+ public void deleteFeature(SequenceFeature sf);
+
+ public void setDatasetSequence(SequenceI seq);
+
+ public SequenceI getDatasetSequence();
+
+ public AlignmentAnnotation[] getAnnotation();
+
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
+
+ /**
+ * Derive a sequence (using this one's dataset or as the dataset)
+ * @return duplicate sequence with valid dataset sequence
+ */
+ public SequenceI deriveSequence();
+ /**
+ * set the array of associated AlignmentAnnotation for this sequenceI
+ * @param revealed
+ */
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+ /**
+ * Get one or more alignment annotations with a particular label.
+ * @param label string which each returned annotation must have as a label.
+ * @return null or array of annotations.
+ */
+ public AlignmentAnnotation[] getAnnotation(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.
+ * @return dataset sequence for this sequence
+ */
+ public SequenceI createDatasetSequence();
+
+ /**
+ * Transfer any database references or annotation from entry
+ * under a sequence mapping.
+ * @param entry
+ * @param mp null or mapping from entry's numbering to local start/end
+ */
+ public void transferAnnotation(SequenceI entry, Mapping mp);
}