-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
- * Copyright (C) 2014 The Jalview Authors\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3\r
- * of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- * The Jalview Authors are detailed in the 'AUTHORS' file.\r
- */\r
-package jalview.datamodel;\r
-\r
-import java.util.Vector;\r
-\r
-import fr.orsay.lri.varna.models.rna.RNA;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public interface SequenceI\r
-{\r
- /**\r
- * Set the display name for the sequence\r
- * \r
- * @param name\r
- */\r
- public void setName(String name);\r
-\r
- /**\r
- * Get the display name\r
- */\r
- public String getName();\r
-\r
- /**\r
- * Set start position of first non-gapped symbol in sequence\r
- * \r
- * @param start\r
- * new start position\r
- */\r
- public void setStart(int start);\r
-\r
- /**\r
- * get start position of first non-gapped residue in sequence\r
- * \r
- * @return\r
- */\r
- public int getStart();\r
-\r
- /**\r
- * get the displayed id of the sequence\r
- * \r
- * @return true means the id will be returned in the form\r
- * DisplayName/Start-End\r
- */\r
- public String getDisplayId(boolean jvsuffix);\r
-\r
- /**\r
- * set end position for last residue in sequence\r
- * \r
- * @param end\r
- */\r
- public void setEnd(int end);\r
-\r
- /**\r
- * get end position for last residue in sequence getEnd()>getStart() unless\r
- * sequence only consists of gap characters\r
- * \r
- * @return\r
- */\r
- public int getEnd();\r
-\r
- /**\r
- * @return length of sequence including gaps\r
- * \r
- */\r
- public int getLength();\r
-\r
- /**\r
- * Replace the sequence with the given string\r
- * \r
- * @param sequence\r
- * new sequence string\r
- */\r
- public void setSequence(String sequence);\r
-\r
- /**\r
- * @return sequence as string\r
- */\r
- public String getSequenceAsString();\r
-\r
- /**\r
- * get a range on the sequence as a string\r
- * \r
- * @param start\r
- * position relative to start of sequence including gaps (from 0)\r
- * @param end\r
- * position relative to start of sequence including gaps (from 0)\r
- * \r
- * @return String containing all gap and symbols in specified range\r
- */\r
- public String getSequenceAsString(int start, int end);\r
-\r
- /**\r
- * Get the sequence as a character array\r
- * \r
- * @return seqeunce and any gaps\r
- */\r
- public char[] getSequence();\r
-\r
- /**\r
- * get stretch of sequence characters in an array\r
- * \r
- * @param start\r
- * absolute index into getSequence()\r
- * @param end\r
- * exclusive index of last position in segment to be returned.\r
- * \r
- * @return char[max(0,end-start)];\r
- */\r
- public char[] getSequence(int start, int end);\r
-\r
- /**\r
- * create a new sequence object from start to end of this sequence\r
- * \r
- * @param start\r
- * int\r
- * @param end\r
- * int\r
- * @return SequenceI\r
- */\r
- public SequenceI getSubSequence(int start, int end);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param i\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public char getCharAt(int i);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param desc\r
- * DOCUMENT ME!\r
- */\r
- public void setDescription(String desc);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public String getDescription();\r
-\r
- /**\r
- * Return the alignment column for a sequence position * Return the alignment\r
- * position for a sequence position\r
- * \r
- * @param pos\r
- * lying from start to end\r
- * \r
- * @return aligned column for residue (0 if residue is upstream from\r
- * alignment, -1 if residue is downstream from alignment) note.\r
- * Sequence object returns sequence.getEnd() for positions upstream\r
- * currently. TODO: change sequence for\r
- * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs\r
- * \r
- */\r
- public int findIndex(int pos);\r
-\r
- /**\r
- * Returns the sequence position for an alignment position\r
- * \r
- * @param i\r
- * column index in alignment (from 1)\r
- * \r
- * @return residue number for residue (left of and) nearest ith column\r
- */\r
- public int findPosition(int i);\r
-\r
- /**\r
- * Returns an int array where indices correspond to each residue in the\r
- * sequence and the element value gives its position in the alignment\r
- * \r
- * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no\r
- * residues in SequenceI object\r
- */\r
- public int[] gapMap();\r
-\r
- /**\r
- * Returns an int array where indices correspond to each position in sequence\r
- * char array and the element value gives the result of findPosition for that\r
- * index in the sequence.\r
- * \r
- * @return int[SequenceI.getLength()]\r
- */\r
- public int[] findPositionMap();\r
-\r
- /**\r
- * Delete a range of aligned sequence columns, creating a new dataset sequence\r
- * if necessary and adjusting start and end positions accordingly.\r
- * \r
- * @param i\r
- * first column in range to delete\r
- * @param j\r
- * last column in range to delete\r
- */\r
- public void deleteChars(int i, int j);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param i\r
- * DOCUMENT ME!\r
- * @param c\r
- * DOCUMENT ME!\r
- */\r
- public void insertCharAt(int i, char c);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param i\r
- * DOCUMENT ME!\r
- * @param c\r
- * DOCUMENT ME!\r
- */\r
- public void insertCharAt(int i, int length, char c);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceFeature[] getSequenceFeatures();\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param v\r
- * DOCUMENT ME!\r
- */\r
- public void setSequenceFeatures(SequenceFeature[] features);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param id\r
- * DOCUMENT ME!\r
- */\r
- public void setPDBId(Vector ids);\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getPDBId();\r
-\r
- /**\r
- * add entry to the vector of PDBIds, if it isn't in the list already\r
- * \r
- * @param entry\r
- */\r
- public void addPDBId(PDBEntry entry);\r
-\r
- /**\r
- * update the list of PDBEntrys to include any DBRefEntrys citing structural\r
- * databases\r
- * \r
- * @return true if PDBEntry list was modified\r
- */\r
- public boolean updatePDBIds();\r
-\r
- public String getVamsasId();\r
-\r
- public void setVamsasId(String id);\r
-\r
- public void setDBRef(DBRefEntry[] dbs);\r
-\r
- public DBRefEntry[] getDBRef();\r
-\r
- /**\r
- * add the given entry to the list of DBRefs for this sequence, or replace a\r
- * similar one if entry contains a map object and the existing one doesnt.\r
- * \r
- * @param entry\r
- */\r
- public void addDBRef(DBRefEntry entry);\r
-\r
- public void addSequenceFeature(SequenceFeature sf);\r
-\r
- public void deleteFeature(SequenceFeature sf);\r
-\r
- public void setDatasetSequence(SequenceI seq);\r
-\r
- public SequenceI getDatasetSequence();\r
-\r
- public AlignmentAnnotation[] getAnnotation();\r
-\r
- public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
-\r
- public void removeAlignmentAnnotation(AlignmentAnnotation annotation);\r
-\r
- /**\r
- * Derive a sequence (using this one's dataset or as the dataset)\r
- * \r
- * @return duplicate sequence with valid dataset sequence\r
- */\r
- public SequenceI deriveSequence();\r
-\r
- /**\r
- * set the array of associated AlignmentAnnotation for this sequenceI\r
- * \r
- * @param revealed\r
- */\r
- public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);\r
-\r
- /**\r
- * Get one or more alignment annotations with a particular label.\r
- * \r
- * @param label\r
- * string which each returned annotation must have as a label.\r
- * @return null or array of annotations.\r
- */\r
- public AlignmentAnnotation[] getAnnotation(String label);\r
-\r
- /**\r
- * create a new dataset sequence (if necessary) for this sequence and sets\r
- * this sequence to refer to it. This call will move any features or\r
- * references on the sequence onto the dataset. It will also make a duplicate\r
- * of existing annotation rows for the dataset sequence, rather than relocate\r
- * them in order to preserve external references (since 2.8.2).\r
- * \r
- * @return dataset sequence for this sequence\r
- */\r
- public SequenceI createDatasetSequence();\r
-\r
- /**\r
- * Transfer any database references or annotation from entry under a sequence\r
- * mapping. <br/>\r
- * <strong>Note: DOES NOT transfer sequence associated alignment\r
- * annotation </strong><br/>\r
- * \r
- * @param entry\r
- * @param mp\r
- * null or mapping from entry's numbering to local start/end\r
- */\r
- public void transferAnnotation(SequenceI entry, Mapping mp);\r
-\r
- /**\r
- * @param index\r
- * The sequence index in the MSA\r
- */\r
- public void setIndex(int index);\r
-\r
- /**\r
- * @return The index of the sequence in the alignment\r
- */\r
- public int getIndex();\r
-\r
- /**\r
- * @return The RNA of the sequence in the alignment\r
- */\r
-\r
- public RNA getRNA();\r
-\r
- /**\r
- * @param rna\r
- * The RNA.\r
- */\r
- public void setRNA(RNA rna);\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import jalview.datamodel.Sequence.DBModList;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
+
+import java.util.BitSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+/**
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public interface SequenceI extends ASequenceI
+{
+ /**
+ * 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 sequence as a string
+ *
+ * @param start
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
+ * @param end
+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
+ *
+ * @return String containing all gap and symbols in specified range
+ */
+ public String getSequenceAsString(int start, int end);
+
+ /**
+ * Answers a copy of the sequence as a character array
+ *
+ * @return
+ */
+ 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 with a subsequence of this one but sharing the
+ * same dataset sequence
+ *
+ * @param start
+ * int index for start position (base 0, inclusive)
+ * @param end
+ * 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);
+
+ /**
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
+ *
+ * @param i
+ * index
+ * @return character or ' '
+ */
+ public char getCharAt(int i);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
+ */
+ public void setDescription(String desc);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription();
+
+ /**
+ * Return the alignment column (from 1..) for a sequence position
+ *
+ * @param pos
+ * 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
+ *
+ */
+ public int findIndex(int pos);
+
+ /**
+ * Returns the sequence position for an alignment (column) position. If at a
+ * gap, returns the position of the next residue to the right. If beyond the
+ * end of the sequence, returns 1 more than the last residue position.
+ *
+ * @param i
+ * column index in alignment (from 0..<length)
+ *
+ * @return
+ */
+ public int findPosition(int i);
+
+ /**
+ * Returns the sequence positions for first and last residues lying within the
+ * given column positions [fromColum,toColumn] (where columns are numbered
+ * from 1), or null if no residues are included in the range
+ *
+ * @param fromColum
+ * - first column base 1
+ * @param toColumn
+ * - last column, base 1
+ * @return
+ */
+ public ContiguousI findPositions(int fromColum, int toColumn);
+
+ /**
+ * 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();
+
+ /**
+ * Build a bitset corresponding to sequence gaps
+ *
+ * @return a BitSet where set values correspond to gaps in the sequence
+ */
+ public BitSet gapBitset();
+
+ /**
+ * Returns an int array where indices correspond to each position in sequence
+ * char array and the element value gives the result of findPosition for that
+ * index in the sequence.
+ *
+ * @return int[SequenceI.getLength()]
+ */
+ public int[] findPositionMap();
+
+ /**
+ * Answers true if the sequence is composed of amino acid characters. Note
+ * that implementations may use heuristic methods which are not guaranteed to
+ * give the biologically 'right' answer.
+ *
+ * @return
+ */
+ public boolean isProtein();
+
+ /**
+ * 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 (inclusive)
+ * @param j
+ * last column in range to delete (exclusive)
+ */
+ public void deleteChars(int i, int j);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * alignment column number
+ * @param c
+ * character to insert
+ */
+ public void insertCharAt(int i, char c);
+
+ /**
+ * insert given character at alignment column position
+ *
+ * @param position
+ * alignment column number
+ * @param count
+ * length of insert
+ * @param ch
+ * character to insert
+ */
+ public void insertCharAt(int position, int count, char ch);
+
+ /**
+ * Answers a list of all sequence features associated with this sequence. The
+ * list may be held by the sequence's dataset sequence if that is defined.
+ *
+ * @return
+ */
+ public List<SequenceFeature> getSequenceFeatures();
+
+ /**
+ * Answers the object holding features for the sequence
+ *
+ * @return
+ */
+ SequenceFeaturesI getFeatures();
+
+ /**
+ * Replaces the sequence features associated with this sequence with the given
+ * features. If this sequence has a dataset sequence, then this method will
+ * update the dataset sequence's features instead.
+ *
+ * @param features
+ */
+ public void setSequenceFeatures(List<SequenceFeature> features);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ public void setPDBId(Vector<PDBEntry> ids);
+
+ /**
+ * Returns a list
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector<PDBEntry> getAllPDBEntries();
+
+ /**
+ * Adds the entry to the *normalised* list of PDBIds.
+ *
+ * If a PDBEntry is passed with the same entry.getID() string as one already
+ * in the list, or one is added that appears to be the same but has a chain ID
+ * appended, then the existing PDBEntry will be updated with the new
+ * attributes instead, unless the entries have distinct chain codes or
+ * associated structure files.
+ *
+ * @param entry
+ * @return true if the entry was added, false if updated
+ */
+ public boolean 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);
+
+ /**
+ * set the array of Database references for the sequence.
+ *
+ * BH 2019.02.04 changes param to DBModlist
+ *
+ * @param dbs
+ * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+ * set are not normalised.
+ * @throws InvalidArgumentException
+ * if the is not one created by Sequence itself
+ */
+ @Deprecated
+ public void setDBRefs(DBModList<DBRefEntry> dbs);
+
+ public DBModList<DBRefEntry> getDBRefs();
+
+ /**
+ * 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);
+
+ /**
+ * Adds the given sequence feature and returns true, or returns false if it is
+ * already present on the sequence, or if the feature type is null.
+ *
+ * @param sf
+ * @return
+ */
+ public boolean addSequenceFeature(SequenceFeature sf);
+
+ public void deleteFeature(SequenceFeature sf);
+
+ public void setDatasetSequence(SequenceI seq);
+
+ 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);
+
+ /**
+ * 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);
+
+ /**
+ * 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<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source), label (type) and description (observation instance). Null
+ * values do not match.
+ *
+ * @param calcId
+ * @param label
+ * @param description
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description);
+
+ /**
+ * 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. 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
+ */
+ public SequenceI createDatasetSequence();
+
+ /**
+ * Transfer any database references or annotation from entry under a sequence
+ * mapping. <br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+ * </strong><br/>
+ *
+ * @param entry
+ * @param mp
+ * null or mapping from entry's numbering to local start/end
+ */
+ public void transferAnnotation(SequenceI entry, Mapping mp);
+
+ /**
+ * @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<int[]> getInsertions();
+
+ /**
+ * Given a pdbId String, return the equivalent PDBEntry if available in the
+ * given sequence
+ *
+ * @param pdbId
+ * @return
+ */
+ public PDBEntry getPDBEntry(String pdbId);
+
+ /**
+ * Get all primary database/accessions for this sequence's data. These
+ * DBRefEntry are expected to resolve to a valid record in the associated
+ * external database, either directly or via a provided 1:1 Mapping.
+ *
+ * @return just the primary references (if any) for this sequence, or an empty
+ * list
+ */
+ public List<DBRefEntry> getPrimaryDBRefs();
+
+ /**
+ * Returns a (possibly empty) list of sequence features that overlap the given
+ * alignment column range, optionally restricted to one or more specified
+ * feature types. If the range is all gaps, then features which enclose it are
+ * included (but not contact features).
+ *
+ * @param fromCol
+ * start column of range inclusive (1..)
+ * @param toCol
+ * end column of range inclusive (1..)
+ * @param types
+ * optional feature types to restrict results to
+ * @return
+ */
+ List<SequenceFeature> findFeatures(int fromCol, int toCol,
+ String... types);
+
+ /**
+ * Method to call to indicate that the sequence (characters or alignment/gaps)
+ * has been modified. Provided to allow any cursors on residue/column
+ * positions to be invalidated.
+ */
+ void sequenceChanged();
+
+ /**
+ *
+ * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+ * returns true.
+ */
+ BitSet getInsertionsAsBits();
+
+ /**
+ * Replaces every occurrence of c1 in the sequence with c2 and returns the
+ * number of characters changed
+ *
+ * @param c1
+ * @param c2
+ */
+ public int replace(char c1, char c2);
+
+ /**
+ * Answers the GeneLociI, or null if not known
+ *
+ * @return
+ */
+ GeneLociI getGeneLoci();
+
+ /**
+ * Sets the mapping to gene loci for the sequence
+ *
+ * @param speciesId
+ * @param assemblyId
+ * @param chromosomeId
+ * @param map
+ */
+ void setGeneLoci(String speciesId, String assemblyId, String chromosomeId,
+ MapList map);
+
+ /**
+ * Returns the sequence string constructed from the substrings of a sequence
+ * defined by the int[] ranges provided by an iterator. E.g. the iterator
+ * could iterate over all visible regions of the alignment
+ *
+ * @param it
+ * the iterator to use
+ * @return a String corresponding to the sequence
+ */
+ public String getSequenceStringFromIterator(Iterator<int[]> it);
+
+ /**
+ * Locate the first position in this sequence which is not contained in an
+ * iterator region. If no such position exists, return 0
+ *
+ * @param it
+ * iterator over regions
+ * @return first residue not contained in regions
+ */
+ public int firstResidueOutsideIterator(Iterator<int[]> it);
+
+}
git://source.jalview.org / jalview.git / blobdiff