/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
public interface AlignmentI extends AnnotatedCollectionI
{
/**
* Calculates the number of sequences in an alignment, excluding hidden
* sequences
*
* @return Number of sequences in alignment
*/
int getHeight();
/**
* Calculates the number of sequences in an alignment, including hidden
* sequences
*
* @return Number of sequences in alignment
*/
int getAbsoluteHeight();
/**
*
* Answers the width of the alignment, including gaps, that is, the length of
* the longest sequence, or -1 if there are no sequences. Avoid calling this
* method repeatedly where possible, as it has to perform a calculation. Note
* that this width includes any hidden columns.
*
* @return
* @see AlignmentI#getVisibleWidth()
*/
@Override
int getWidth();
/**
*
* Answers the visible width of the alignment, including gaps, that is, the
* length of the longest sequence, excluding any hidden columns. Answers -1 if
* there are no sequences. Avoid calling this method repeatedly where
* possible, as it has to perform a calculation.
*
* @return
*/
int getVisibleWidth();
/**
* Calculates if this set of sequences (visible and invisible) are all the
* same length
*
* @return true if all sequences in alignment are the same length
*/
boolean isAligned();
/**
* Calculates if this set of sequences is all the same length
*
* @param includeHidden
* optionally exclude hidden sequences from test
* @return true if all (or just visible) sequences are the same length
*/
boolean isAligned(boolean includeHidden);
/**
* Answers if the sequence at alignmentIndex is hidden
*
* @param alignmentIndex
* the index to check
* @return true if the sequence is hidden
*/
boolean isHidden(int alignmentIndex);
/**
* Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
*/
@Override
List getSequences();
/**
* Gets sequences as a SequenceI[]
*
* @return All sequences in alignment.
*/
SequenceI[] getSequencesArray();
/**
* Find a specific sequence in this alignment.
*
* @param i
* Index of required sequence.
*
* @return SequenceI at given index.
*/
SequenceI getSequenceAt(int i);
/**
* Find a specific sequence in this alignment.
*
* @param i
* Index of required sequence in full alignment, i.e. if all columns
* were visible
*
* @return SequenceI at given index.
*/
SequenceI getSequenceAtAbsoluteIndex(int i);
/**
* Returns a map of lists of sequences keyed by sequence name.
*
* @return
*/
Map> getSequencesByName();
/**
* Add a new sequence to this alignment.
*
* @param seq
* New sequence will be added at end of alignment.
*/
void addSequence(SequenceI seq);
/**
* Used to set a particular index of the alignment with the given sequence.
*
* @param i
* Index of sequence to be updated. if i>length, sequence will be
* added to end, with no intervening positions.
* @param seq
* New sequence to be inserted. The existing sequence at position i
* will be replaced.
* @return existing sequence (or null if i>current length)
*/
SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment. Updates hidden sequences to account
* for the removed sequence. Do NOT use this method to delete sequences which
* are just hidden.
*
* @param s
* Sequence to be deleted.
*/
void deleteSequence(SequenceI s);
/**
* Deletes a sequence from the alignment. Updates hidden sequences to account
* for the removed sequence. Do NOT use this method to delete sequences which
* are just hidden.
*
* @param i
* Index of sequence to be deleted.
*/
void deleteSequence(int i);
/**
* Deletes a sequence in the alignment which has been hidden.
*
* @param i
* Index of sequence to be deleted
*/
void deleteHiddenSequence(int i);
/**
* Finds sequence in alignment using sequence name as query.
*
* @param name
* Id of sequence to search for.
*
* @return Sequence matching query, if found. If not found returns null.
*/
SequenceI findName(String name);
SequenceI[] findSequenceMatch(String name);
/**
* Finds index of a given sequence in the alignment.
*
* @param s
* Sequence to look for.
*
* @return Index of sequence within the alignment or -1 if not found
*/
int findIndex(SequenceI s);
/**
* Returns the first group (in the order in which groups were added) that
* includes the given sequence instance and aligned position (base 0), or null
* if none found
*
* @param seq
* - must be contained in the alignment (not a dataset sequence)
* @param position
*
* @return
*/
SequenceGroup findGroup(SequenceI seq, int position);
/**
* Finds all groups that a given sequence is part of.
*
* @param s
* Sequence in alignment.
*
* @return All groups containing given sequence.
*/
SequenceGroup[] findAllGroups(SequenceI s);
/**
* Adds a new SequenceGroup to this alignment.
*
* @param sg
* New group to be added.
*/
void addGroup(SequenceGroup sg);
/**
* Deletes a specific SequenceGroup
*
* @param g
* Group will be deleted from alignment.
*/
void deleteGroup(SequenceGroup g);
/**
* Get all the groups associated with this alignment.
*
* @return All groups as a list.
*/
List getGroups();
/**
* Deletes all groups from this alignment.
*/
void deleteAllGroups();
/**
* 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.
*/
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
*/
void setAnnotationIndex(AlignmentAnnotation aa, int index);
/**
* Delete all annotations, including auto-calculated if the flag is set true.
* Returns true if at least one annotation was deleted, else false.
*
* @param includingAutoCalculated
* @return
*/
boolean deleteAllAnnotations(boolean includingAutoCalculated);
/**
* Deletes a specific AlignmentAnnotation from the alignment, and removes its
* reference from any SequenceI or SequenceGroup object's annotation if and
* only if aa is contained within the alignment's annotation vector.
* Otherwise, it will do nothing.
*
* @param aa
* the annotation to delete
* @return true if annotation was deleted from this alignment.
*/
boolean deleteAnnotation(AlignmentAnnotation aa);
/**
* Deletes a specific AlignmentAnnotation from the alignment, and optionally
* removes any reference from any SequenceI or SequenceGroup object's
* annotation if and only if aa is contained within the alignment's annotation
* vector. Otherwise, it will do nothing.
*
* @param aa
* the annotation to delete
* @param unhook
* flag indicating if any references should be removed from
* annotation - use this if you intend to add the annotation back
* into the alignment
* @return true if annotation was deleted from this alignment.
*/
boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
/**
* Get the annotation associated with this alignment (this can be null if no
* annotation has ever been created on the alignment)
*
* @return array of AlignmentAnnotation objects
*/
@Override
AlignmentAnnotation[] getAlignmentAnnotation();
/**
* Change the gap character used in this alignment to 'gc'
*
* @param gc
* the new gap character.
*/
void setGapCharacter(char gc);
/**
* Get the gap character used in this alignment
*
* @return gap character
*/
char getGapCharacter();
/**
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
*/
boolean hasRNAStructure();
/**
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
* dataset.
*/
AlignmentI getDataset();
/**
* Set the associated dataset for the alignment, or create one.
*
* @param dataset
* The dataset alignment or null to construct one.
*/
void setDataset(AlignmentI dataset);
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
*
* @return boolean true if alignment was modified
*/
boolean padGaps();
HiddenSequences getHiddenSequences();
HiddenColumns getHiddenColumns();
/**
* Compact representation of alignment
*
* @return CigarArray
*/
CigarArray getCompactAlignment();
/**
* Set an arbitrary key value pair for an alignment. Note: both key and value
* objects should return a meaningful, human readable response to .toString()
*
* @param key
* @param value
*/
void setProperty(Object key, Object value);
/**
* Get a named property from the alignment.
*
* @param key
* @return value of property
*/
Object getProperty(Object key);
/**
* Get the property hashtable.
*
* @return hashtable of alignment properties (or null if none are defined)
*/
Map