X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=558b38d69665439b4e5e65b7081f4d10664be707;hb=9efc6af45120e24f7a11cc8ce6409139844e5001;hp=e14c1e96db8aa9edcb1dff11d617de9967b5ca88;hpb=c1ffd6dd15b79a56ec0a37eebbe4df05341ca57c;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index e14c1e9..558b38d 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -1,301 +1,305 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* 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. -* -* 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 -*/ -package jalview.datamodel; - -import java.util.*; - - -/** Data structure to hold and manipulate a multiple sequence alignment - */ -public interface AlignmentI -{ - /** - * Calculates the number of sequences in an alignment - * - * @return Number of sequences in alignment - */ - public int getHeight(); - - /** - * Calculates the maximum width of the alignment, including gaps. - * - * @return Greatest sequence length within alignment. - */ - public int getWidth(); - - /** - * Calculates the longest sequence Id of the alignment - * - * @return Number of characters in longest sequence Id. - */ - public int getMaxIdLength(); - - /** - * Calculates if this set of sequences is all the same length - * - * @return true if all sequences in alignment are the same length - */ - public boolean isAligned(); - - /** - * Gets sequences as a Vector - * - * @return All sequences in alignment. - */ - public Vector getSequences(); - - /** - * Gets sequences as a SequenceI[] - * - * @return All sequences in alignment. - */ - public SequenceI [] getSequencesArray(); - - /** - * Find a specific sequence in this alignment. - * - * @param i Index of required sequence. - * - * @return SequenceI at given index. - */ - public SequenceI getSequenceAt(int i); - - /** - * Add a new sequence to this alignment. - * - * @param seq New sequence will be added at end of alignment. - */ - public 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. - * @param seq New sequence to be inserted. - */ - public void setSequenceAt(int i, SequenceI seq); - - /** - * Deletes a sequence from the alignment. - * - * @param s Sequence to be deleted. - */ - public void deleteSequence(SequenceI s); - - /** - * Deletes a sequence from the alignment. - * - * @param i Index of sequence to be deleted. - */ - public void deleteSequence(int i); - - /** - * Deletes all residues in every sequence of alignment within given columns. - * - * @param start Start index of columns to delete. - * @param end End index to columns to delete. - */ - public void deleteColumns(int start, int end); - - /** - * Deletes all residues in every sequence of alignment within given columns. - * - * @param seq1 Index of first sequence to delete columns from. - * @param seq2 Index of last sequence to delete columns from. - * @param start Start index of columns to delete. - * @param end End index of columns to delete. - */ - public void deleteColumns(int seq1, int seq2, int start, int end); - - /** - * 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. - */ - public SequenceI findName(String name); - - - /** - * Finds index of a given sequence in the alignment. - * - * @param s Sequence to look for. - * - * @return Index of sequence within the alignment. - */ - public int findIndex(SequenceI s); - - /** - * All sequences will be cut from beginning to given index. - * - * @param i Remove all residues in sequences up to this column. - */ - public void trimLeft(int i); - - /** - * All sequences will be cut from given index. - * - * @param i Remove all residues in sequences beyond this column. - */ - public void trimRight(int i); - - /** - * Removes all columns containing entirely gap characters. - */ - public void removeGaps(); - - /** - * Removes redundant sequences from alignment. - * - * @param threshold Remove all sequences above the given threshold. - * @param sel Set of sequences which will have redundant sequences removed from. - * - * @return All sequences below redundancy threshold. - */ - public Vector removeRedundancy(float threshold, Vector sel); - - /** - * Finds group that sequence at index i in alignment is part of. - * - * @param i Index in alignment. - * - * @return First group found for sequence at position i. WARNING : - * Sequences may be members of several groups. This method is incomplete. - */ - public SequenceGroup findGroup(int i); - - /** - * Finds group that given sequence is part of. - * - * @param s Sequence in alignment. - * - * @return First group found for sequence. WARNING : - * Sequences may be members of several groups. This method is incomplete. - */ - public SequenceGroup findGroup(SequenceI s); - - /** - * Finds all groups that a given sequence is part of. - * - * @param s Sequence in alignment. - * - * @return All groups containing given sequence. - */ - public SequenceGroup[] findAllGroups(SequenceI s); - - /** - * Adds a new SequenceGroup to this alignment. - * - * @param sg New group to be added. - */ - public void addGroup(SequenceGroup sg); - - /** - * Deletes a specific SequenceGroup - * - * @param g Group will be deleted from alignment. - */ - public void deleteGroup(SequenceGroup g); - - /** - * Get all the groups associated with this alignment. - * - * @return All groups as a Vector. - */ - public Vector getGroups(); - - /** - * Deletes all groups from this alignment. - */ - public void deleteAllGroups(); - - - /** - * Adds a new AlignmentAnnotation to this alignment - */ - public void addAnnotation(AlignmentAnnotation aa); - - - public void setAnnotationIndex(AlignmentAnnotation aa, int index); - - /** - * Deletes a specific AlignmentAnnotation from the alignment. - * - * @param aa DOCUMENT ME! - */ - public void deleteAnnotation(AlignmentAnnotation aa); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public AlignmentAnnotation[] getAlignmentAnnotation(); - - /** - * DOCUMENT ME! - * - * @param gc DOCUMENT ME! - */ - public void setGapCharacter(char gc); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getGapCharacter(); - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Vector getAAFrequency(); - - /** - * Returns true if alignment is nucleotide sequence - * - * @return DOCUMENT ME! - */ - public boolean isNucleotide(); - - /** - * Set true if the alignment is a nucleotide sequence - * - * @return - */ - public void setNucleotide(boolean b); - - - public Alignment getDataset(); - - public void setDataset(Alignment dataset); - /** - * pads sequences with gaps (to ensure the set looks like an alignment) - * @return boolean true if alignment was modified - */ - public boolean padGaps(); - - public void adjustSequenceAnnotations(); - - public HiddenSequences getHiddenSequences(); - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * 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 + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * 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. + * + * 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 + */ +package jalview.datamodel; + +import java.util.*; + +/** Data structure to hold and manipulate a multiple sequence alignment + */ +public interface AlignmentI +{ + /** + * Calculates the number of sequences in an alignment + * + * @return Number of sequences in alignment + */ + public int getHeight(); + + /** + * Calculates the maximum width of the alignment, including gaps. + * + * @return Greatest sequence length within alignment. + */ + public int getWidth(); + + /** + * Calculates if this set of sequences is all the same length + * + * @return true if all sequences in alignment are the same length + */ + public boolean isAligned(); + + /** + * Gets sequences as a Vector + * + * @return All sequences in alignment. + */ + public Vector getSequences(); + + /** + * Gets sequences as a SequenceI[] + * + * @return All sequences in alignment. + */ + public SequenceI[] getSequencesArray(); + + /** + * Find a specific sequence in this alignment. + * + * @param i Index of required sequence. + * + * @return SequenceI at given index. + */ + public SequenceI getSequenceAt(int i); + + /** + * Add a new sequence to this alignment. + * + * @param seq New sequence will be added at end of alignment. + */ + public 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. + * @param seq New sequence to be inserted. + */ + public void setSequenceAt(int i, SequenceI seq); + + /** + * Deletes a sequence from the alignment + * + * @param s Sequence to be deleted. + */ + public void deleteSequence(SequenceI s); + + /** + * Deletes a sequence from the alignment. + * + * @param i Index of sequence to be deleted. + */ + public void deleteSequence(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. + */ + public SequenceI findName(String name); + + public 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. + */ + public int findIndex(SequenceI s); + + /** + * Finds group that given sequence is part of. + * + * @param s Sequence in alignment. + * + * @return First group found for sequence. WARNING : + * Sequences may be members of several groups. This method is incomplete. + */ + public SequenceGroup findGroup(SequenceI s); + + /** + * Finds all groups that a given sequence is part of. + * + * @param s Sequence in alignment. + * + * @return All groups containing given sequence. + */ + public SequenceGroup[] findAllGroups(SequenceI s); + + /** + * Adds a new SequenceGroup to this alignment. + * + * @param sg New group to be added. + */ + public void addGroup(SequenceGroup sg); + + /** + * Deletes a specific SequenceGroup + * + * @param g Group will be deleted from alignment. + */ + public void deleteGroup(SequenceGroup g); + + /** + * Get all the groups associated with this alignment. + * + * @return All groups as a Vector. + */ + public Vector getGroups(); + + + /** + * Deletes all groups from this alignment. + */ + public 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. + */ + public 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 + */ + public void setAnnotationIndex(AlignmentAnnotation aa, int index); + + /** + * Deletes a specific AlignmentAnnotation from the alignment, + * and removes its reference from any SequenceI 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. + */ + public boolean deleteAnnotation(AlignmentAnnotation aa); + + /** + * Get the annotation associated with this alignment + * + * @return array of AlignmentAnnotation objects + */ + public AlignmentAnnotation[] getAlignmentAnnotation(); + + /** + * Change the gap character used in this alignment to 'gc' + * + * @param gc the new gap character. + */ + public void setGapCharacter(char gc); + + /** + * Get the gap character used in this alignment + * + * @return gap character + */ + public char getGapCharacter(); + + /** + * Test for all nucleotide alignment + * + * @return true if alignment is nucleotide sequence + */ + public boolean isNucleotide(); + + /** + * Set alignment to be a nucleotide sequence + * + */ + public void setNucleotide(boolean b); + + /** + * Get the associated dataset for the alignment. + * @return Alignment containing dataset sequences or null of this is a dataset. + */ + public Alignment getDataset(); + + /** + * Set the associated dataset for the alignment, or create one. + * @param dataset The dataset alignment or null to construct one. + */ + public void setDataset(Alignment dataset); + + /** + * pads sequences with gaps (to ensure the set looks like an alignment) + * @return boolean true if alignment was modified + */ + public boolean padGaps(); + + public HiddenSequences getHiddenSequences(); + + /** + * Compact representation of alignment + * @return CigarArray + */ + public 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 + */ + public void setProperty(Object key, Object value); + /** + * Get a named property from the alignment. + * @param key + * @return value of property + */ + public Object getProperty(Object key); + /** + * Get the property hashtable. + * @return hashtable of alignment properties (or null if none are defined) + */ + public Hashtable getProperties(); + + /** + * add a reference to a frame of aligned codons for this alignment + * @param codons + */ + public void addCodonFrame(AlignedCodonFrame codons); + /** + * remove a particular codon frame reference from this alignment + * @param codons + * @return true if codon frame was removed. + */ + public boolean removeCodonFrame(AlignedCodonFrame codons); + /** + * get all codon frames associated with this alignment + * @return + */ + public AlignedCodonFrame[] getCodonFrames(); + /** + * get a particular codon frame + * @param index + * @return + */ + public AlignedCodonFrame getCodonFrame(int index); + /** + * get codon frames involving sequenceI + */ + public AlignedCodonFrame[] getCodonFrame(SequenceI seq); + /** + * find sequence with given name in alignment + * @param token name to find + * @param b true implies that case insensitive matching will also be tried + * @return matched sequence or null + */ + public SequenceI findName(String token, boolean b); + +}