X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=ebfb0ce3cc8a21c2f5dabece7e8497e50edada15;hb=601989c95175f5ad883e73c4aa07a76713510d1f;hp=182b68769dc990df3bc38538db9eca945c2b4953;hpb=2a64503d035e47cf9a40e5de979fd22980e50106;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 182b687..ebfb0ce 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -1,73 +1,294 @@ +/* +* 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 jalview.jbgui.*; import java.util.*; + /** Data structure to hold and manipulate a multiple sequence alignment */ -public interface AlignmentI { +public interface AlignmentI +{ + /** + * Calculates the number of sequences in an alignment + * + * @return Number of sequences in alignment + */ + public int getHeight(); - public int getHeight() ; - public int getWidth() ; - public int getMaxIdLength() ; + /** + * Calculates the maximum width of the alignment, including gaps. + * + * @return Greatest sequence length within alignment. + */ + public int getWidth(); - public boolean isAligned(); + /** + * Calculates the longest sequence Id of the alignment + * + * @return Number of characters in longest sequence Id. + */ + public int getMaxIdLength(); - public Vector getSequences(); - public SequenceI getSequenceAt(int i); + /** + * 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(); - public void addSequence(SequenceI seq) ; - public void setSequenceAt(int i,SequenceI seq); + /** + * Gets sequences as a Vector + * + * @return All sequences in alignment. + */ + public Vector getSequences(); - public void deleteSequence(SequenceI s) ; - public void deleteSequence(int i) ; + /** + * Find a specific sequence in this alignment. + * + * @param i Index of required sequence. + * + * @return SequenceI at given index. + */ + public SequenceI getSequenceAt(int i); - public SequenceI[] getColumns(int start, int end) ; - public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ; + /** + * Add a new sequence to this alignment. + * + * @param seq New sequence will be added at end of alignment. + */ + public void addSequence(SequenceI seq); - public void deleteColumns(int start, int end) ; - public void deleteColumns(int seq1, int seq2, int start, int end) ; + /** + * 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); - public void insertColumns(SequenceI[] seqs, int pos) ; + /** + * Deletes a sequence from the alignment. + * + * @param s Sequence to be deleted. + */ + public void deleteSequence(SequenceI s); - public SequenceI findName(String name) ; - public SequenceI findbyDisplayId(String name); + /** + * Deletes a sequence from the alignment. + * + * @param i Index of sequence to be deleted. + */ + public void deleteSequence(int i); - public int findIndex(SequenceI s) ; + /** + * 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); - // Modifying - public void trimLeft(int i) ; - public void trimRight(int i) ; + /** + * 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); - public void removeGaps() ; - public Vector removeRedundancy(float threshold, Vector sel) ; + /** + * 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); - // Grouping methods - public SequenceGroup findGroup(int i) ; - public SequenceGroup findGroup(SequenceI s) ; - public SequenceGroup [] findAllGroups(SequenceI s); - public void addToGroup(SequenceGroup g, SequenceI s) ; - public void removeFromGroup(SequenceGroup g,SequenceI s) ; - public void addGroup(SequenceGroup sg) ; - public void deleteGroup(SequenceGroup g) ; - public Vector getGroups(); - public void deleteAllGroups(); + /** + * 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); - public void addSuperGroup(SuperGroup sg); - public void removeSuperGroup(SuperGroup sg); - public SuperGroup getSuperGroup(SequenceGroup sg); + /** + * 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); - // Sorting - public void sortGroups() ; - public void sortByPID(SequenceI s) ; - public void sortByID() ; + /** + * All sequences will be cut from given index. + * + * @param i Remove all residues in sequences beyond this column. + */ + public void trimRight(int i); - public void setGapCharacter(char gc); - public char getGapCharacter(); + /** + * 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 Vector getAAFrequency(); -} + 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(); + +}