X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=82aff3329e5190320ad2de32b8726bf69f9bc478;hb=6a91de2e48559da8034762a7d77a143435362029;hp=8a14a08d2f1e2fc34f08ea212636baa69c456d99;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 8a14a08..82aff33 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -1,116 +1,298 @@ -/* -* 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 { - public int getHeight(); - - public int getWidth(); - - public int getMaxIdLength(); - - public boolean isAligned(); - - public Vector getSequences(); - - public SequenceI getSequenceAt(int i); - - public void addSequence(SequenceI seq); - - public void setSequenceAt(int i, SequenceI seq); - - public void deleteSequence(SequenceI s); - - public void deleteSequence(int i); - - public SequenceI[] getColumns(int start, int end); - - public SequenceI[] getColumns(int seq1, int seq2, int start, int end); - - public void deleteColumns(int start, int end); - - public void deleteColumns(int seq1, int seq2, int start, int end); - - public void insertColumns(SequenceI[] seqs, int pos); - - public SequenceI findName(String name); - - public SequenceI findbyDisplayId(String name); - - public int findIndex(SequenceI s); - - // Modifying - public void trimLeft(int i); - - public void trimRight(int i); - - public void removeGaps(); - - public Vector removeRedundancy(float threshold, Vector sel); - - // 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(); - - public void addSuperGroup(SuperGroup sg); - - public void removeSuperGroup(SuperGroup sg); - - public SuperGroup getSuperGroup(SequenceGroup sg); - - // Sorting - public void sortGroups(); - - public void sortByPID(SequenceI s); - - public void sortByID(); - - //Annotations - public void addAnnotation(AlignmentAnnotation aa); - - public void deleteAnnotation(AlignmentAnnotation aa); - - public AlignmentAnnotation[] getAlignmentAnnotation(); - - public void setGapCharacter(char gc); - - public char getGapCharacter(); - - public Vector getAAFrequency(); -} +/* + * 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); + +}