/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
* 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
+ * 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
+ *
+ * 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/>.
*/
package jalview.datamodel;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
-public interface AlignmentI
+public interface AlignmentI extends AnnotatedCollectionI
{
/**
* 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.
*/
+ @Override
public int getWidth();
/**
* 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
*/
public 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
public boolean isAligned(boolean includeHidden);
/**
- * Gets sequences as a Vector
- *
+ * Gets sequences as a Synchronized collection
+ *
* @return All sequences in alignment.
*/
- public Vector getSequences();
+ @Override
+ public List<SequenceI> 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
/**
* Deletes a sequence from the alignment
- *
+ *
* @param s
* Sequence to be deleted.
*/
/**
* Deletes a sequence from the alignment.
- *
+ *
* @param i
* Index of sequence to be deleted.
*/
/**
* 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 or -1 if not found
*/
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.
*/
/**
* 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.
*/
/**
* Deletes a specific SequenceGroup
- *
+ *
* @param g
* Group will be deleted from alignment.
*/
/**
* Get all the groups associated with this alignment.
- *
- * @return All groups as a Vector.
+ *
+ * @return All groups as a list.
*/
- public Vector getGroups();
+ public List<SequenceGroup> getGroups();
/**
* Deletes all groups from this alignment.
/**
* 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.
*/
/**
* moves annotation to a specified index in alignment annotation display stack
- *
+ *
* @param aa
* the annotation object to be moved
* @param index
* 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.
* 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
/**
* 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
public AlignmentAnnotation[] getAlignmentAnnotation();
/**
* Change the gap character used in this alignment to 'gc'
- *
+ *
* @param gc
* the new gap character.
*/
/**
* 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();
/**
* Test if alignment contains RNA structure
- *
+ *
* @return true if RNA structure AligmnentAnnotation was added to alignment
*/
public boolean hasRNAStructure();
/**
* 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.
*/
/**
* Set the associated dataset for the alignment, or create one.
- *
+ *
* @param dataset
* The dataset alignment or null to construct one.
*/
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
- *
+ *
* @return boolean true if alignment was modified
*/
public boolean padGaps();
/**
* 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
*/
/**
* Get a named property from the alignment.
- *
+ *
* @param key
* @return value of property
*/
/**
* 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.
*/
/**
* get all codon frames associated with this alignment
- *
+ *
* @return
*/
public AlignedCodonFrame[] getCodonFrames();
/**
* get a particular codon frame
- *
+ *
* @param index
* @return
*/
/**
* find sequence with given name in alignment
- *
+ *
* @param token
* name to find
* @param b
/**
* find next sequence with given name in alignment starting after a given
* sequence
- *
+ *
* @param startAfter
* the sequence after which the search will be started (usually the
* result of the last call to findName)
/**
* find first sequence in alignment which is involved in the given search
* result object
- *
+ *
* @param results
* @return -1 or index of sequence in alignment
*/
* gap characters, etc...). If you are uncertain, use the copy Alignment copy
* constructor to create a new version which can be appended without side
* effect.
- *
+ *
* @param toappend
* - the alignment to be appended.
*/
/**
* Justify the sequences to the left or right by deleting and inserting gaps
* before the initial residue or after the terminal residue
- *
+ *
* @param right
* true if alignment padded to right, false to justify to left
* @return true if alignment was changed TODO: return undo object
/**
* add given annotation row at given position (0 is start, -1 is end)
- *
+ *
* @param consensus
* @param i
*/
public void addAnnotation(AlignmentAnnotation consensus, int i);
+
+ /**
+ * search for or create a specific annotation row on the alignment
+ *
+ * @param method - CalcId for the annotation (must match)
+ * @param autoCalc - value of autocalc flag for the annotation
+ * @param seqRef - null or specific sequence reference
+ * @param groupRef - null or specific group reference
+ * @return existing annotation matching the given attributes
+ */
+ public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
+ SequenceI seqRef, SequenceGroup groupRef);
+
+ /**
+ * move the given group up or down in the alignment by the given number of rows.
+ * Implementor assumes given group is already present on alignment - no recalculations are triggered.
+ * @param sg
+ * @param map
+ * @param up
+ * @param i
+ */
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up);
}
git://source.jalview.org / jalview.git / blobdiff