/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * modify it under the terms of the GNU General 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.
+ * PURPOSE. See the GNU General 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/>.
+ * You should have received a copy of the GNU General License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Hashtable;
+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
+public interface AlignmentI extends AnnotatedCollectionI
{
/**
* Calculates the number of sequences in an alignment
*
* @return Number of sequences in alignment
*/
- public int getHeight();
+ int getHeight();
/**
+ *
* Calculates the maximum width of the alignment, including gaps.
*
* @return Greatest sequence length within alignment.
*/
- public int getWidth();
+ @Override
+ int getWidth();
/**
* Calculates if this set of sequences (visible and invisible) are all the
*
* @return true if all sequences in alignment are the same length
*/
- public boolean isAligned();
+ boolean isAligned();
/**
* Calculates if this set of sequences is all the same length
* optionally exclude hidden sequences from test
* @return true if all (or just visible) sequences are the same length
*/
- public boolean isAligned(boolean includeHidden);
+ boolean isAligned(boolean includeHidden);
/**
- * Gets sequences as a Vector
+ * Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
*/
- public Vector getSequences();
+ @Override
+ List<SequenceI> getSequences();
/**
* Gets sequences as a SequenceI[]
*
* @return All sequences in alignment.
*/
- public SequenceI[] getSequencesArray();
+ SequenceI[] getSequencesArray();
/**
* Find a specific sequence in this alignment.
*
* @return SequenceI at given index.
*/
- public SequenceI getSequenceAt(int i);
+ SequenceI getSequenceAt(int i);
+
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ Map<String, List<SequenceI>> getSequencesByName();
/**
* Add a new sequence to this alignment.
* @param seq
* New sequence will be added at end of alignment.
*/
- public void addSequence(SequenceI seq);
+ void addSequence(SequenceI seq);
/**
* Used to set a particular index of the alignment with the given sequence.
* @param seq
* New sequence to be inserted.
*/
- public void setSequenceAt(int i, SequenceI seq);
+ void setSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment
* @param s
* Sequence to be deleted.
*/
- public void deleteSequence(SequenceI s);
+ void deleteSequence(SequenceI s);
/**
* Deletes a sequence from the alignment.
* @param i
* Index of sequence to be deleted.
*/
- public void deleteSequence(int i);
+ void deleteSequence(int i);
/**
* Finds sequence in alignment using sequence name as query.
*
* @return Sequence matching query, if found. If not found returns null.
*/
- public SequenceI findName(String name);
+ SequenceI findName(String name);
- public SequenceI[] findSequenceMatch(String name);
+ SequenceI[] findSequenceMatch(String name);
/**
* Finds index of a given sequence in the alignment.
*
* @return Index of sequence within the alignment or -1 if not found
*/
- public int findIndex(SequenceI s);
+ int findIndex(SequenceI s);
/**
* Finds group that given sequence is part of.
* @return First group found for sequence. WARNING : Sequences may be members
* of several groups. This method is incomplete.
*/
- public SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI s);
/**
* Finds all groups that a given sequence is part of.
*
* @return All groups containing given sequence.
*/
- public SequenceGroup[] findAllGroups(SequenceI s);
+ SequenceGroup[] findAllGroups(SequenceI s);
/**
* Adds a new SequenceGroup to this alignment.
* @param sg
* New group to be added.
*/
- public void addGroup(SequenceGroup sg);
+ void addGroup(SequenceGroup sg);
/**
* Deletes a specific SequenceGroup
* @param g
* Group will be deleted from alignment.
*/
- public void deleteGroup(SequenceGroup g);
+ void deleteGroup(SequenceGroup g);
/**
* Get all the groups associated with this alignment.
*
- * @return All groups as a Vector.
+ * @return All groups as a list.
*/
- public Vector getGroups();
+ List<SequenceGroup> getGroups();
/**
* Deletes all groups from this alignment.
*/
- public void deleteAllGroups();
+ 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);
+ void addAnnotation(AlignmentAnnotation aa);
/**
* moves annotation to a specified index in alignment annotation display stack
* @param index
* the destination position
*/
- public void setAnnotationIndex(AlignmentAnnotation aa, int index);
+ 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 object's annotation if and only if aa is
- * contained within the alignment's annotation vector. Otherwise, it will do
- * nothing.
+ * 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.
*/
- public boolean deleteAnnotation(AlignmentAnnotation aa);
+ boolean deleteAnnotation(AlignmentAnnotation aa);
/**
- * Get the annotation associated with this alignment
+ * 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
*/
- public AlignmentAnnotation[] getAlignmentAnnotation();
+ @Override
+ AlignmentAnnotation[] getAlignmentAnnotation();
/**
* Change the gap character used in this alignment to 'gc'
* @param gc
* the new gap character.
*/
- public void setGapCharacter(char gc);
+ void setGapCharacter(char gc);
/**
* Get the gap character used in this alignment
*
* @return gap character
*/
- public char getGapCharacter();
+ char getGapCharacter();
/**
* Test for all nucleotide alignment
*
* @return true if alignment is nucleotide sequence
*/
- public boolean isNucleotide();
+ boolean isNucleotide();
+
+ /**
+ * Test if alignment contains RNA structure
+ *
+ * @return true if RNA structure AligmnentAnnotation was added to alignment
+ */
+ boolean hasRNAStructure();
/**
* Set alignment to be a nucleotide sequence
*
*/
- public void setNucleotide(boolean b);
+ 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();
+ 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);
+ 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();
+ boolean padGaps();
- public HiddenSequences getHiddenSequences();
+ HiddenSequences getHiddenSequences();
/**
* Compact representation of alignment
*
* @return CigarArray
*/
- public CigarArray getCompactAlignment();
+ CigarArray getCompactAlignment();
/**
* Set an arbitrary key value pair for an alignment. Note: both key and value
* @param key
* @param value
*/
- public void setProperty(Object key, Object value);
+ void setProperty(Object key, Object value);
/**
* Get a named property from the alignment.
* @param key
* @return value of property
*/
- public Object getProperty(Object key);
+ Object getProperty(Object key);
/**
* Get the property hashtable.
*
* @return hashtable of alignment properties (or null if none are defined)
*/
- public Hashtable getProperties();
+ Hashtable getProperties();
/**
* add a reference to a frame of aligned codons for this alignment
*
* @param codons
*/
- public void addCodonFrame(AlignedCodonFrame codons);
+ 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);
+ boolean removeCodonFrame(AlignedCodonFrame codons);
/**
* get all codon frames associated with this alignment
*
* @return
*/
- public AlignedCodonFrame[] getCodonFrames();
+ Set<AlignedCodonFrame> getCodonFrames();
/**
- * get a particular codon frame
- *
- * @param index
- * @return
+ * Set the codon frame mappings (replacing any existing set).
*/
- public AlignedCodonFrame getCodonFrame(int index);
+ void setCodonFrames(Set<AlignedCodonFrame> acfs);
/**
* get codon frames involving sequenceI
*/
- public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+ List<AlignedCodonFrame> getCodonFrame(SequenceI seq);
/**
* find sequence with given name in alignment
* tried
* @return matched sequence or null
*/
- public SequenceI findName(String token, boolean b);
+ SequenceI findName(String token, boolean b);
/**
* find next sequence with given name in alignment starting after a given
* tried
* @return matched sequence or null
*/
- public SequenceI findName(SequenceI startAfter, String token, boolean b);
+ SequenceI findName(SequenceI startAfter, String token, boolean b);
/**
* find first sequence in alignment which is involved in the given search
* @param results
* @return -1 or index of sequence in alignment
*/
- public int findIndex(SearchResults results);
+ int findIndex(SearchResults results);
/**
* append sequences and annotation from another alignment object to this one.
* @param toappend
* - the alignment to be appended.
*/
- public void append(AlignmentI toappend);
+ void append(AlignmentI toappend);
/**
* Justify the sequences to the left or right by deleting and inserting gaps
* true if alignment padded to right, false to justify to left
* @return true if alignment was changed TODO: return undo object
*/
- public boolean justify(boolean right);
+ boolean justify(boolean right);
/**
* add given annotation row at given position (0 is start, -1 is end)
* @param consensus
* @param i
*/
- public void addAnnotation(AlignmentAnnotation consensus, int i);
+ void addAnnotation(AlignmentAnnotation consensus, int i);
+
+ /**
+ * search for or create a specific annotation row on the alignment
+ *
+ * @param name
+ * name for annotation (must match)
+ * @param calcId
+ * calcId for the annotation (null or 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
+ * @param method
+ * - CalcId for the annotation (must match)
+ *
+ * @return existing annotation matching the given attributes
+ */
+ AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+ 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
+ */
+ void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up);
+
+ /**
+ * validate annotation after an edit and update any alignment state flags
+ * accordingly
+ *
+ * @param alignmentAnnotation
+ */
+ void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
+
+ /**
+ * Align this alignment the same as the given one. If both of the same type
+ * (nucleotide/protein) then align both identically. If this is nucleotide and
+ * the other is protein, make 3 gaps for each gap in the protein sequences. If
+ * this is protein and the other is nucleotide, insert a gap for each 3 gaps
+ * (or part thereof) between nucleotide bases. Returns the number of mapped
+ * sequences that were realigned .
+ *
+ * @param al
+ * @return
+ */
+ int alignAs(AlignmentI al);
+
+ /**
+ * Returns the set of distinct sequence names in the alignment.
+ *
+ * @return
+ */
+ Set<String> getSequenceNames();
+
+ /**
+ * Checks if the alignment has at least one sequence with one non-gaped
+ * residue
+ *
+ * @return
+ */
+ public boolean hasValidSequence();
}
git://source.jalview.org / jalview.git / blobdiff