/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-*/
+ * 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 jalview.util.ShiftList;
-
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
- */
- 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();
-
-
- /**
- * 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();
- /**
- * Compact representation of alignment
- * @return CigarArray
- */
- public CigarArray getCompactAlignment();
+ /**
+ * 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 <em>also</em> be tried
+ * @return matched sequence or null
+ */
+ public SequenceI findName(String token, boolean b);
+
}
git://source.jalview.org / jalview.git / blobdiff