X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=a193997a288937ad7976a1eee9137ffc7d79a00a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=06e93d7a4322aea1f8b8feb2267d0a071e4f2c22;hpb=e33cdacd2ac2836504375c538574a0f1cafec7e3;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 06e93d7..a193997 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,278 +1,434 @@
-/*
-* 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
-{
-    /**
-     *  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 the longest sequence Id of the alignment
-     *
-     * @return Number of characters in longest sequence Id.
-     */
-    public int getMaxIdLength();
-
-    /**
-     * 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);
-
-    /**
-     * 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(SequenceI seqs [], int start, int end);
-
-
-    /**
-     * 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.
-     */
-    public int findIndex(SequenceI s);
-
-    /**
-    * 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);
-
-    /**
-     * All sequences will be cut from given index.
-     *
-     * @param i Remove all residues in sequences beyond this column.
-     */
-    public void trimRight(int i);
-
-    /**
-     * Removes all columns containing entirely gap characters.
-     */
-    public void removeGaps();
-
-
-
-    /**
-     * 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();
-
-    /**
-     * 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();
-    /**
-     * Compact representation of alignment
-     * @return CigarArray
-     */
-    public CigarArray getCompactAlignment();
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * 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 
+ * 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.
+ * 
+ * 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;
+
+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 (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
+   * 
+   * @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 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.
+   */
+  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 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);
+
+  /**
+   * 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.
+   */
+  public 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();
+
+  /**
+   * 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();
+
+  /**
+   * 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.
+   */
+  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);
+
+  /**
+   * 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)
+   * @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(SequenceI startAfter, String token, boolean b);
+
+  /**
+   * find first sequence in alignment which is involved in the given search
+   * result object
+   * 
+   * @param results
+   * @return -1 or index of sequence in alignment
+   */
+  public int findIndex(SearchResults results);
+
+  /**
+   * append sequences and annotation from another alignment object to this one.
+   * Note: this is a straight transfer of object references, and may result in
+   * toappend's dependent data being transformed to fit the alignment (changing
+   * 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.
+   */
+  public void append(AlignmentI toappend);
+
+  /**
+   * 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
+   */
+  public 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);
+}