X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=e99563b9586694800c734989812d3b84c655f9b1;hb=HEAD;hp=af5b7c45d4c0b814f397380f38fd11d1777e04d9;hpb=961b10e4c895aadb7fc9df82a641c6c53c0d5c70;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index af5b7c4..e99563b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,179 +1,265 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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
+   * Calculates the number of sequences in an alignment, excluding hidden
+   * sequences
    * 
    * @return Number of sequences in alignment
    */
-  public int getHeight();
+  int getHeight();
 
   /**
-   * Calculates the maximum width of the alignment, including gaps.
+   * Calculates the number of sequences in an alignment, including hidden
+   * sequences
    * 
-   * @return Greatest sequence length within alignment.
+   * @return Number of sequences in alignment
    */
-  public int getWidth();
+  int getAbsoluteHeight();
 
   /**
-   * Calculates if this set of sequences is all the same length
+   * 
+   * Answers the width of the alignment, including gaps, that is, the length of
+   * the longest sequence, or -1 if there are no sequences. Avoid calling this
+   * method repeatedly where possible, as it has to perform a calculation. Note
+   * that this width includes any hidden columns.
+   * 
+   * @return
+   * @see AlignmentI#getVisibleWidth()
+   */
+  @Override
+  int getWidth();
+
+  /**
+   * 
+   * Answers the visible width of the alignment, including gaps, that is, the
+   * length of the longest sequence, excluding any hidden columns. Answers -1 if
+   * there are no sequences. Avoid calling this method repeatedly where
+   * possible, as it has to perform a calculation.
+   * 
+   * @return
+   */
+  int getVisibleWidth();
+
+  /**
+   * 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();
+  boolean isAligned();
 
   /**
-   * Gets sequences as a Vector
+   * 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
+   */
+  boolean isAligned(boolean includeHidden);
+
+  /**
+   * Answers if the sequence at alignmentIndex is hidden
+   * 
+   * @param alignmentIndex
+   *          the index to check
+   * @return true if the sequence is hidden
+   */
+  boolean isHidden(int alignmentIndex);
+
+  /**
+   * 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.
+   * 
+   * @param i
+   *          Index of required sequence.
+   * 
+   * @return SequenceI at given index.
+   */
+  SequenceI getSequenceAt(int i);
 
   /**
    * Find a specific sequence in this alignment.
    * 
    * @param i
-   *                Index of required sequence.
+   *          Index of required sequence in full alignment, i.e. if all columns
+   *          were visible
    * 
    * @return SequenceI at given index.
    */
-  public SequenceI getSequenceAt(int i);
+  SequenceI getSequenceAtAbsoluteIndex(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.
+   *          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 i
-   *                Index of sequence to be updated.
+   *          Index of sequence to be updated. if i>length, sequence will be
+   *          added to end, with no intervening positions.
    * @param seq
-   *                New sequence to be inserted.
+   *          New sequence to be inserted. The existing sequence at position i
+   *          will be replaced.
+   * @return existing sequence (or null if i>current length)
    */
-  public void setSequenceAt(int i, SequenceI seq);
+  SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
-   * Deletes a sequence from the alignment
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param s
-   *                Sequence to be deleted.
+   *          Sequence to be deleted.
    */
-  public void deleteSequence(SequenceI s);
+  void deleteSequence(SequenceI s);
 
   /**
-   * Deletes a sequence from the alignment.
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param i
-   *                Index of sequence to be deleted.
+   *          Index of sequence to be deleted.
    */
-  public void deleteSequence(int i);
+  void deleteSequence(int i);
+
+  /**
+   * Deletes a sequence in the alignment which has been hidden.
+   * 
+   * @param i
+   *          Index of sequence to be deleted
+   */
+  void deleteHiddenSequence(int i);
 
   /**
    * Finds sequence in alignment using sequence name as query.
    * 
    * @param name
-   *                Id of sequence to search for.
+   *          Id of sequence to search for.
    * 
    * @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.
    * 
    * @param s
-   *                Sequence to look for.
+   *          Sequence to look for.
    * 
    * @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.
+   * Returns the first group (in the order in which groups were added) that
+   * includes the given sequence instance and aligned position (base 0), or null
+   * if none found
    * 
-   * @param s
-   *                Sequence in alignment.
+   * @param seq
+   *          - must be contained in the alignment (not a dataset sequence)
+   * @param position
    * 
-   * @return First group found for sequence. WARNING : Sequences may be members
-   *         of several groups. This method is incomplete.
+   * @return
    */
-  public SequenceGroup findGroup(SequenceI s);
+  SequenceGroup findGroup(SequenceI seq, int position);
 
   /**
    * Finds all groups that a given sequence is part of.
    * 
    * @param s
-   *                Sequence in alignment.
+   *          Sequence in alignment.
    * 
    * @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.
+   *          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.
+   *          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
@@ -181,64 +267,85 @@ public interface AlignmentI
    * @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 aa
-   *                the annotation object to be moved
+   *          the annotation object to be moved
    * @param index
-   *                the destination position
+   *          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.
+   */
+  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
+   *          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 deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
 
   /**
-   * Get the annotation associated with this alignment
+   * 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.
+   *          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();
-
-  /**
-   * Test for all nucleotide alignment
-   * 
-   * @return true if alignment is nucleotide sequence
-   */
-  public boolean isNucleotide();
+  char getGapCharacter();
 
   /**
-   * Set alignment to be a nucleotide sequence
+   * Test if alignment contains RNA structure
    * 
+   * @return true if RNA structure AligmnentAnnotation was added to alignment
    */
-  public void setNucleotide(boolean b);
+  boolean hasRNAStructure();
 
   /**
    * Get the associated dataset for the alignment.
@@ -246,31 +353,33 @@ public interface AlignmentI
    * @return Alignment containing dataset sequences or null of this is a
    *         dataset.
    */
-  public Alignment getDataset();
+  AlignmentI getDataset();
 
   /**
    * Set the associated dataset for the alignment, or create one.
    * 
    * @param dataset
-   *                The dataset alignment or null to construct one.
+   *          The dataset alignment or null to construct one.
    */
-  public void setDataset(Alignment dataset);
+  void setDataset(AlignmentI 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();
+
+  HiddenSequences getHiddenSequences();
 
-  public HiddenSequences getHiddenSequences();
+  HiddenColumns getHiddenColumns();
 
   /**
    * 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
@@ -279,7 +388,7 @@ public interface AlignmentI
    * @param key
    * @param value
    */
-  public void setProperty(Object key, Object value);
+  void setProperty(Object key, Object value);
 
   /**
    * Get a named property from the alignment.
@@ -287,21 +396,21 @@ public interface AlignmentI
    * @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
@@ -309,61 +418,209 @@ public interface AlignmentI
    * @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();
+  List<AlignedCodonFrame> getCodonFrames();
 
   /**
-   * get a particular codon frame
-   * 
-   * @param index
-   * @return
+   * Set the codon frame mappings (replacing any existing list).
    */
-  public AlignedCodonFrame getCodonFrame(int index);
+  void setCodonFrames(List<AlignedCodonFrame> acfs);
 
   /**
    * get codon frames involving sequenceI
    */
-  public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+  List<AlignedCodonFrame> getCodonFrame(SequenceI seq);
 
   /**
    * find sequence with given name in alignment
    * 
    * @param token
-   *                name to find
+   *          name to find
    * @param b
-   *                true implies that case insensitive matching will
-   *                <em>also</em> be tried
+   *          true implies that case insensitive matching will <em>also</em> be
+   *          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
    * sequence
    * 
    * @param startAfter
-   *                the sequence after which the search will be started (usually
-   *                the result of the last call to findName)
+   *          the sequence after which the search will be started (usually the
+   *          result of the last call to findName)
    * @param token
-   *                name to find
+   *          name to find
    * @param b
-   *                true implies that case insensitive matching will
-   *                <em>also</em> be tried
+   *          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);
+  SequenceI findName(SequenceI startAfter, String token, boolean b);
 
   /**
-   * find first sequence in alignment which is involved in the given search result object
+   * 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);
+  int findIndex(SearchResultsI 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.
+   */
+  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
+   */
+  boolean justify(boolean right);
+
+  /**
+   * add given annotation row at given position (0 is start, -1 is end)
+   * 
+   * @param consensus
+   * @param 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();
+
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  int realiseMappings(List<SequenceI> seqs);
+
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+
+  /**
+   * Set the hidden columns collection on the alignment. Answers true if the
+   * hidden column selection changed, else false.
+   * 
+   * @param cols
+   * @return
+   */
+  public boolean setHiddenColumns(HiddenColumns cols);
+
+  /**
+   * Set the first sequence as representative and hide its insertions. Typically
+   * used when loading JPred files.
+   */
+  public void setupJPredAlignment();
+
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @param input
+   *          alignment view where sequence corresponding to profileseq is first
+   *          entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input);
 }