X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=2190fa83ed649f9d70524663531e37c1684e1485;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=3e9e265efde038461f63eea0435003629296e119;hpb=c39e588784c0fbb64c7dabfcae8db4faedde10e6;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 3e9e265..2190fa8 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,107 +1,127 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
 import java.util.*;
 
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * 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
+   * 
    * @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 is all the same length
-   *
+   * 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();
 
   /**
-   * 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
+   */
+  public boolean isAligned(boolean includeHidden);
+
+  /**
+   * 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.
-   *
+   * 
+   * @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.
+   * 
+   * @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.
+   * 
+   * @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.
+   * 
+   * @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.
+   * 
+   * @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.
-   *
+   * 
+   * @param name
+   *          Id of sequence to search for.
+   * 
    * @return Sequence matching query, if found. If not found returns null.
    */
   public SequenceI findName(String name);
@@ -110,54 +130,57 @@ public interface AlignmentI
 
   /**
    * Finds index of a given sequence in the alignment.
-   *
-   * @param s Sequence to look for.
-   *
-   * @return Index of sequence within 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.
+   * 
+   * @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.
-   *
+   * 
+   * @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.
+   * 
+   * @param sg
+   *          New group to be added.
    */
   public void addGroup(SequenceGroup sg);
 
   /**
    * Deletes a specific SequenceGroup
-   *
-   * @param g Group will be deleted from alignment.
+   * 
+   * @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.
+   * 
+   * @return All groups as a list.
    */
-  public Vector getGroups();
-
-  public void destroyAlignment();
+  public List<SequenceGroup> getGroups();
 
   /**
    * Deletes all groups from this alignment.
@@ -166,59 +189,113 @@ public interface AlignmentI
 
   /**
    * 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.
-   *
-   * @param aa DOCUMENT ME!
+   * 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 void deleteAnnotation(AlignmentAnnotation aa);
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * 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();
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param gc DOCUMENT ME!
+   * Change the gap character used in this alignment to 'gc'
+   * 
+   * @param gc
+   *          the new gap character.
    */
   public void setGapCharacter(char gc);
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Get the gap character used in this alignment
+   * 
+   * @return gap character
    */
   public char getGapCharacter();
 
   /**
-   * Returns true if alignment is nucleotide sequence
-   *
-   * @return DOCUMENT ME!
+   * Test for all nucleotide alignment
+   * 
+   * @return true if alignment is nucleotide sequence
    */
   public boolean isNucleotide();
 
   /**
-   * Set true if the alignment is a nucleotide sequence
-   *
-   * @return
+   * 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();
@@ -227,7 +304,176 @@ public interface AlignmentI
 
   /**
    * 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);
+
+  /**
+   * 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
+   */
+  public 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
+   */
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up);
+
+  /**
+   * validate annotation after an edit and update any alignment state flags accordingly
+   * @param alignmentAnnotation
+   */
+  public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
 }