X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=2190fa83ed649f9d70524663531e37c1684e1485;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=d09c41d4b49fbcf4d0143fec5f373911363dbb50;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index d09c41d..2190fa8 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,19 +1,20 @@
 /*
- * 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
- *
+ * 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
+ * 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
+ *  
+ * 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;
 
@@ -26,14 +27,14 @@ public interface AlignmentI extends AnnotatedCollectionI
 {
   /**
    * 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
@@ -42,14 +43,14 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * 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
@@ -58,7 +59,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Gets sequences as a Synchronized collection
-   *
+   * 
    * @return All sequences in alignment.
    */
   @Override
@@ -66,33 +67,32 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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
@@ -102,7 +102,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Deletes a sequence from the alignment
-   *
+   * 
    * @param s
    *          Sequence to be deleted.
    */
@@ -110,7 +110,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Deletes a sequence from the alignment.
-   *
+   * 
    * @param i
    *          Index of sequence to be deleted.
    */
@@ -118,10 +118,10 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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);
@@ -130,20 +130,20 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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.
    */
@@ -151,17 +151,17 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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.
    */
@@ -169,7 +169,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Deletes a specific SequenceGroup
-   *
+   * 
    * @param g
    *          Group will be deleted from alignment.
    */
@@ -177,7 +177,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Get all the groups associated with this alignment.
-   *
+   * 
    * @return All groups as a list.
    */
   public List<SequenceGroup> getGroups();
@@ -189,7 +189,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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.
    */
@@ -197,7 +197,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * moves annotation to a specified index in alignment annotation display stack
-   *
+   * 
    * @param aa
    *          the annotation object to be moved
    * @param index
@@ -210,7 +210,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 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.
@@ -222,7 +222,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 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
@@ -236,7 +236,7 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * 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
@@ -244,7 +244,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Change the gap character used in this alignment to 'gc'
-   *
+   * 
    * @param gc
    *          the new gap character.
    */
@@ -252,34 +252,34 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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.
    */
@@ -287,7 +287,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Set the associated dataset for the alignment, or create one.
-   *
+   * 
    * @param dataset
    *          The dataset alignment or null to construct one.
    */
@@ -295,7 +295,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * pads sequences with gaps (to ensure the set looks like an alignment)
-   *
+   * 
    * @return boolean true if alignment was modified
    */
   public boolean padGaps();
@@ -304,7 +304,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Compact representation of alignment
-   *
+   * 
    * @return CigarArray
    */
   public CigarArray getCompactAlignment();
@@ -312,7 +312,7 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * 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
    */
@@ -320,7 +320,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Get a named property from the alignment.
-   *
+   * 
    * @param key
    * @return value of property
    */
@@ -328,21 +328,21 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 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.
    */
@@ -350,14 +350,14 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * get all codon frames associated with this alignment
-   *
+   * 
    * @return
    */
   public AlignedCodonFrame[] getCodonFrames();
 
   /**
    * get a particular codon frame
-   *
+   * 
    * @param index
    * @return
    */
@@ -370,7 +370,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * find sequence with given name in alignment
-   *
+   * 
    * @param token
    *          name to find
    * @param b
@@ -383,7 +383,7 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * 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)
@@ -399,7 +399,7 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * find first sequence in alignment which is involved in the given search
    * result object
-   *
+   * 
    * @param results
    * @return -1 or index of sequence in alignment
    */
@@ -412,7 +412,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 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.
    */
@@ -421,7 +421,7 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * 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
@@ -430,7 +430,7 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * add given annotation row at given position (0 is start, -1 is end)
-   *
+   * 
    * @param consensus
    * @param i
    */
@@ -438,19 +438,31 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * search for or create a specific annotation row on the alignment
-   *
-   * @param method - CalcId for the annotation (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 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, boolean autoCalc,
-          SequenceI seqRef, SequenceGroup groupRef);
+  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.
+   * 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
@@ -458,4 +470,10 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   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);
 }