X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=975f9facf8100307be69035eb9986ab74ca132c1;hb=066a11f5ce0580b9d7bf0f855432c341aa279bd4;hp=d09c41d4b49fbcf4d0143fec5f373911363dbb50;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index d09c41d..975f9fa 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 2.8.1)
+ * 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 .
+ * 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 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 map, boolean up);
+
+ /**
+ * validate annotation after an edit and update any alignment state flags accordingly
+ * @param alignmentAnnotation
+ */
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
}