X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=975f9facf8100307be69035eb9986ab74ca132c1;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=9f1334286e5aede03cb3e517e9cc4acd4926f4aa;hpb=2ac096ecd8ee1a5c11480e864fce7cf78d661c66;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 9f13342..975f9fa 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,20 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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
+ * 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;
@@ -23,7 +23,7 @@ import java.util.*;
/**
* 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
@@ -37,26 +37,33 @@ public interface AlignmentI
*
* @return Greatest sequence length within alignment.
*/
+ @Override
public int getWidth();
/**
- * Calculates if this set of sequences (visible and invisible) are 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();
+
/**
* 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
+ *
+ * @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
+ * Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
*/
- public Vector getSequences();
+ @Override
+ public List getSequences();
/**
* Gets sequences as a SequenceI[]
@@ -69,7 +76,7 @@ public interface AlignmentI
* Find a specific sequence in this alignment.
*
* @param i
- * Index of required sequence.
+ * Index of required sequence.
*
* @return SequenceI at given index.
*/
@@ -79,7 +86,7 @@ public interface AlignmentI
* 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);
@@ -87,9 +94,9 @@ public interface AlignmentI
* 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.
* @param seq
- * New sequence to be inserted.
+ * New sequence to be inserted.
*/
public void setSequenceAt(int i, SequenceI seq);
@@ -97,7 +104,7 @@ public interface AlignmentI
* Deletes a sequence from the alignment
*
* @param s
- * Sequence to be deleted.
+ * Sequence to be deleted.
*/
public void deleteSequence(SequenceI s);
@@ -105,7 +112,7 @@ public interface AlignmentI
* Deletes a sequence from the alignment.
*
* @param i
- * Index of sequence to be deleted.
+ * Index of sequence to be deleted.
*/
public void deleteSequence(int i);
@@ -113,7 +120,7 @@ public interface AlignmentI
* 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.
*/
@@ -125,7 +132,7 @@ public interface AlignmentI
* 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
*/
@@ -135,7 +142,7 @@ public interface AlignmentI
* Finds group that given sequence is part of.
*
* @param s
- * Sequence in alignment.
+ * Sequence in alignment.
*
* @return First group found for sequence. WARNING : Sequences may be members
* of several groups. This method is incomplete.
@@ -146,7 +153,7 @@ public interface AlignmentI
* Finds all groups that a given sequence is part of.
*
* @param s
- * Sequence in alignment.
+ * Sequence in alignment.
*
* @return All groups containing given sequence.
*/
@@ -156,7 +163,7 @@ public interface AlignmentI
* Adds a new SequenceGroup to this alignment.
*
* @param sg
- * New group to be added.
+ * New group to be added.
*/
public void addGroup(SequenceGroup sg);
@@ -164,16 +171,16 @@ public interface AlignmentI
* Deletes a specific SequenceGroup
*
* @param g
- * Group will be deleted from alignment.
+ * 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 List getGroups();
/**
* Deletes all groups from this alignment.
@@ -192,36 +199,54 @@ public interface AlignmentI
* 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);
/**
* 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
+ * the annotation to delete
* @return true if annotation was deleted from this alignment.
*/
public boolean deleteAnnotation(AlignmentAnnotation aa);
/**
- * Get the annotation associated with this alignment
+ * 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
*/
+ @Override
public 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);
@@ -240,6 +265,13 @@ public interface AlignmentI
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
*
*/
@@ -257,7 +289,7 @@ public interface AlignmentI
* 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);
@@ -340,10 +372,10 @@ public interface AlignmentI
* find sequence with given name in alignment
*
* @param token
- * name to find
+ * name to find
* @param b
- * true implies that case insensitive matching will
- * also be tried
+ * true implies that case insensitive matching will also be
+ * tried
* @return matched sequence or null
*/
public SequenceI findName(String token, boolean b);
@@ -353,19 +385,21 @@ public interface AlignmentI
* 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
- * also be tried
+ * true implies that case insensitive matching will also 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
+ * find first sequence in alignment which is involved in the given search
+ * result object
+ *
* @param results
* @return -1 or index of sequence in alignment
*/
@@ -373,25 +407,73 @@ public interface AlignmentI
/**
* 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.
+ * 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
+ * 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 map, boolean up);
+
+ /**
+ * validate annotation after an edit and update any alignment state flags accordingly
+ * @param alignmentAnnotation
+ */
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
}