-package jalview.datamodel;\r
-\r
-import jalview.jbgui.*;\r
-import java.util.*;\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public interface AlignmentI {\r
-\r
- public int getHeight() ;\r
- public int getWidth() ;\r
- public int getMaxIdLength() ;\r
-\r
- public boolean isAligned();\r
-\r
- public Vector getSequences();\r
- public SequenceI getSequenceAt(int i);\r
-\r
- public void addSequence(SequenceI seq) ;\r
- public void setSequenceAt(int i,SequenceI seq);\r
-\r
- public void deleteSequence(SequenceI s) ;\r
- public void deleteSequence(int i) ;\r
-\r
- public SequenceI[] getColumns(int start, int end) ;\r
- public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ;\r
-\r
- public void deleteColumns(int start, int end) ;\r
- public void deleteColumns(int seq1, int seq2, int start, int end) ;\r
-\r
- public void insertColumns(SequenceI[] seqs, int pos) ;\r
-\r
- public SequenceI findName(String name) ;\r
- public SequenceI findbyDisplayId(String name);\r
-\r
- public int findIndex(SequenceI s) ;\r
-\r
- // Modifying\r
- public void trimLeft(int i) ;\r
- public void trimRight(int i) ;\r
-\r
- public void removeGaps() ;\r
- public Vector removeRedundancy(float threshold, Vector sel) ;\r
-\r
-\r
- // Grouping methods\r
- public SequenceGroup findGroup(int i) ;\r
- public SequenceGroup findGroup(SequenceI s) ;\r
- public SequenceGroup [] findAllGroups(SequenceI s);\r
- public void addToGroup(SequenceGroup g, SequenceI s) ;\r
- public void removeFromGroup(SequenceGroup g,SequenceI s) ;\r
- public void addGroup(SequenceGroup sg) ;\r
- public void deleteGroup(SequenceGroup g) ;\r
- public Vector getGroups();\r
- public void deleteAllGroups();\r
-\r
- public void addSuperGroup(SuperGroup sg);\r
- public void removeSuperGroup(SuperGroup sg);\r
- public SuperGroup getSuperGroup(SequenceGroup sg);\r
-\r
- // Sorting\r
- public void sortGroups() ;\r
- public void sortByPID(SequenceI s) ;\r
- public void sortByID() ;\r
-\r
- public void setGapCharacter(char gc);\r
- public char getGapCharacter();\r
-\r
- public Vector getAAFrequency();\r
-}\r
-\r
-\r
-\r
+/*
+ * 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
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+/** Data structure to hold and manipulate a multiple sequence alignment
+ */
+public interface AlignmentI
+{
+ /**
+ * 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.
+ */
+ public int getWidth();
+
+ /**
+ * Calculates if this set of sequences is all the same length
+ *
+ * @return true if all sequences in alignment are the same length
+ */
+ public boolean isAligned();
+
+ /**
+ * Gets sequences as a Vector
+ *
+ * @return All sequences in alignment.
+ */
+ public Vector 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.
+ *
+ * @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 New sequence to be inserted.
+ */
+ public void setSequenceAt(int i, SequenceI seq);
+
+ /**
+ * Deletes a sequence from the alignment
+ *
+ * @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.
+ */
+ public void deleteSequence(int i);
+
+ /**
+ * 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);
+
+ public SequenceI[] findSequenceMatch(String name);
+
+ /**
+ * Finds index of a given sequence in the alignment.
+ *
+ * @param s Sequence to look for.
+ *
+ * @return Index of sequence within the alignment.
+ */
+ 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.
+ */
+ public SequenceGroup findGroup(SequenceI s);
+
+ /**
+ * 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.
+ */
+ public void addGroup(SequenceGroup sg);
+
+ /**
+ * Deletes a specific SequenceGroup
+ *
+ * @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.
+ */
+ public Vector getGroups();
+
+ /**
+ * Deletes all groups from this alignment.
+ */
+ public void deleteAllGroups();
+
+ /**
+ * Adds a new AlignmentAnnotation to this alignment
+ */
+ public void addAnnotation(AlignmentAnnotation aa);
+
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);
+
+ /**
+ * Deletes a specific AlignmentAnnotation from the alignment.
+ *
+ * @param aa DOCUMENT ME!
+ */
+ public void deleteAnnotation(AlignmentAnnotation aa);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gc DOCUMENT ME!
+ */
+ public void setGapCharacter(char gc);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter();
+
+ /**
+ * Returns true if alignment is nucleotide sequence
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean isNucleotide();
+
+ /**
+ * Set true if the alignment is a nucleotide sequence
+ *
+ * @return
+ */
+ public void setNucleotide(boolean b);
+
+ public Alignment getDataset();
+
+ 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();
+
+ public HiddenSequences getHiddenSequences();
+
+ /**
+ * Compact representation of alignment
+ * @return CigarArray
+ */
+ public CigarArray getCompactAlignment();
+}
git://source.jalview.org / jalview.git / blobdiff