X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=64a21dd44919f5961a2af6f9e44d11ef423855e0;hb=50a8dcccc09f983c21f0c9a8a3653c379c348a4b;hp=f16c009d1e7a1c848a5a4ca14fdf140431e422a8;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index f16c009..64a21dd 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,82 +1,279 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 jalview.jbgui.*; - -import java.awt.*; - -import java.util.Vector; - - -public interface SequenceI { - public void setName(String name); - - public String getName(); - - public void setStart(int start); - - public int getStart(); - - public String getDisplayId(); - - public void setEnd(int end); - - public int getEnd(); - - public int getLength(); - - public void setSequence(String sequence); - - public String getSequence(); - - public String getSequence(int start, int end); - - public char getCharAt(int i); - - public void setDescription(String desc); - - public String getDescription(); - - public int findIndex(int pos); - - public int findPosition(int i); - - public int[] gapMap(); - - public void deleteChars(int i, int j); - - public void deleteCharAt(int i); - - public void insertCharAt(int i, char c); - - public void insertCharAt(int i, char c, boolean chop); - - public void setColor(Color c); - - public Color getColor(); - - public Vector getSequenceFeatures(); - - public void setSequenceFeatures(Vector v); - - public void setPDBId(String id); - - public String getPDBId(); -} +/* + * 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.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public interface SequenceI +{ + /** + * DOCUMENT ME! + * + * @param name DOCUMENT ME! + */ + public void setName(String name); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getName(); + + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + */ + public void setStart(int start); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStart(); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getDisplayId(boolean jvsuffix); + + /** + * DOCUMENT ME! + * + * @param end DOCUMENT ME! + */ + public void setEnd(int end); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEnd(); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getLength(); + + /** + * DOCUMENT ME! + * + * @param sequence DOCUMENT ME! + */ + public void setSequence(String sequence); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getSequenceAsString(); + + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getSequenceAsString(int start, int end); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char[] getSequence(); + + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char[] getSequence(int start, int end); + + /** + * create a new sequence object from start to end of this sequence + * @param start int + * @param end int + * @return SequenceI + */ + public SequenceI getSubSequence(int start, int end); + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getCharAt(int i); + + /** + * DOCUMENT ME! + * + * @param desc DOCUMENT ME! + */ + public void setDescription(String desc); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getDescription(); + + /** + * DOCUMENT ME! + * + * @param pos DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int findIndex(int pos); + + /** + * Returns the sequence position for an alignment position + * + * @param i column index in alignment (from 1) + * + * @return residue number for residue (left of and) nearest ith column + */ + public int findPosition(int i); + + /** + * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment + * + * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object + */ + public int[] gapMap(); + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param j DOCUMENT ME! + */ + public void deleteChars(int i, int j); + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param c DOCUMENT ME! + */ + public void insertCharAt(int i, char c); + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param c DOCUMENT ME! + */ + public void insertCharAt(int i, int length, char c); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceFeature[] getSequenceFeatures(); + + /** + * DOCUMENT ME! + * + * @param v DOCUMENT ME! + */ + public void setSequenceFeatures(SequenceFeature[] features); + + /** + * DOCUMENT ME! + * + * @param id DOCUMENT ME! + */ + public void setPDBId(Vector ids); + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Vector getPDBId(); + + public void addPDBId(PDBEntry entry); + + public String getVamsasId(); + + public void setVamsasId(String id); + + public void setDBRef(DBRefEntry[] dbs); + + public DBRefEntry[] getDBRef(); + + public void addDBRef(DBRefEntry entry); + + public void addSequenceFeature(SequenceFeature sf); + + public void deleteFeature(SequenceFeature sf); + + public void setDatasetSequence(SequenceI seq); + + public SequenceI getDatasetSequence(); + + public AlignmentAnnotation[] getAnnotation(); + + public void addAlignmentAnnotation(AlignmentAnnotation annotation); + + public void removeAlignmentAnnotation(AlignmentAnnotation annotation); + + /** + * Derive a sequence (using this one's dataset or as the dataset) + * @return duplicate sequence with valid dataset sequence + */ + public SequenceI deriveSequence(); + /** + * set the array of associated AlignmentAnnotation for this sequenceI + * @param revealed + */ + public void setAlignmentAnnotation(AlignmentAnnotation[] annotation); + /** + * Get one or more alignment annotations with a particular label. + * @param label string which each returned annotation must have as a label. + * @return null or array of annotations. + */ + public AlignmentAnnotation[] getAnnotation(String label); + +}