-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 SequenceGroup getHiddenSequences();
-
- public void addHiddenSequence(SequenceI seq);
-
- public void showHiddenSequence(SequenceI seq);
-
- /**
- * Derive a sequence (using this one's dataset or as the dataset)
- * @return duplicate sequence with valid dataset sequence
- */
- public SequenceI deriveSequence();
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
+ * Copyright (C) 2014 The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.datamodel;\r
+\r
+import java.util.Vector;\r
+\r
+import fr.orsay.lri.varna.models.rna.RNA;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public interface SequenceI\r
+{\r
+ /**\r
+ * Set the display name for the sequence\r
+ * \r
+ * @param name\r
+ */\r
+ public void setName(String name);\r
+\r
+ /**\r
+ * Get the display name\r
+ */\r
+ public String getName();\r
+\r
+ /**\r
+ * Set start position of first non-gapped symbol in sequence\r
+ * \r
+ * @param start\r
+ * new start position\r
+ */\r
+ public void setStart(int start);\r
+\r
+ /**\r
+ * get start position of first non-gapped residue in sequence\r
+ * \r
+ * @return\r
+ */\r
+ public int getStart();\r
+\r
+ /**\r
+ * get the displayed id of the sequence\r
+ * \r
+ * @return true means the id will be returned in the form\r
+ * DisplayName/Start-End\r
+ */\r
+ public String getDisplayId(boolean jvsuffix);\r
+\r
+ /**\r
+ * set end position for last residue in sequence\r
+ * \r
+ * @param end\r
+ */\r
+ public void setEnd(int end);\r
+\r
+ /**\r
+ * get end position for last residue in sequence getEnd()>getStart() unless\r
+ * sequence only consists of gap characters\r
+ * \r
+ * @return\r
+ */\r
+ public int getEnd();\r
+\r
+ /**\r
+ * @return length of sequence including gaps\r
+ * \r
+ */\r
+ public int getLength();\r
+\r
+ /**\r
+ * Replace the sequence with the given string\r
+ * \r
+ * @param sequence\r
+ * new sequence string\r
+ */\r
+ public void setSequence(String sequence);\r
+\r
+ /**\r
+ * @return sequence as string\r
+ */\r
+ public String getSequenceAsString();\r
+\r
+ /**\r
+ * get a range on the sequence as a string\r
+ * \r
+ * @param start\r
+ * position relative to start of sequence including gaps (from 0)\r
+ * @param end\r
+ * position relative to start of sequence including gaps (from 0)\r
+ * \r
+ * @return String containing all gap and symbols in specified range\r
+ */\r
+ public String getSequenceAsString(int start, int end);\r
+\r
+ /**\r
+ * Get the sequence as a character array\r
+ * \r
+ * @return seqeunce and any gaps\r
+ */\r
+ public char[] getSequence();\r
+\r
+ /**\r
+ * get stretch of sequence characters in an array\r
+ * \r
+ * @param start\r
+ * absolute index into getSequence()\r
+ * @param end\r
+ * exclusive index of last position in segment to be returned.\r
+ * \r
+ * @return char[max(0,end-start)];\r
+ */\r
+ public char[] getSequence(int start, int end);\r
+\r
+ /**\r
+ * create a new sequence object from start to end of this sequence\r
+ * \r
+ * @param start\r
+ * int\r
+ * @param end\r
+ * int\r
+ * @return SequenceI\r
+ */\r
+ public SequenceI getSubSequence(int start, int end);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param i\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getCharAt(int i);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param desc\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setDescription(String desc);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription();\r
+\r
+ /**\r
+ * Return the alignment column for a sequence position * Return the alignment\r
+ * position for a sequence position\r
+ * \r
+ * @param pos\r
+ * lying from start to end\r
+ * \r
+ * @return aligned column for residue (0 if residue is upstream from\r
+ * alignment, -1 if residue is downstream from alignment) note.\r
+ * Sequence object returns sequence.getEnd() for positions upstream\r
+ * currently. TODO: change sequence for\r
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs\r
+ * \r
+ */\r
+ public int findIndex(int pos);\r
+\r
+ /**\r
+ * Returns the sequence position for an alignment position\r
+ * \r
+ * @param i\r
+ * column index in alignment (from 1)\r
+ * \r
+ * @return residue number for residue (left of and) nearest ith column\r
+ */\r
+ public int findPosition(int i);\r
+\r
+ /**\r
+ * Returns an int array where indices correspond to each residue in the\r
+ * sequence and the element value gives its position in the alignment\r
+ * \r
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no\r
+ * residues in SequenceI object\r
+ */\r
+ public int[] gapMap();\r
+\r
+ /**\r
+ * Returns an int array where indices correspond to each position in sequence\r
+ * char array and the element value gives the result of findPosition for that\r
+ * index in the sequence.\r
+ * \r
+ * @return int[SequenceI.getLength()]\r
+ */\r
+ public int[] findPositionMap();\r
+\r
+ /**\r
+ * Delete a range of aligned sequence columns, creating a new dataset sequence\r
+ * if necessary and adjusting start and end positions accordingly.\r
+ * \r
+ * @param i\r
+ * first column in range to delete\r
+ * @param j\r
+ * last column in range to delete\r
+ */\r
+ public void deleteChars(int i, int j);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param i\r
+ * DOCUMENT ME!\r
+ * @param c\r
+ * DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, char c);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param i\r
+ * DOCUMENT ME!\r
+ * @param c\r
+ * DOCUMENT ME!\r
+ */\r
+ public void insertCharAt(int i, int length, char c);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceFeature[] getSequenceFeatures();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param v\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(SequenceFeature[] features);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param id\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setPDBId(Vector ids);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getPDBId();\r
+\r
+ /**\r
+ * add entry to the vector of PDBIds, if it isn't in the list already\r
+ * \r
+ * @param entry\r
+ */\r
+ public void addPDBId(PDBEntry entry);\r
+\r
+ /**\r
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural\r
+ * databases\r
+ * \r
+ * @return true if PDBEntry list was modified\r
+ */\r
+ public boolean updatePDBIds();\r
+\r
+ public String getVamsasId();\r
+\r
+ public void setVamsasId(String id);\r
+\r
+ public void setDBRef(DBRefEntry[] dbs);\r
+\r
+ public DBRefEntry[] getDBRef();\r
+\r
+ /**\r
+ * add the given entry to the list of DBRefs for this sequence, or replace a\r
+ * similar one if entry contains a map object and the existing one doesnt.\r
+ * \r
+ * @param entry\r
+ */\r
+ public void addDBRef(DBRefEntry entry);\r
+\r
+ public void addSequenceFeature(SequenceFeature sf);\r
+\r
+ public void deleteFeature(SequenceFeature sf);\r
+\r
+ public void setDatasetSequence(SequenceI seq);\r
+\r
+ public SequenceI getDatasetSequence();\r
+\r
+ public AlignmentAnnotation[] getAnnotation();\r
+\r
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+ /**\r
+ * Derive a sequence (using this one's dataset or as the dataset)\r
+ * \r
+ * @return duplicate sequence with valid dataset sequence\r
+ */\r
+ public SequenceI deriveSequence();\r
+\r
+ /**\r
+ * set the array of associated AlignmentAnnotation for this sequenceI\r
+ * \r
+ * @param revealed\r
+ */\r
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);\r
+\r
+ /**\r
+ * Get one or more alignment annotations with a particular label.\r
+ * \r
+ * @param label\r
+ * string which each returned annotation must have as a label.\r
+ * @return null or array of annotations.\r
+ */\r
+ public AlignmentAnnotation[] getAnnotation(String label);\r
+\r
+ /**\r
+ * create a new dataset sequence (if necessary) for this sequence and sets\r
+ * this sequence to refer to it. This call will move any features or\r
+ * references on the sequence onto the dataset. It will also make a duplicate\r
+ * of existing annotation rows for the dataset sequence, rather than relocate\r
+ * them in order to preserve external references (since 2.8.2).\r
+ * \r
+ * @return dataset sequence for this sequence\r
+ */\r
+ public SequenceI createDatasetSequence();\r
+\r
+ /**\r
+ * Transfer any database references or annotation from entry under a sequence\r
+ * mapping. <br/>\r
+ * <strong>Note: DOES NOT transfer sequence associated alignment\r
+ * annotation </strong><br/>\r
+ * \r
+ * @param entry\r
+ * @param mp\r
+ * null or mapping from entry's numbering to local start/end\r
+ */\r
+ public void transferAnnotation(SequenceI entry, Mapping mp);\r
+\r
+ /**\r
+ * @param index\r
+ * The sequence index in the MSA\r
+ */\r
+ public void setIndex(int index);\r
+\r
+ /**\r
+ * @return The index of the sequence in the alignment\r
+ */\r
+ public int getIndex();\r
+\r
+ /**\r
+ * @return The RNA of the sequence in the alignment\r
+ */\r
+\r
+ public RNA getRNA();\r
+\r
+ /**\r
+ * @param rna\r
+ * The RNA.\r
+ */\r
+ public void setRNA(RNA rna);\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff