X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=64a57bae376b10bbfbdf36ed1d56233348679118;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=75b17eb9f37d1ac092389bc08e64de454c47f3dd;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 75b17eb..64a57ba 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,57 +1,406 @@
-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 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 (Version 2.8.2b1)
+ * 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
+ * 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.List;
+import java.util.Vector;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public interface SequenceI
+{
+ /**
+ * Set the display name for the sequence
+ *
+ * @param name
+ */
+ public void setName(String name);
+
+ /**
+ * Get the display name
+ */
+ public String getName();
+
+ /**
+ * Set start position of first non-gapped symbol in sequence
+ *
+ * @param start
+ * new start position
+ */
+ public void setStart(int start);
+
+ /**
+ * get start position of first non-gapped residue in sequence
+ *
+ * @return
+ */
+ public int getStart();
+
+ /**
+ * get the displayed id of the sequence
+ *
+ * @return true means the id will be returned in the form
+ * DisplayName/Start-End
+ */
+ public String getDisplayId(boolean jvsuffix);
+
+ /**
+ * set end position for last residue in sequence
+ *
+ * @param end
+ */
+ public void setEnd(int end);
+
+ /**
+ * get end position for last residue in sequence getEnd()>getStart() unless
+ * sequence only consists of gap characters
+ *
+ * @return
+ */
+ public int getEnd();
+
+ /**
+ * @return length of sequence including gaps
+ *
+ */
+ public int getLength();
+
+ /**
+ * Replace the sequence with the given string
+ *
+ * @param sequence
+ * new sequence string
+ */
+ public void setSequence(String sequence);
+
+ /**
+ * @return sequence as string
+ */
+ public String getSequenceAsString();
+
+ /**
+ * get a range on the sequence as a string
+ *
+ * @param start
+ * position relative to start of sequence including gaps (from 0)
+ * @param end
+ * position relative to start of sequence including gaps (from 0)
+ *
+ * @return String containing all gap and symbols in specified range
+ */
+ public String getSequenceAsString(int start, int end);
+
+ /**
+ * Get the sequence as a character array
+ *
+ * @return seqeunce and any gaps
+ */
+ public char[] getSequence();
+
+ /**
+ * get stretch of sequence characters in an array
+ *
+ * @param start
+ * absolute index into getSequence()
+ * @param end
+ * exclusive index of last position in segment to be returned.
+ *
+ * @return char[max(0,end-start)];
+ */
+ public char[] getSequence(int start, int end);
+
+ /**
+ * create a new sequence object from start to end of this sequence
+ *
+ * @param start
+ * int index for start position
+ * @param end
+ * int index for end position
+ *
+ * @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
+ */
+ 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();
+
+ /**
+ * Return the alignment column for a sequence position * Return the alignment
+ * position for a sequence position
+ *
+ * @param pos
+ * lying from start to end
+ *
+ * @return aligned column for residue (0 if residue is upstream from
+ * alignment, -1 if residue is downstream from alignment) note.
+ * Sequence object returns sequence.getEnd() for positions upstream
+ * currently. TODO: change sequence for
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+ *
+ */
+ public int findIndex(int pos);
+
+ /**
+ * Returns the sequence position for an alignment position
+ *
+ * @param i
+ * column index in alignment (from 0.. getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
+ * create a new dataset sequence (if necessary) for this sequence and sets
+ * this sequence to refer to it. This call will move any features or
+ * references on the sequence onto the dataset. It will also make a duplicate
+ * of existing annotation rows for the dataset sequence, rather than relocate
+ * them in order to preserve external references (since 2.8.2).
+ *
+ * @return dataset sequence for this sequence
+ */
+ public SequenceI createDatasetSequence();
+
+ /**
+ * Transfer any database references or annotation from entry under a sequence
+ * mapping.
+ * Note: DOES NOT transfer sequence associated alignment
+ * annotation
+ *
+ * @param entry
+ * @param mp
+ * null or mapping from entry's numbering to local start/end
+ */
+ public void transferAnnotation(SequenceI entry, Mapping mp);
+
+ /**
+ * @param index
+ * The sequence index in the MSA
+ */
+ public void setIndex(int index);
+
+ /**
+ * @return The index of the sequence in the alignment
+ */
+ public int getIndex();
+
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna
+ * The RNA.
+ */
+ public void setRNA(RNA rna);
+
+}