/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
import java.util.*;
-import java.awt.*;
-
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String getSequence();
+ public String getSequenceAsString();
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String getSequence(int start, int end);
+ 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
public int findIndex(int pos);
/**
- * DOCUMENT ME!
+ * Returns the sequence position for an alignment position
*
- * @param i DOCUMENT ME!
+ * @param i column index in alignment (from 1)
*
- * @return DOCUMENT ME!
+ * @return residue number for residue (left of and) nearest ith column
*/
public int findPosition(int i);
/**
- * DOCUMENT ME!
+ * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
*
- * @return DOCUMENT ME!
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
*/
public int[] gapMap();
*/
public void deleteChars(int i, int j);
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i);
/**
* DOCUMENT ME!
*/
public void insertCharAt(int i, char c);
-
/**
* DOCUMENT ME!
*
+ * @param i DOCUMENT ME!
* @param c DOCUMENT ME!
*/
- public void setColor(Color c);
+ public void insertCharAt(int i, int length, char c);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor();
/**
* DOCUMENT ME!
public void addSequenceFeature(SequenceFeature sf);
+ public void deleteFeature(SequenceFeature sf);
+
public void setDatasetSequence(SequenceI seq);
public SequenceI getDatasetSequence();
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
- public SequenceGroup getHiddenSequences();
-
- public void addHiddenSequence(SequenceI seq);
-
- public void showHiddenSequence(SequenceI seq);
-
- public void changeCase(boolean toUpper, int start, int end);
-
- public void toggleCase(int start, int end);
-
- /**
- * getSubSequence from start to end of sequence
- * @param start first residue in subSequence
- * @return SequenceI
- */
- public SequenceI getSubSequence(int start);
- /**
- * remove all gaps in the sequence
- * @return number of gaps removed
- */
- public int removeGaps();
- /**
- * remove all gaps from start to end columns in sequence
- * @param start
- * @param end
- * @return number of gaps removed
- */
- public int removeGaps(int start, int end);
+
+ /**
+ * Derive a sequence (using this one's dataset or as the dataset)
+ * @return duplicate sequence with valid dataset sequence
+ */
+ public SequenceI deriveSequence();
}