\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
*/\r
-public interface AlignmentI {\r
+public interface AlignmentI\r
+{\r
+ /**\r
+ * Calculates the number of sequences in an alignment\r
+ *\r
+ * @return Number of sequences in alignment\r
+ */\r
public int getHeight();\r
\r
+ /**\r
+ * Calculates the maximum width of the alignment, including gaps.\r
+ *\r
+ * @return Greatest sequence length within alignment.\r
+ */\r
public int getWidth();\r
\r
+ /**\r
+ * Calculates the longest sequence Id of the alignment\r
+ *\r
+ * @return Number of characters in longest sequence Id.\r
+ */\r
public int getMaxIdLength();\r
\r
+ /**\r
+ * Calculates if this set of sequences is all the same length\r
+ *\r
+ * @return true if all sequences in alignment are the same length\r
+ */\r
public boolean isAligned();\r
\r
+ /**\r
+ * Gets sequences as a Vector\r
+ *\r
+ * @return All sequences in alignment.\r
+ */\r
public Vector getSequences();\r
\r
+ /**\r
+ * Gets sequences as a SequenceI[]\r
+ *\r
+ * @return All sequences in alignment.\r
+ */\r
+ public SequenceI [] getSequencesArray();\r
+\r
+ /**\r
+ * Find a specific sequence in this alignment.\r
+ *\r
+ * @param i Index of required sequence.\r
+ *\r
+ * @return SequenceI at given index.\r
+ */\r
public SequenceI getSequenceAt(int i);\r
\r
+ /**\r
+ * Add a new sequence to this alignment.\r
+ *\r
+ * @param seq New sequence will be added at end of alignment.\r
+ */\r
public void addSequence(SequenceI seq);\r
\r
+ /**\r
+ * Used to set a particular index of the alignment with the given sequence.\r
+ *\r
+ * @param i Index of sequence to be updated.\r
+ * @param seq New sequence to be inserted.\r
+ */\r
public void setSequenceAt(int i, SequenceI seq);\r
\r
+ /**\r
+ * Deletes a sequence from the alignment.\r
+ *\r
+ * @param s Sequence to be deleted.\r
+ */\r
public void deleteSequence(SequenceI s);\r
\r
+ /**\r
+ * Deletes a sequence from the alignment.\r
+ *\r
+ * @param i Index of sequence to be deleted.\r
+ */\r
public void deleteSequence(int i);\r
\r
- public SequenceI[] getColumns(int start, int end);\r
-\r
- public SequenceI[] getColumns(int seq1, int seq2, int start, int end);\r
-\r
+ /**\r
+ * Deletes all residues in every sequence of alignment within given columns.\r
+ *\r
+ * @param start Start index of columns to delete.\r
+ * @param end End index to columns to delete.\r
+ */\r
public void deleteColumns(int start, int end);\r
\r
+ /**\r
+ * Deletes all residues in every sequence of alignment within given columns.\r
+ *\r
+ * @param seq1 Index of first sequence to delete columns from.\r
+ * @param seq2 Index of last sequence to delete columns from.\r
+ * @param start Start index of columns to delete.\r
+ * @param end End index of columns to delete.\r
+ */\r
public void deleteColumns(int seq1, int seq2, int start, int end);\r
\r
- public void insertColumns(SequenceI[] seqs, int pos);\r
-\r
+ /**\r
+ * Finds sequence in alignment using sequence name as query.\r
+ *\r
+ * @param name Id of sequence to search for.\r
+ *\r
+ * @return Sequence matching query, if found. If not found returns null.\r
+ */\r
public SequenceI findName(String name);\r
\r
- public SequenceI findbyDisplayId(String name);\r
\r
+ /**\r
+ * Finds index of a given sequence in the alignment.\r
+ *\r
+ * @param s Sequence to look for.\r
+ *\r
+ * @return Index of sequence within the alignment.\r
+ */\r
public int findIndex(SequenceI s);\r
\r
- // Modifying\r
+ /**\r
+ * All sequences will be cut from beginning to given index.\r
+ *\r
+ * @param i Remove all residues in sequences up to this column.\r
+ */\r
public void trimLeft(int i);\r
\r
+ /**\r
+ * All sequences will be cut from given index.\r
+ *\r
+ * @param i Remove all residues in sequences beyond this column.\r
+ */\r
public void trimRight(int i);\r
\r
+ /**\r
+ * Removes all columns containing entirely gap characters.\r
+ */\r
public void removeGaps();\r
\r
- public Vector removeRedundancy(float threshold, Vector sel);\r
\r
- // Grouping methods\r
- public SequenceGroup findGroup(int i);\r
\r
+ /**\r
+ * Finds group that given sequence is part of.\r
+ *\r
+ * @param s Sequence in alignment.\r
+ *\r
+ * @return First group found for sequence. WARNING :\r
+ * Sequences may be members of several groups. This method is incomplete.\r
+ */\r
public SequenceGroup findGroup(SequenceI s);\r
\r
+ /**\r
+ * Finds all groups that a given sequence is part of.\r
+ *\r
+ * @param s Sequence in alignment.\r
+ *\r
+ * @return All groups containing given sequence.\r
+ */\r
public SequenceGroup[] findAllGroups(SequenceI s);\r
\r
- public void addToGroup(SequenceGroup g, SequenceI s);\r
-\r
- public void removeFromGroup(SequenceGroup g, SequenceI s);\r
-\r
+ /**\r
+ * Adds a new SequenceGroup to this alignment.\r
+ *\r
+ * @param sg New group to be added.\r
+ */\r
public void addGroup(SequenceGroup sg);\r
\r
+ /**\r
+ * Deletes a specific SequenceGroup\r
+ *\r
+ * @param g Group will be deleted from alignment.\r
+ */\r
public void deleteGroup(SequenceGroup g);\r
\r
+ /**\r
+ * Get all the groups associated with this alignment.\r
+ *\r
+ * @return All groups as a Vector.\r
+ */\r
public Vector getGroups();\r
\r
+ /**\r
+ * Deletes all groups from this alignment.\r
+ */\r
public void deleteAllGroups();\r
\r
- public void addSuperGroup(SuperGroup sg);\r
\r
- public void removeSuperGroup(SuperGroup sg);\r
-\r
- public SuperGroup getSuperGroup(SequenceGroup sg);\r
-\r
- // Sorting\r
- public void sortGroups();\r
-\r
- public void sortByPID(SequenceI s);\r
+ /**\r
+ * Adds a new AlignmentAnnotation to this alignment\r
+ */\r
+ public void addAnnotation(AlignmentAnnotation aa);\r
\r
- public void sortByID();\r
\r
- //Annotations\r
- public void addAnnotation(AlignmentAnnotation aa);\r
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
\r
+ /**\r
+ * Deletes a specific AlignmentAnnotation from the alignment.\r
+ *\r
+ * @param aa DOCUMENT ME!\r
+ */\r
public void deleteAnnotation(AlignmentAnnotation aa);\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public AlignmentAnnotation[] getAlignmentAnnotation();\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param gc DOCUMENT ME!\r
+ */\r
public void setGapCharacter(char gc);\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public char getGapCharacter();\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public Vector getAAFrequency();\r
+\r
+ /**\r
+ * Returns true if alignment is nucleotide sequence\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean isNucleotide();\r
+\r
+ /**\r
+ * Set true if the alignment is a nucleotide sequence\r
+ *\r
+ * @return\r
+ */\r
+ public void setNucleotide(boolean b);\r
+\r
+\r
+ public Alignment getDataset();\r
+\r
+ public void setDataset(Alignment dataset);\r
+ /**\r
+ * pads sequences with gaps (to ensure the set looks like an alignment)\r
+ * @return boolean true if alignment was modified\r
+ */\r
+ public boolean padGaps();\r
+\r
+ public void adjustSequenceAnnotations();\r
+\r
+ public HiddenSequences getHiddenSequences();\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff