Formatted source

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index e48ff36..8a14a08 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -16,81 +16,101 @@
 * along with this program; if not, write to the Free Software\r
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
 */\r
-\r
 package jalview.datamodel;\r
 \r
 import java.util.*;\r
 \r
+\r
 /** Data structure to hold and manipulate a multiple sequence alignment\r
  */\r
 public interface AlignmentI {\r
+    public int getHeight();\r
 \r
-  public int         getHeight() ;\r
-  public int         getWidth() ;\r
-  public int         getMaxIdLength() ;\r
+    public int getWidth();\r
 \r
-  public boolean isAligned();\r
+    public int getMaxIdLength();\r
 \r
-  public Vector      getSequences();\r
-  public SequenceI   getSequenceAt(int i);\r
+    public boolean isAligned();\r
 \r
-  public void        addSequence(SequenceI seq) ;\r
-  public void        setSequenceAt(int i,SequenceI seq);\r
+    public Vector getSequences();\r
 \r
-  public void        deleteSequence(SequenceI s) ;\r
-  public void        deleteSequence(int i) ;\r
+    public SequenceI getSequenceAt(int i);\r
 \r
-  public SequenceI[] getColumns(int start, int end) ;\r
-  public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ;\r
+    public void addSequence(SequenceI seq);\r
 \r
-  public void        deleteColumns(int start, int end) ;\r
-  public void        deleteColumns(int seq1, int seq2, int start, int end) ;\r
+    public void setSequenceAt(int i, SequenceI seq);\r
 \r
-  public void        insertColumns(SequenceI[] seqs, int pos) ;\r
+    public void deleteSequence(SequenceI s);\r
 \r
-  public SequenceI   findName(String name) ;\r
-  public SequenceI   findbyDisplayId(String name);\r
+    public void deleteSequence(int i);\r
 \r
-  public int         findIndex(SequenceI s) ;\r
+    public SequenceI[] getColumns(int start, int end);\r
 \r
-  // Modifying\r
-  public void        trimLeft(int i) ;\r
-  public void        trimRight(int i) ;\r
+    public SequenceI[] getColumns(int seq1, int seq2, int start, int end);\r
 \r
-  public void        removeGaps() ;\r
-  public Vector      removeRedundancy(float threshold, Vector sel) ;\r
+    public void deleteColumns(int start, int end);\r
 \r
+    public void deleteColumns(int seq1, int seq2, int start, int end);\r
 \r
-  // Grouping methods\r
-  public SequenceGroup findGroup(int i) ;\r
-  public SequenceGroup findGroup(SequenceI s) ;\r
-  public SequenceGroup [] findAllGroups(SequenceI s);\r
-  public void          addToGroup(SequenceGroup g, SequenceI s) ;\r
-  public void          removeFromGroup(SequenceGroup g,SequenceI s) ;\r
-  public void          addGroup(SequenceGroup sg) ;\r
-  public void          deleteGroup(SequenceGroup g) ;\r
-  public Vector        getGroups();\r
-  public void deleteAllGroups();\r
+    public void insertColumns(SequenceI[] seqs, int pos);\r
 \r
-  public void          addSuperGroup(SuperGroup sg);\r
-  public void          removeSuperGroup(SuperGroup sg);\r
-  public SuperGroup    getSuperGroup(SequenceGroup sg);\r
+    public SequenceI findName(String name);\r
 \r
-  // Sorting\r
-  public void          sortGroups() ;\r
-  public void          sortByPID(SequenceI s) ;\r
-  public void          sortByID() ;\r
+    public SequenceI findbyDisplayId(String name);\r
 \r
-  //Annotations\r
-  public void addAnnotation(AlignmentAnnotation aa);\r
-  public void deleteAnnotation(AlignmentAnnotation aa);\r
-  public AlignmentAnnotation [] getAlignmentAnnotation();\r
+    public int findIndex(SequenceI s);\r
 \r
-  public void          setGapCharacter(char gc);\r
-  public char          getGapCharacter();\r
+    // Modifying\r
+    public void trimLeft(int i);\r
 \r
-  public Vector        getAAFrequency();\r
-}\r
+    public void trimRight(int i);\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
+    public SequenceGroup findGroup(SequenceI s);\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
+    public void addGroup(SequenceGroup sg);\r
+\r
+    public void deleteGroup(SequenceGroup g);\r
 \r
+    public Vector getGroups();\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
+    public void sortByID();\r
+\r
+    //Annotations\r
+    public void addAnnotation(AlignmentAnnotation aa);\r
+\r
+    public void deleteAnnotation(AlignmentAnnotation aa);\r
+\r
+    public AlignmentAnnotation[] getAlignmentAnnotation();\r
+\r
+    public void setGapCharacter(char gc);\r
+\r
+    public char getGapCharacter();\r
+\r
+    public Vector getAAFrequency();\r
+}\r