+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program 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 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* 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 jalview.jbgui.*;\r
import java.util.*;\r
\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
public int getWidth() ;\r
public int getMaxIdLength() ;\r
\r
+ public boolean isAligned();\r
+\r
public Vector getSequences();\r
public SequenceI getSequenceAt(int i);\r
\r
public void insertColumns(SequenceI[] seqs, int pos) ;\r
\r
public SequenceI findName(String name) ;\r
- public SequenceI findbyDisplayId(String name);\r
+ public SequenceI findbyDisplayId(String name);\r
\r
public int findIndex(SequenceI s) ;\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 SequenceGroup addGroup() ;\r
public void deleteGroup(SequenceGroup g) ;\r
public Vector getGroups();\r
+ public void deleteAllGroups();\r
+\r
+ public void addSuperGroup(SuperGroup sg);\r
+ public void removeSuperGroup(SuperGroup sg);\r
+ public SuperGroup getSuperGroup(SequenceGroup sg);\r
\r
// Sorting\r
public void sortGroups() ;\r
public void sortByPID(SequenceI s) ;\r
public void sortByID() ;\r
\r
+ //Annotations\r
+ public void addAnnotation(AlignmentAnnotation aa);\r
+ public void deleteAnnotation(AlignmentAnnotation aa);\r
+ public AlignmentAnnotation [] getAlignmentAnnotation();\r
+\r
public void setGapCharacter(char gc);\r
public char getGapCharacter();\r
\r
- public Vector getAAFrequency();\r
+ public Vector getAAFrequency();\r
}\r
\r
\r