X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=0842d94801128a4a74762077dd7365b82f822cee;hb=6bfaf3d3a82e4eece77dc1c2d83aede7c4dbb690;hp=75b17eb9f37d1ac092389bc08e64de454c47f3dd;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 75b17eb..0842d94 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,57 +1,274 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
-import jalview.jbgui.*;
+import java.util.*;
+
 import java.awt.*;
 
-import java.util.Vector;
 
-public interface SequenceI {
-  public void        setName(String name);
-  public String      getName();
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public interface SequenceI
+{
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName();
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
+    public void setStart(int start);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStart();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId(boolean jvsuffix);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
+    public void setEnd(int end);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getLength();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sequence DOCUMENT ME!
+     */
+    public void setSequence(String sequence);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence(int start, int end);
+    /**
+     * create a new sequence object from start to end of this sequence
+     * @param start int
+     * @param end int
+     * @return SequenceI
+     */
+    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();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findIndex(int pos);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findPosition(int i);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] gapMap();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void deleteChars(int i, int j);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteCharAt(int i);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c);
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(Color c);
 
-  public void        setStart(int start);
-  public int         getStart();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getColor();
 
-  public String      getDisplayId();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceFeature[] getSequenceFeatures();
 
-  public void        setEnd(int end);
-  public int         getEnd();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
+    public void setSequenceFeatures(SequenceFeature [] features);
 
-  public int         getLength();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(Vector ids);
 
-  public void        setSequence(String sequence);
-  public String      getSequence();
-  public String      getSequence(int start,int end);
-  public char        getCharAt(int i);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getPDBId();
 
-  public void        setDescription(String desc);
-  public String      getDescription();
+    public void addPDBId(PDBEntry entry);
 
-  public int         findIndex(int pos);
-  public int         findPosition(int i);
+    public String getVamsasId();
 
-  public void       deleteCharAt(int i);
-  public void       insertCharAt(int i, char c);
-  public void       insertCharAt(int i,char c,boolean chop);
+    public void setVamsasId(String id);
 
-  public void        setColor(Color c);
-  public Color       getColor();
+    public void setDBRef(DBRefEntry[] dbs);
 
-  public Vector     getSequenceFeatures();
-  public void       setSequenceFeatures(Vector v);
+    public DBRefEntry [] getDBRef();
 
-  public void setPDBId(String id);
-  public String getPDBId();
+    public void addDBRef(DBRefEntry entry);
 
-  }
+    public void addSequenceFeature(SequenceFeature sf);
 
+    public void setDatasetSequence(SequenceI seq);
 
+    public SequenceI getDatasetSequence();
 
+    public AlignmentAnnotation [] getAnnotation();
 
+    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);
 
+}