new SequenceI method for making a sub sequence from a range on the

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index b7c9197..d711788 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -45,6 +45,7 @@ public interface SequenceI
      */\r
     public String getName();\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -64,7 +65,7 @@ public interface SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getDisplayId();\r
+    public String getDisplayId(boolean jvsuffix);\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -110,7 +111,13 @@ public interface SequenceI
      * @return DOCUMENT ME!\r
      */\r
     public String getSequence(int start, int end);\r
-\r
+    /**\r
+     * create a new sequence object from start to end of this sequence\r
+     * @param start int\r
+     * @param end int\r
+     * @return SequenceI\r
+     */\r
+    public SequenceI getSubSequence(int start, int end);\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -182,14 +189,6 @@ public interface SequenceI
      */\r
     public void insertCharAt(int i, char c);\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     * @param c DOCUMENT ME!\r
-     * @param chop DOCUMENT ME!\r
-     */\r
-    public void insertCharAt(int i, char c, boolean chop);\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -210,26 +209,59 @@ public interface SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public Vector getSequenceFeatures();\r
+    public SequenceFeature[] getSequenceFeatures();\r
 \r
     /**\r
      * DOCUMENT ME!\r
      *\r
      * @param v DOCUMENT ME!\r
      */\r
-    public void setSequenceFeatures(Vector v);\r
+    public void setSequenceFeatures(SequenceFeature [] features);\r
 \r
     /**\r
      * DOCUMENT ME!\r
      *\r
      * @param id DOCUMENT ME!\r
      */\r
-    public void setPDBId(String id);\r
+    public void setPDBId(Vector ids);\r
 \r
     /**\r
      * DOCUMENT ME!\r
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getPDBId();\r
+    public Vector getPDBId();\r
+\r
+    public void addPDBId(PDBEntry entry);\r
+\r
+    public String getVamsasId();\r
+\r
+    public void setVamsasId(String id);\r
+\r
+    public void setDBRef(DBRefEntry[] dbs);\r
+\r
+    public DBRefEntry [] getDBRef();\r
+\r
+    public void addDBRef(DBRefEntry entry);\r
+\r
+    public void addSequenceFeature(SequenceFeature sf);\r
+\r
+    public void setDatasetSequence(SequenceI seq);\r
+\r
+    public SequenceI getDatasetSequence();\r
+\r
+    public AlignmentAnnotation [] getAnnotation();\r
+\r
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
+\r
+    public SequenceGroup getHiddenSequences();\r
+\r
+    public void addHiddenSequence(SequenceI seq);\r
+\r
+    public void showHiddenSequence(SequenceI seq);\r
+\r
+    public void changeCase(boolean toUpper, int start, int end);\r
+\r
+    public void toggleCase(int start, int end);\r
+\r
 }\r