X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=916d785222d04f1ed7be7375dda8d219a5eee26e;hb=c394157681d10261bd6f7883b19eaf88d6784609;hp=9f328ee1134df680a04cfe19b5ff3a9f70a1358e;hpb=4660fcf0745dbc1f6f6e7241b398301f93edb548;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9f328ee..916d785 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,6 +20,9 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
@@ -27,9 +30,6 @@ import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
 
-import jalview.analysis.AlignSeq;
-import jalview.util.StringUtils;
-
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -37,7 +37,7 @@ import jalview.util.StringUtils;
  * @author $author$
  * @version $Revision$
  */
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
 {
   SequenceI datasetSequence;
 
@@ -59,7 +59,6 @@ public class Sequence implements SequenceI
 
   RNA rna;
 
-  private boolean hidden;
 
   /**
    * This annotation is displayed below the alignment but the positions are tied
@@ -92,20 +91,30 @@ public class Sequence implements SequenceI
    */
   public Sequence(String name, String sequence, int start, int end)
   {
-    this.name = name;
-    this.sequence = sequence.toCharArray();
-    this.start = start;
-    this.end = end;
-    parseId();
-    checkValidRange();
+    initSeqAndName(name, sequence.toCharArray(), start, end);
   }
 
   public Sequence(String name, char[] sequence, int start, int end)
   {
-    this.name = name;
-    this.sequence = sequence;
-    this.start = start;
-    this.end = end;
+    initSeqAndName(name, sequence, start, end);
+  }
+
+  /**
+   * Stage 1 constructor - assign name, sequence, and set start and end fields.
+   * start and end are updated values from name2 if it ends with /start-end
+   * 
+   * @param name2
+   * @param sequence2
+   * @param start2
+   * @param end2
+   */
+  protected void initSeqAndName(String name2, char[] sequence2, int start2,
+          int end2)
+  {
+    this.name = name2;
+    this.sequence = sequence2;
+    this.start = start2;
+    this.end = end2;
     parseId();
     checkValidRange();
   }
@@ -198,7 +207,15 @@ public class Sequence implements SequenceI
    */
   public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
   {
-    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    initSeqFrom(seq, alAnnotation);
+
+  }
+
+  protected void initSeqFrom(SequenceI seq,
+          AlignmentAnnotation[] alAnnotation)
+  {
+    initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+            seq.getEnd());
     description = seq.getDescription();
     if (seq.getSequenceFeatures() != null)
     {
@@ -751,7 +768,7 @@ public class Sequence implements SequenceI
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
-    if (i >= sequence.length)
+    if (i >= sequence.length || i < 0)
     {
       return;
     }
@@ -1285,16 +1302,9 @@ public class Sequence implements SequenceI
     return result;
   }
 
-  @Override
-  public boolean isHidden()
-  {
-    return this.hidden;
-  }
-
-  @Override
-  public void setHidden(Boolean hidden)
+  public String toString()
   {
-    this.hidden = hidden;
+    return getDisplayId(false);
   }
 
 }