featuresAdded = false

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 0875450..5adb70d 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -13,6 +13,7 @@ public class Alignment implements AlignmentI
   protected Vector      groups = new Vector();\r
   protected ArrayList   superGroup = new ArrayList();\r
   protected char        gapCharacter = '-';\r
+  public boolean featuresAdded = false;\r
 \r
   /** Make an alignment from an array of Sequences.\r
   *\r
@@ -40,14 +41,11 @@ public class Alignment implements AlignmentI
   }\r
 \r
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.\r
-   * Should put the new sequence in a sequence group!!!\r
    *\r
    * @param snew\r
    */\r
   public void addSequence(SequenceI snew) {\r
     sequences.addElement(snew);\r
-\r
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);\r
   }\r
 \r
   public void addSequence(SequenceI[] seq) {\r
@@ -57,8 +55,7 @@ public class Alignment implements AlignmentI
   }\r
 \r
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.\r
-   * Should put the new sequence in a sequence group!!!\r
-   *\r
+    *\r
    * @param snew\r
    */\r
   public void setSequenceAt(int i,SequenceI snew) {\r
@@ -66,8 +63,6 @@ public class Alignment implements AlignmentI
     deleteSequence(oldseq);\r
 \r
     sequences.setElementAt(snew,i);\r
-\r
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);\r
   }\r
 \r
   public Vector getGroups() {\r
@@ -500,6 +495,17 @@ public class Alignment implements AlignmentI
   {\r
     return AAFrequency.calculate(sequences, 0, getWidth());\r
   }\r
+\r
+  public boolean isAligned()\r
+  {\r
+    int width = getWidth();\r
+    for (int i = 0; i < sequences.size(); i++)\r
+      if (getSequenceAt(i).getLength() != width)\r
+        return false;\r
+\r
+    return true;\r
+\r
+  }\r
 }\r
 \r
 \r