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
}\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
}\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
deleteSequence(oldseq);\r
\r
sequences.setElementAt(snew,i);\r
-\r
- ((SequenceGroup)groups.lastElement()).addSequence(snew);\r
}\r
\r
public Vector getGroups() {\r
{\r
groups.clear();\r
superGroup.clear();\r
+ int i=0;\r
+ while (i < sequences.size()) {\r
+ SequenceI s = getSequenceAt(i);\r
+ s.setColor(java.awt.Color.white);\r
+ i++;\r
+ }\r
+\r
+\r
}\r
\r
/** */\r
{\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