- while ((i < s.length) && (s[i] != null))\r
- {\r
- out.append(">" + printId(s[i]));\r
- if(s[i].getDescription()!=null)\r
- out.append(" "+s[i].getDescription());\r
+ else if (!firstLine)\r
+ {\r
+ seq.setSequence(sb.toString());\r
+ seqs.addElement(seq);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * called by AppletFormatAdapter to generate\r
+ * an annotated alignment, rather than bare\r
+ * sequences.\r
+ * @param al\r
+ */\r
+ public void addAnnotations(Alignment al)\r
+ {\r
+ addProperties(al);\r
+ for (int i = 0; i < annotations.size(); i++)\r
+ {\r
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);\r
+ aa.setPadGaps(true, al.getGapCharacter());\r
+ al.addAnnotation( aa );\r
+ }\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param len DOCUMENT ME!\r
+ * @param gaps DOCUMENT ME!\r
+ * @param displayId DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print(SequenceI[] s)\r
+ {\r
+ out = new StringBuffer();\r
+ int i = 0;\r
+\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
+ out.append(">" + printId(s[i]));\r
+ if (s[i].getDescription() != null)\r
+ {\r
+ out.append(" " + s[i].getDescription());\r
+ }\r