*/\r
public class MSFfile extends AlignFile\r
{\r
- private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",\r
- "-");\r
- private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(\r
- "[" + jalview.util.Comparison.GapChars + "]", "\\~");\r
+\r
\r
/**\r
* Creates a new MSFfile object.\r
*/\r
public void parse()\r
{\r
+ com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",\r
+ "-");\r
+\r
int i = 0;\r
boolean seqFlag = false;\r
String key = new String();\r
String seq = seqhash.get(head).toString();\r
\r
int start = 1;\r
- int end = seq.length();\r
+ int end = -1;\r
\r
if (maxLength < head.length())\r
{\r
}\r
}\r
\r
+\r
// Replace ~ with a sensible gap character\r
seq = gapre.replaceAll(seq);\r
\r
*/\r
public static String print(SequenceI[] s, boolean is_NA)\r
{\r
+ com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(\r
+ "[" + jalview.util.Comparison.GapChars + "]", "\\~");\r
+\r
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
"_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
\r