import java.util.*;\r
\r
\r
-public abstract class AlignFile extends FileParse {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public abstract class AlignFile extends FileParse\r
+{\r
int noSeqs = 0;\r
int maxLength = 0;\r
Vector seqs;\r
long start;\r
long end;\r
\r
- public AlignFile() {\r
+ /**\r
+ * Creates a new AlignFile object.\r
+ */\r
+ public AlignFile()\r
+ {\r
}\r
\r
- public AlignFile(String inStr) {\r
+ /**\r
+ * Creates a new AlignFile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public AlignFile(String inStr)\r
+ {\r
initData();\r
System.out.println("is this ever called??");\r
\r
- try {\r
+ try\r
+ {\r
parse();\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
* @param inFile Filename to read from.\r
* @param type What type of file to read from (File, URL)\r
*/\r
- public AlignFile(String inFile, String type) throws IOException {\r
+ public AlignFile(String inFile, String type) throws IOException\r
+ {\r
super(inFile, type);\r
\r
initData();\r
/**\r
* Return the seqs Vector\r
*/\r
- public Vector getSeqs() {\r
+ public Vector getSeqs()\r
+ {\r
return seqs;\r
}\r
\r
/**\r
* Return the Sequences in the seqs Vector as an array of Sequences\r
*/\r
- public SequenceI[] getSeqsAsArray() {\r
+ public SequenceI[] getSeqsAsArray()\r
+ {\r
SequenceI[] s = new SequenceI[seqs.size()];\r
\r
- for (int i = 0; i < seqs.size(); i++) {\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
s[i] = (SequenceI) seqs.elementAt(i);\r
}\r
\r
/**\r
* Initialise objects to store sequence data in.\r
*/\r
- protected void initData() {\r
+ protected void initData()\r
+ {\r
seqs = new Vector();\r
headers = new Vector();\r
}\r
\r
- protected void setSeqs(SequenceI[] s) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ */\r
+ protected void setSeqs(SequenceI[] s)\r
+ {\r
seqs = new Vector();\r
\r
- for (int i = 0; i < s.length; i++) {\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
seqs.addElement(s[i]);\r
}\r
}\r
\r
// Checks whether sequence is valid aa characters\r
- protected boolean isValidProteinSequence(String sequence) {\r
+ protected boolean isValidProteinSequence(String sequence)\r
+ {\r
for (int i = 0; i < sequence.length(); i++)\r
if (!jalview.schemes.ResidueProperties.aaHash.containsKey(\r
- String.valueOf(sequence.charAt(i)))) {\r
+ String.valueOf(sequence.charAt(i))))\r
+ {\r
return false;\r
}\r
\r