import java.util.*;\r
\r
\r
-public class BLCFile extends AlignFile {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class BLCFile extends AlignFile\r
+{\r
Vector titles;\r
\r
- public BLCFile() {\r
+ /**\r
+ * Creates a new BLCFile object.\r
+ */\r
+ public BLCFile()\r
+ {\r
}\r
\r
- public BLCFile(String inStr) {\r
+ /**\r
+ * Creates a new BLCFile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public BLCFile(String inStr)\r
+ {\r
super(inStr);\r
}\r
\r
- public BLCFile(String inFile, String type) throws IOException {\r
+ /**\r
+ * Creates a new BLCFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public BLCFile(String inFile, String type) throws IOException\r
+ {\r
super(inFile, type);\r
}\r
\r
- public void initData() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void initData()\r
+ {\r
super.initData();\r
titles = new Vector();\r
}\r
\r
- public void parse() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void parse()\r
+ {\r
boolean idsFound = false;\r
Vector ids = new Vector();\r
StringBuffer[] seqstrings;\r
\r
String line = null;\r
\r
- try {\r
- do {\r
+ try\r
+ {\r
+ do\r
+ {\r
line = nextLine();\r
\r
// seek end of ids\r
- if (line.indexOf("*") > -1) {\r
+ if (line.indexOf("*") > -1)\r
+ {\r
idsFound = true;\r
\r
break;\r
\r
int abracket = line.indexOf(">");\r
\r
- if (abracket > -1) {\r
+ if (abracket > -1)\r
+ {\r
if (line.indexOf(" ") > -1) //\r
- {\r
+ {\r
///Colur it be this format?\r
//>54402046 0 1 137 137:\r
// or this??\r
// 1 >L1H14 30539 343\r
- try {\r
+ try\r
+ {\r
ids.addElement(line.substring(abracket + 1,\r
line.indexOf(" ", abracket + 1)));\r
\r
value = Integer.parseInt(line.substring(0,\r
line.indexOf(" ")));\r
ends.addElement(value + "");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
System.err.println("Error during blockfile read.");\r
ex.printStackTrace();\r
- starts.addElement("0");\r
- ends.addElement("0");\r
+ starts.addElement("1");\r
+ ends.addElement("-1");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (line.indexOf("/") > -1)\r
+ {\r
+ ids.addElement(line.substring(abracket + 1,\r
+ line.indexOf("/")));\r
+ line = line.substring(line.indexOf("/") + 1);\r
+ starts.addElement(line.substring(0,\r
+ line.indexOf("-")));\r
+ ends.addElement(line.substring(line.indexOf("-") +\r
+ 1));\r
+ }\r
+ else\r
+ {\r
+ ids.addElement(line.substring(abracket + 1));\r
+ starts.addElement("1");\r
+ ends.addElement("-1");\r
}\r
- } else {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf("/")));\r
- line = line.substring(line.indexOf("/") + 1);\r
- starts.addElement(line.substring(0, line.indexOf("-")));\r
- ends.addElement(line.substring(line.indexOf("-") + 1));\r
}\r
}\r
- } while (!idsFound);\r
+ }\r
+ while (!idsFound);\r
\r
int starCol = line.indexOf("*");\r
seqstrings = new StringBuffer[ids.size()];\r
\r
- for (int i = 0; i < ids.size(); i++) {\r
- if (seqstrings[i] == null) {\r
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
+ if (seqstrings[i] == null)\r
+ {\r
seqstrings[i] = new StringBuffer();\r
}\r
}\r
\r
- while ((line = nextLine()).indexOf("*") == -1) {\r
- for (int i = 0; i < ids.size(); i++) {\r
- if (line.length() > (i + starCol)) {\r
+ while ((line = nextLine()).indexOf("*") == -1)\r
+ {\r
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
+ if (line.length() > (i + starCol))\r
+ {\r
seqstrings[i].append(line.charAt(i + starCol));\r
}\r
}\r
}\r
\r
- for (int i = 0; i < ids.size(); i++) {\r
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
seqstrings[i].toString(),\r
Integer.parseInt(starts.elementAt(i).toString()),\r
Integer.parseInt(ends.elementAt(i).toString()));\r
seqs.addElement(newSeq);\r
}\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
ex.printStackTrace();\r
}\r
}\r
\r
- public String print() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
+ {\r
return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String print(SequenceI[] s)\r
+ {\r
StringBuffer out = new StringBuffer();\r
\r
int i = 0;\r
int max = -1;\r
\r
- while ((i < s.length) && (s[i] != null)) {\r
+ while ((i < s.length) && (s[i] != null))\r
+ {\r
out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
s[i].getEnd() + "\n");\r
\r
- if (s[i].getSequence().length() > max) {\r
+ if (s[i].getSequence().length() > max)\r
+ {\r
max = s[i].getSequence().length();\r
}\r
\r
\r
out.append("* iteration 1\n");\r
\r
- for (int j = 0; j < max; j++) {\r
+ for (int j = 0; j < max; j++)\r
+ {\r
i = 0;\r
\r
- while ((i < s.length) && (s[i] != null)) {\r
- if (s[i].getSequence().length() > j) {\r
+ while ((i < s.length) && (s[i] != null))\r
+ {\r
+ if (s[i].getSequence().length() > j)\r
+ {\r
out.append(s[i].getSequence().substring(j, j + 1));\r
- } else {\r
+ }\r
+ else\r
+ {\r
out.append("-");\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff