/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
import jalview.datamodel.*;\r
import jalview.util.*;\r
\r
-public class PileUpfile extends MSFfile\r
+public class PileUpfile\r
+ extends MSFfile\r
{\r
\r
- /**\r
- * Creates a new MSFfile object.\r
- */\r
- public PileUpfile()\r
- {\r
- }\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ */\r
+ public PileUpfile()\r
+ {\r
+ }\r
\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public PileUpfile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
\r
- /**\r
- * Creates a new MSFfile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public PileUpfile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
- /**\r
+ /**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
public String print()\r
{\r
- return print(getSeqsAsArray());\r
+ return print(getSeqsAsArray());\r
}\r
\r
-\r
- public String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("PileUp\n\n");\r
\r
int[] checksums = new int[s.length];\r
while (i < s.length)\r
{\r
- checksums[i] = checkSum(s[i].getSequence());\r
+ checksums[i] = checkSum(s[i].getSequenceAsString());\r
bigChecksum += checksums[i];\r
i++;\r
}\r
\r
- out.append(" MSF: " + s[0].getSequence().length() +\r
- " Type: P Check: " + bigChecksum%10000 + " ..\n\n\n");\r
+ out.append(" MSF: " + s[0].getSequence().length +\r
+ " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n");\r
\r
- i=0;\r
+ i = 0;\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String seq = s[i].getSequence();\r
+ String seq = s[i].getSequenceAsString();\r
out.append(" Name: " + printId(s[i]) +\r
" oo Len: " +\r
- s[i].getSequence().length() + " Check: " + checksums[i] +\r
+ seq.length() + " Check: " + checksums[i] +\r
" Weight: 1.00\n");\r
\r
if (seq.length() > max)\r
{\r
String name = printId(s[j]);\r
\r
- out.append(new Format("%-" + maxid + "s").form(name + " "));\r
+ out.append(new Format("%-" + maxid + "s").form(name + " "));\r
\r
for (int k = 0; k < 5; k++)\r
{\r
int start = (i * 50) + (k * 10);\r
int end = start + 10;\r
\r
- if ( (end < s[j].getSequence().length()) &&\r
- (start < s[j].getSequence().length()))\r
+ if ( (end < s[j].getSequence().length) &&\r
+ (start < s[j].getSequence().length))\r
{\r
- out.append(s[j].getSequence().substring(start, end));\r
+ out.append(s[j].getSequence(start, end));\r
\r
if (k < 4)\r
{\r
}\r
else\r
{\r
- if (start < s[j].getSequence().length())\r
+ if (start < s[j].getSequence().length)\r
{\r
- out.append(s[j].getSequence().substring(start));\r
+ out.append(s[j].getSequenceAsString().substring(start));\r
out.append("\n");\r
}\r
else\r