*\r
**/\r
import java.io.*;\r
-import java.util.*;\r
\r
import jalview.datamodel.*;\r
import jalview.util.*;\r
\r
-public class PileUpfile\r
- extends AlignFile\r
+public class PileUpfile extends MSFfile\r
{\r
- public PileUpfile()\r
- {\r
- }\r
-\r
- public PileUpfile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
\r
- public PileUpfile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public void parse()\r
- {\r
- int i = 0;\r
- boolean seqFlag = false;\r
- String key = new String();\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- String line;\r
-\r
- try\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ */\r
+ public PileUpfile()\r
{\r
- while ( (line = nextLine()) != null)\r
- {\r
- StringTokenizer str = new StringTokenizer(line);\r
-\r
- while (str.hasMoreTokens())\r
- {\r
- String inStr = str.nextToken();\r
-\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1)\r
- {\r
- key = str.nextToken();\r
- headers.addElement(key);\r
- }\r
-\r
- //if line has // set SeqFlag to 1 so we know sequences are coming\r
- if (inStr.indexOf("//") != -1)\r
- {\r
- seqFlag = true;\r
- }\r
-\r
- //Process lines as sequence lines if seqFlag is set\r
- if ( (inStr.indexOf("//") == -1) && (seqFlag == true))\r
- {\r
- //seqeunce id is the first field\r
- key = inStr;\r
-\r
- StringBuffer tempseq;\r
-\r
- //Get sequence from hash if it exists\r
- if (seqhash.containsKey(key))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(key);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key, tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens())\r
- {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
}\r
- catch (IOException e)\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public PileUpfile(String inStr)\r
{\r
- System.err.println("Exception parsing PileUpfile " + e);\r
- e.printStackTrace();\r
+ super(inStr);\r
}\r
\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\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
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
-\r
- int start = 1;\r
- int end = -1;\r
-\r
- if (maxLength < head.length())\r
- {\r
- maxLength = head.length();\r
- }\r
-\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
- Sequence newSeq = new Sequence(head, seq, start, end);\r
-\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- System.err.println(\r
- "PileUpfile Parser: Can't find sequence for " +\r
- headers.elementAt(i));\r
- }\r
+ super(inFile, type);\r
}\r
- }\r
-\r
- public static int checkSum(String seq)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
{\r
-\r
- int check = 0;\r
-\r
- String sequence = seq.toUpperCase();\r
-\r
- for (int i = 0; i < sequence.length(); i++)\r
- {\r
- if (i < sequence.length())\r
- {\r
- int value = sequence.charAt(i);\r
- if (value != -1)\r
- {\r
- check += (i % 57 + 1) * value;\r
- }\r
- }\r
-\r
- }\r
-\r
- return check % 10000;\r
+ return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
+\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("PileUp\n\n");\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
String seq = s[i].getSequence();\r
- out.append(" Name: " + s[i].getName() +\r
- "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+ out.append(" Name: " + printId(s[i]) +\r
" oo Len: " +\r
s[i].getSequence().length() + " Check: " + checksums[i] +\r
" Weight: 1.00\n");\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- String name = s[j].getName();\r
- // out.append(new Format("%-" + maxid + "s").form(name) + " ");\r
+ String name = printId(s[j]);\r
\r
- out.append(new Format("%-" + maxid + "s").form(name\r
- + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form(name + " "));\r
\r
for (int k = 0; k < 5; k++)\r
{\r
\r
return out.toString();\r
}\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff