-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-/**\r
- * <p>Title: </p>\r
- * PileUpfile\r
- * <p>Description: </p>\r
- *\r
- * Read and write PileUp style MSF Files.\r
- * This used to be the MSFFile class, and was written according to the EBI's idea\r
- * of a subset of the MSF alignment format. But, that was updated to reflect current\r
- * GCG style IO fashion, as found in Emboss (thanks David Martin!)\r
- *\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
-{\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
- 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
- System.err.println("Exception parsing PileUpfile " + e);\r
- e.printStackTrace();\r
- }\r
-\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\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
- }\r
- }\r
-\r
- public static int checkSum(String seq)\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
- }\r
-\r
- public static String print(SequenceI[] s)\r
- {\r
- StringBuffer out = new StringBuffer("PileUp\n\n");\r
-\r
- int max = 0;\r
- int maxid = 0;\r
-\r
- int i = 0;\r
- int bigChecksum = 0;\r
- int[] checksums = new int[s.length];\r
- while (i < s.length)\r
- {\r
- checksums[i] = checkSum(s[i].getSequence());\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
-\r
- i=0;\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
- " oo Len: " +\r
- s[i].getSequence().length() + " Check: " + checksums[i] +\r
- " Weight: 1.00\n");\r
-\r
- if (seq.length() > max)\r
- {\r
- max = seq.length();\r
- }\r
-\r
- if (s[i].getName().length() > maxid)\r
- {\r
- maxid = s[i].getName().length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 10)\r
- {\r
- maxid = 10;\r
- }\r
-\r
- maxid++;\r
- out.append("\n\n//\n\n");\r
-\r
- int len = 50;\r
-\r
- int nochunks = (max / len) + 1;\r
-\r
- if ( (max % len) == 0)\r
- {\r
- nochunks--;\r
- }\r
-\r
- for (i = 0; i < nochunks; i++)\r
- {\r
- int j = 0;\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
-\r
- out.append(new Format("%-" + maxid + "s").form(name\r
- + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\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
- {\r
- out.append(s[j].getSequence().substring(start, end));\r
-\r
- if (k < 4)\r
- {\r
- out.append(" ");\r
- }\r
- else\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- else\r
- {\r
- if (start < s[j].getSequence().length())\r
- {\r
- out.append(s[j].getSequence().substring(start));\r
- out.append("\n");\r
- }\r
- else\r
- {\r
- if (k == 0)\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- }\r
- }\r
-\r
- j++;\r
- }\r
-\r
- out.append("\n");\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * PileUpfile
+ * <p>
+ * Description:
+ * </p>
+ *
+ * Read and write PileUp style MSF Files. This used to be the MSFFile class, and
+ * was written according to the EBI's idea of a subset of the MSF alignment
+ * format. But, that was updated to reflect current GCG style IO fashion, as
+ * found in Emboss (thanks David Martin!)
+ *
+ */
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+
+import java.io.IOException;
+
+public class PileUpfile extends MSFfile
+{
+
+ /**
+ * Creates a new MSFfile object.
+ */
+ public PileUpfile()
+ {
+ }
+
+ /**
+ * Creates a new MSFfile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param sourceType
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public PileUpfile(String inFile, DataSourceType sourceType)
+ throws IOException
+ {
+ super(inFile, sourceType);
+ }
+
+ public PileUpfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
+ {
+ StringBuffer out = new StringBuffer("PileUp");
+ out.append(newline);
+ out.append(newline);
+
+ int max = 0;
+ int maxid = 0;
+
+ int i = 0;
+ int bigChecksum = 0;
+ int[] checksums = new int[s.length];
+ while (i < s.length)
+ {
+ checksums[i] = checkSum(s[i].getSequenceAsString());
+ bigChecksum += checksums[i];
+ i++;
+ }
+
+ out.append(" MSF: " + s[0].getLength()
+ + " Type: P Check: " + bigChecksum % 10000 + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
+
+ i = 0;
+ while ((i < s.length) && (s[i] != null))
+ {
+ String seq = s[i].getSequenceAsString();
+ out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
+ + seq.length() + " Check: " + checksums[i]
+ + " Weight: 1.00");
+ out.append(newline);
+
+ if (seq.length() > max)
+ {
+ max = seq.length();
+ }
+
+ if (s[i].getName().length() > maxid)
+ {
+ maxid = s[i].getName().length();
+ }
+
+ i++;
+ }
+
+ if (maxid < 10)
+ {
+ maxid = 10;
+ }
+
+ maxid++;
+ out.append(newline);
+ out.append(newline);
+ out.append("//");
+ out.append(newline);
+ out.append(newline);
+
+ int len = 50;
+
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
+
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
+
+ while ((j < s.length) && (s[j] != null))
+ {
+ String name = printId(s[j], jvsuffix);
+
+ out.append(new Format("%-" + maxid + "s").form(name + " "));
+
+ for (int k = 0; k < 5; k++)
+ {
+ int start = (i * 50) + (k * 10);
+ int end = start + 10;
+
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
+ {
+ out.append(s[j].getSequence(start, end));
+
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append(newline);
+ }
+ }
+ else
+ {
+ if (start < length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ out.append(newline);
+ }
+ else
+ {
+ if (k == 0)
+ {
+ out.append(newline);
+ }
+ }
+ }
+ }
+
+ j++;
+ }
+
+ out.append(newline);
+ }
+
+ return out.toString();
+ }
+}