/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/\r
-package jalview.io;\r
-\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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!)
- *
- **/\r
-import jalview.datamodel.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class PileUpfile extends AlignFile {\r
- public PileUpfile() {\r
- }\r
-\r
- public PileUpfile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public PileUpfile(String inFile, String type) throws IOException {\r
- super(inFile, type);\r
- }\r
-\r
- public void parse() {\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
- while ((line = nextLine()) != null) {\r
- StringTokenizer str = new StringTokenizer(line);\r
-\r
- while (str.hasMoreTokens()) {\r
- String inStr = str.nextToken();\r
-\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1) {\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
- seqFlag = true;\r
- }\r
-\r
- //Process lines as sequence lines if seqFlag is set\r
- if ((inStr.indexOf("//") == -1) && (seqFlag == true)) {\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
- tempseq = (StringBuffer) seqhash.get(key);\r
- } else {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key, tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens()) {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
- } catch (IOException e) {\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
- if (seqhash.get(headers.elementAt(i)) != null) {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
-\r
- int start = 1;\r
- int end = seq.length();\r
-\r
- if (maxLength < head.length()) {\r
- maxLength = head.length();\r
- }\r
-\r
- if (head.indexOf("/") > 0) {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2) {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2) {\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
- } else {\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
- //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
- int check = 0;\r
-\r
- String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
- index += "--------------------------------------------------------------------------------------------------------------------------------";\r
-\r
- for (int i = 0; i < seq.length(); i++) {\r
- try {\r
- if (i < seq.length()) {\r
- int pos = index.indexOf(seq.substring(i, i + 1));\r
-\r
- if (!index.substring(pos, pos + 1).equals("_")) {\r
- check += (((i % 57) + 1) * pos);\r
- }\r
- }\r
- } catch (Exception e) {\r
- System.err.println("Exception during MSF Checksum calculation");\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- return check % 10000;\r
- }\r
-\r
- public static String print(SequenceI[] s) {\r
- StringBuffer out = new StringBuffer("PileUp\n\n");\r
-\r
- int max = 0;\r
- int maxid = 0;\r
-\r
- int i = 0;\r
- String big = "";\r
-\r
- while ((i < s.length) && (s[i] != null)) {\r
- big += s[i].getSequence();\r
- i++;\r
- }\r
-\r
- i = 0;\r
-\r
- int bigcheck = checkSum(big);\r
-\r
- out.append(" MSF: " + s[0].getSequence().length() +\r
- " Type: P Check: " + bigcheck + " ..\n\n\n");\r
-\r
- while ((i < s.length) && (s[i] != null)) {\r
- String seq = s[i].getSequence();\r
- String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd();\r
- int check = checkSum(s[i].getSequence());\r
- out.append(" Name: " + name + " oo Len: " +\r
- s[i].getSequence().length() + " Check: " + check +\r
- " Weight: 1.00\n");\r
-\r
- if (seq.length() > max) {\r
- max = seq.length();\r
- }\r
-\r
- if (name.length() > maxid) {\r
- maxid = name.length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 10) {\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
- nochunks--;\r
- }\r
-\r
- for (i = 0; i < nochunks; i++) {\r
- int j = 0;\r
-\r
- while ((j < s.length) && (s[j] != null)) {\r
- String name = s[j].getName();\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
- 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
- out.append(s[j].getSequence().substring(start, end));\r
-\r
- if (k < 4) {\r
- out.append(" ");\r
- } else {\r
- out.append("\n");\r
- }\r
- } else {\r
- if (start < s[j].getSequence().length()) {\r
- out.append(s[j].getSequence().substring(start));\r
- out.append("\n");\r
- } else {\r
- if (k == 0) {\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
- return print(getSeqsAsArray());\r
- }\r
-}\r
+ * <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 type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public PileUpfile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public PileUpfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ public String print(SequenceI[] s)
+ {
+ 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].getSequence().length
+ + " 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]) + " 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) + 1;
+
+ if ((max % len) == 0)
+ {
+ nochunks--;
+ }
+
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
+
+ while ((j < s.length) && (s[j] != null))
+ {
+ String name = printId(s[j]);
+
+ 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;
+
+ if ((end < s[j].getSequence().length)
+ && (start < s[j].getSequence().length))
+ {
+ out.append(s[j].getSequence(start, end));
+
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append(newline);
+ }
+ }
+ else
+ {
+ if (start < s[j].getSequence().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();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff