Title:
- * PileUpfile - *Description:
- * - * 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.*; -import jalview.util.*; - -import java.io.*; -import java.util.*; - - -public class PileUpfile - extends AlignFile -{ - -public PileUpfile() -{} - -public PileUpfile(String inStr) { - super(inStr); -} - -public PileUpfile(String inFile, String type) throws IOException { - super(inFile,type); -} - -public void parse() { - - int i = 0; - boolean seqFlag = false; - String key = new String(); - Vector headers = new Vector(); - Hashtable seqhash = new Hashtable(); - String line; - - try { - while ((line = nextLine()) != null) { - - StringTokenizer str = new StringTokenizer(line); - - while (str.hasMoreTokens()) { - - String inStr = str.nextToken(); - - //If line has header information add to the headers vector - if (inStr.indexOf("Name:") != -1) { - key = str.nextToken(); - headers.addElement(key); - } - - //if line has // set SeqFlag to 1 so we know sequences are coming - if (inStr.indexOf("//") != -1) { - seqFlag = true; - } - - //Process lines as sequence lines if seqFlag is set - if (( inStr.indexOf("//") == -1) && (seqFlag == true)) { - //seqeunce id is the first field - key = inStr; - StringBuffer tempseq; - - //Get sequence from hash if it exists - if (seqhash.containsKey(key)) { - tempseq = (StringBuffer)seqhash.get(key); - } else { - tempseq = new StringBuffer(); - seqhash.put(key,tempseq); - } - - //loop through the rest of the words - while (str.hasMoreTokens()) { - //append the word to the sequence - tempseq.append(str.nextToken()); - } - } - } - } - } catch (IOException e) { - System.err.println("Exception parsing PileUpfile " + e); - e.printStackTrace(); - } - - this.noSeqs = headers.size(); - - //Add sequences to the hash - for (i = 0; i < headers.size(); i++ ) { - - if ( seqhash.get(headers.elementAt(i)) != null) { - String head = headers.elementAt(i).toString(); - String seq = seqhash.get(head).toString(); - - int start = 1; - int end = seq.length(); - - if (maxLength < head.length() ) { - maxLength = head.length(); - } - - if (head.indexOf("/") > 0 ) { - - StringTokenizer st = new StringTokenizer(head,"/"); - - if (st.countTokens() == 2) { - - head = st.nextToken(); - String tmp = st.nextToken(); - st = new StringTokenizer(tmp,"-"); - if (st.countTokens() == 2) { - start = Integer.valueOf(st.nextToken()).intValue(); - end = Integer.valueOf(st.nextToken()).intValue(); - } - } - } - - Sequence newSeq = new Sequence(head,seq,start,end); - - seqs.addElement(newSeq); - - } else { - System.err.println("PileUpfile Parser: Can't find sequence for " + headers.elementAt(i)); - } - } - -} - -public static int checkSum(String seq) { - //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@"; - int check = 0; - - String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@"; - index += "--------------------------------------------------------------------------------------------------------------------------------"; - - for(int i = 0; i < seq.length(); i++) { - try { - if (iTitle:
+ * PileUpfile + *Description:
+ * + * 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 java.io.*; + +import jalview.datamodel.*; +import jalview.util.*; + +public class PileUpfile extends MSFfile +{ + + /** + * Creates a new MSFfile object. + */ + public PileUpfile() + { + } + /** + * Creates a new MSFfile object. + * + * @param inStr DOCUMENT ME! + */ + public PileUpfile(String inStr) + { + super(inStr); + } + + /** + * 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); + } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() + { + return print(getSeqsAsArray()); + } + + + public String print(SequenceI[] s) + { + StringBuffer out = new StringBuffer("PileUp\n\n"); + + 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].getSequence()); + bigChecksum += checksums[i]; + i++; + } + + out.append(" MSF: " + s[0].getSequence().length() + + " Type: P Check: " + bigChecksum%10000 + " ..\n\n\n"); + + i=0; + while ( (i < s.length) && (s[i] != null)) + { + String seq = s[i].getSequence(); + out.append(" Name: " + printId(s[i]) + + " oo Len: " + + s[i].getSequence().length() + " Check: " + checksums[i] + + " Weight: 1.00\n"); + + 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("\n\n//\n\n"); + + 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().substring(start, end)); + + if (k < 4) + { + out.append(" "); + } + else + { + out.append("\n"); + } + } + else + { + if (start < s[j].getSequence().length()) + { + out.append(s[j].getSequence().substring(start)); + out.append("\n"); + } + else + { + if (k == 0) + { + out.append("\n"); + } + } + } + } + + j++; + } + + out.append("\n"); + } + + return out.toString(); + } +}