X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=179204e44a677d305ca68830775fa87704c69d4f;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=9495f82b972a7b2bae61abdeb56d9c1ab17c499d;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 9495f82..179204e 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -1,232 +1,405 @@ +/* +* 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 +*/ package jalview.io; import jalview.datamodel.*; + import jalview.util.*; import java.io.*; + import java.util.*; -public class MSFfile extends AlignFile { - public MSFfile() - {} +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class MSFfile extends AlignFile +{ - public MSFfile(String inStr) { - super(inStr); - } - public MSFfile(String inFile, String type) throws IOException { - super(inFile,type); - } + /** + * Creates a new MSFfile object. + */ + public MSFfile() + { + } - public void parse() { + /** + * Creates a new MSFfile object. + * + * @param inStr DOCUMENT ME! + */ + public MSFfile(String inStr) + { + super(inStr); + } - int i = 0; - boolean seqFlag = false; - String key = new String(); - Vector headers = new Vector(); - Hashtable seqhash = new Hashtable(); - String line; + /** + * Creates a new MSFfile object. + * + * @param inFile DOCUMENT ME! + * @param type DOCUMENT ME! + * + * @throws IOException DOCUMENT ME! + */ + public MSFfile(String inFile, String type) throws IOException + { + super(inFile, type); + } - try { - while ((line = nextLine()) != null) { + /** + * DOCUMENT ME! + */ + 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 MSFFile " + e); + e.printStackTrace(); + } - StringTokenizer str = new StringTokenizer(line); + this.noSeqs = headers.size(); - while (str.hasMoreTokens()) { + //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(); - String inStr = str.nextToken(); + int start = -1; + int end = -1; - //If line has header information add to the headers vector - if (inStr.indexOf("Name:") != -1) { - key = str.nextToken(); - headers.addElement(key); - } + if (maxLength < head.length()) + { + maxLength = head.length(); + } - //if line has // set SeqFlag to 1 so we know sequences are coming - if (inStr.indexOf("//") != -1) { - seqFlag = true; - } + // Replace ~ with a sensible gap character + seq = seq.replace('~', '-'); - //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()); - } + Sequence newSeq = parseId(head); + newSeq.setSequence(seq); + + seqs.addElement(newSeq); + } + else + { + System.err.println("MSFFile Parser: Can't find sequence for " + + headers.elementAt(i)); + } } - } } - } catch (IOException e) { - System.err.println("Exception parsing MSFFile " + e); - e.printStackTrace(); + + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int checkSum(String seq) + { + int check = 0; + String sequence = seq.toUpperCase(); + + for (int i = 0; i < sequence.length(); i++) + { + try + { + + int value = sequence.charAt(i); + if (value!=-1) + { + check += (i % 57 +1) * value; + } + } + catch (Exception e) + { + System.err.println("Exception during MSF Checksum calculation"); + e.printStackTrace(); + } + } + + return check % 10000; } - this.noSeqs = headers.size(); - //Add sequences to the hash - for (i = 0; i < headers.size(); i++ ) { + /** + * DOCUMENT ME! + * + * @param s DOCUMENT ME! + * @param is_NA DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print(SequenceI[] seqs) + { - if ( seqhash.get(headers.elementAt(i)) != null) { - String head = headers.elementAt(i).toString(); - String seq = seqhash.get(head).toString(); + boolean is_NA = jalview.util.Comparison.isNucleotide(seqs); - int start = 1; - int end = seq.length(); + SequenceI [] s = new SequenceI[seqs.length]; - if (maxLength < head.length() ) { - maxLength = head.length(); - } + StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") + + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet. - if (head.indexOf("/") > 0 ) { + int max = 0; + int maxid = 0; + int i = 0; - StringTokenizer st = new StringTokenizer(head,"/"); + while ((i < seqs.length) && (seqs[i] != null)) + { + // Replace all internal gaps with . and external spaces with ~ + s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.')); - if (st.countTokens() == 2) { + StringBuffer sb = new StringBuffer(s[i].getSequence()); + for (int ii = 0; ii < sb.length(); ii++) + { + if (sb.charAt(ii) == '.') + { + sb.setCharAt(ii, '~'); + } + else + break; + } - 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(); + for (int ii = sb.length() - 1; ii > 0; ii--) + { + if (sb.charAt(ii) == '.') + { + sb.setCharAt(ii,'~'); } + else + break; } + + s[i].setSequence(sb.toString()); + + if (s[i].getSequence().length() > max) + { + max = s[i].getSequence().length(); + } + + i++; } - Sequence newSeq = new Sequence(head,seq,start,end); + Format maxLenpad = new Format("%" + (new String("" + max)).length() + + "d"); + Format maxChkpad = new Format("%" + (new String("1" + max)).length() + + "d"); + 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++; + } - seqs.addElement(newSeq); + long maxNB = 0; + out.append(" MSF: " + s[0].getSequence().length() + " Type: " + + (is_NA ? "N" : "P") + " Check: " + (bigChecksum%10000) + " ..\n\n\n"); - } else { - System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i)); - } - } + String[] nameBlock = new String[s.length]; + String[] idBlock = new String[s.length]; - } + i=0; + while ((i < s.length) && (s[i] != null)) + { - public static int checkSum(String seq) { - //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@"; - int check = 0; + nameBlock[i] = new String(" Name: " + printId(s[i])+" "); - String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@"; - index += "--------------------------------------------------------------------------------------------------------------------------------"; + idBlock[i] = new String("Len: " + + maxLenpad.form(s[i].getSequence().length()) + " Check: " + + maxChkpad.form(checksums[i]) + " Weight: 1.00\n"); - for(int i = 0; i < seq.length(); i++) { - try { - if (i maxid) + { + maxid = s[i].getName().length(); + } - public static String print(SequenceI[] s) { - StringBuffer out = new StringBuffer("PileUp\n\n"); + if (nameBlock[i].length() > maxNB) + { + maxNB = nameBlock[i].length(); + } - int max = 0; - int maxid = 0; + i++; + } - int i = 0; - String big = ""; - while (i < s.length && s[i] != null) { - big += s[i].getSequence(); - i++; - } - i = 0; - int bigcheck = checkSum(big); - - out.append(" MSF: " + s[0].getSequence().length() + " Type: P Check: " + bigcheck + " ..\n\n\n"); - - while (i < s.length && s[i] != null) { - String seq = s[i].getSequence(); - String name = s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd(); - int check = checkSum(s[i].getSequence()); - out.append(" Name: " + name + " oo Len: " + s[i].getSequence().length() + " Check: " + check + " Weight: 1.00\n"); - if (seq.length() > max) { - max = seq.length(); - } - if (name.length() > maxid) { - maxid = name.length(); - } - i++; - } + if (maxid < 10) + { + maxid = 10; + } - if (maxid < 10) { - maxid = 10; - } - maxid++; - out.append( "\n\n//\n\n"); + if (maxNB < 15) + { + maxNB = 15; + } - int len = 50; + Format nbFormat = new Format("%-" + maxNB + "s"); - 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 = s[j].getName(); - out.append( new Format("%-" + maxid + "s").form(name + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " "); - 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"); - } - } - } + for (i = 0; (i < s.length) && (s[i] != null); i++) + { + out.append(nbFormat.form(nameBlock[i]) + idBlock[i]); } - j++; - } - out.append("\n"); - } - return out.toString(); - } - public String print() { - return print(getSeqsAsArray()); - } -} + 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(); + } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() + { + return print(getSeqsAsArray()); + } +}