X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=5f812153ae1bc4d806ac884532087e3505ac7776;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=2a6e10f0dee360545d7cf37987bb789d0a31adb6;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 2a6e10f..5f81215 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -27,24 +27,54 @@ import java.io.*; import java.util.*; -public class MSFfile extends AlignFile { +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class MSFfile extends AlignFile +{ private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~", "-"); private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex( "[" + jalview.util.Comparison.GapChars + "]", "\\~"); - public MSFfile() { + /** + * Creates a new MSFfile object. + */ + public MSFfile() + { } - public MSFfile(String inStr) { + /** + * Creates a new MSFfile object. + * + * @param inStr DOCUMENT ME! + */ + public MSFfile(String inStr) + { super(inStr); } - public MSFfile(String inFile, String type) throws IOException { + /** + * 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); } - public void parse() { + /** + * DOCUMENT ME! + */ + public void parse() + { int i = 0; boolean seqFlag = false; String key = new String(); @@ -52,48 +82,60 @@ public class MSFfile extends AlignFile { Hashtable seqhash = new Hashtable(); String line; - try { - while ((line = nextLine()) != null) { + try + { + while ((line = nextLine()) != null) + { StringTokenizer str = new StringTokenizer(line); - while (str.hasMoreTokens()) { + while (str.hasMoreTokens()) + { String inStr = str.nextToken(); //If line has header information add to the headers vector - if (inStr.indexOf("Name:") != -1) { + 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) { + if (inStr.indexOf("//") != -1) + { seqFlag = true; } //Process lines as sequence lines if seqFlag is set - if ((inStr.indexOf("//") == -1) && (seqFlag == true)) { + 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)) { + if (seqhash.containsKey(key)) + { tempseq = (StringBuffer) seqhash.get(key); - } else { + } + else + { tempseq = new StringBuffer(); seqhash.put(key, tempseq); } //loop through the rest of the words - while (str.hasMoreTokens()) { + while (str.hasMoreTokens()) + { //append the word to the sequence tempseq.append(str.nextToken()); } } } } - } catch (IOException e) { + } + catch (IOException e) + { System.err.println("Exception parsing MSFFile " + e); e.printStackTrace(); } @@ -101,28 +143,34 @@ public class MSFfile extends AlignFile { this.noSeqs = headers.size(); //Add sequences to the hash - for (i = 0; i < headers.size(); i++) { - if (seqhash.get(headers.elementAt(i)) != null) { + 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()) { + if (maxLength < head.length()) + { maxLength = head.length(); } - if (head.indexOf("/") > 0) { + if (head.indexOf("/") > 0) + { StringTokenizer st = new StringTokenizer(head, "/"); - if (st.countTokens() == 2) { + if (st.countTokens() == 2) + { head = st.nextToken(); String tmp = st.nextToken(); st = new StringTokenizer(tmp, "-"); - if (st.countTokens() == 2) { + if (st.countTokens() == 2) + { start = Integer.valueOf(st.nextToken()).intValue(); end = Integer.valueOf(st.nextToken()).intValue(); } @@ -135,30 +183,44 @@ public class MSFfile extends AlignFile { Sequence newSeq = new Sequence(head, seq, start, end); seqs.addElement(newSeq); - } else { + } + else + { System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i)); } } } - public static int checkSum(String seq) { + /** + * DOCUMENT ME! + * + * @param seq DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static int checkSum(String seq) + { //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@"; int check = 0; + String sequence = seq.toUpperCase(); String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@"; - index += "--------------------------------------------------------------------------------------------------------------------------------"; + index += "--------------------------------------------------------------------------------------------------------------------------------"; - for (int i = 0; i < seq.length(); i++) { - try { - if (i < seq.length()) { - int pos = index.indexOf(seq.substring(i, i + 1)); + for (int i = 0; i < sequence.length(); i++) + { + try + { + int pos = index.indexOf(sequence.charAt(i)); - if (!index.substring(pos, pos + 1).equals("_")) { + if (index.charAt(pos)!='_') + { check += (((i % 57) + 1) * pos); } - } - } catch (Exception e) { + } + catch (Exception e) + { System.err.println("Exception during MSF Checksum calculation"); e.printStackTrace(); } @@ -167,11 +229,28 @@ public class MSFfile extends AlignFile { return check % 10000; } - public static String print(SequenceI[] s) { + /** + * DOCUMENT ME! + * + * @param s DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String print(SequenceI[] s) + { return print(s, false); } - public static String print(SequenceI[] s, boolean is_NA) { + /** + * DOCUMENT ME! + * + * @param s DOCUMENT ME! + * @param is_NA DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String print(SequenceI[] s, boolean is_NA) + { StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet. @@ -180,11 +259,13 @@ public class MSFfile extends AlignFile { int i = 0; String big = ""; - while ((i < s.length) && (s[i] != null)) { + while ((i < s.length) && (s[i] != null)) + { String sq; big += (sq = s[i].getSequence()); - if (sq.length() > max) { + if (sq.length() > max) + { max = sq.length(); } @@ -205,8 +286,8 @@ public class MSFfile extends AlignFile { String[] nameBlock = new String[s.length]; String[] idBlock = new String[s.length]; - while ((i < s.length) && (s[i] != null)) { - String seq = s[i].getSequence(); + while ((i < s.length) && (s[i] != null)) + { String name = s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd(); int check = checkSum(s[i].getSequence()); @@ -215,28 +296,33 @@ public class MSFfile extends AlignFile { maxLenpad.form(s[i].getSequence().length()) + " Check:" + maxChkpad.form(check) + " Weight: 1.00\n"); - if (name.length() > maxid) { + if (name.length() > maxid) + { maxid = name.length(); } - if (nameBlock[i].length() > maxNB) { + if (nameBlock[i].length() > maxNB) + { maxNB = nameBlock[i].length(); } i++; } - if (maxid < 10) { + if (maxid < 10) + { maxid = 10; } - if (maxNB < 15) { + if (maxNB < 15) + { maxNB = 15; } Format nbFormat = new Format("%-" + maxNB + "s"); - for (i = 0; (i < s.length) && (s[i] != null); i++) { + for (i = 0; (i < s.length) && (s[i] != null); i++) + { out.append(nbFormat.form(nameBlock[i]) + idBlock[i]); } @@ -247,39 +333,53 @@ public class MSFfile extends AlignFile { int nochunks = (max / len) + 1; - if ((max % len) == 0) { + if ((max % len) == 0) + { nochunks--; } - for (i = 0; i < nochunks; i++) { + for (i = 0; i < nochunks; i++) + { int j = 0; - while ((j < s.length) && (s[j] != null)) { + 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++) { + 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())) { + (start < s[j].getSequence().length())) + { out.append(re2gap.replaceAll(s[j].getSequence() .substring(start, end))); - if (k < 4) { + if (k < 4) + { // out.append(" "); - } else { + } + else + { out.append("\n"); } - } else { - if (start < s[j].getSequence().length()) { + } + else + { + if (start < s[j].getSequence().length()) + { out.append(re2gap.replaceAll( s[j].getSequence().substring(start))); out.append("\n"); - } else { - if (k == 0) { + } + else + { + if (k == 0) + { out.append("\n"); } } @@ -295,7 +395,13 @@ public class MSFfile extends AlignFile { return out.toString(); } - public String print() { + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() + { return print(getSeqsAsArray()); } }