X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=aa8e40684f219d29e9ac3b4db54ecea13db77387;hb=8b27085fa7fc5f2877e078421284c2636b85b8c6;hp=1f28f491581c88e38fee2e5911a9b8f91a3485e2;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 1f28f49..aa8e406 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -26,9 +26,10 @@ import jalview.util.Comparison; import jalview.util.Format; import java.io.IOException; +import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.StringTokenizer; -import java.util.Vector; /** * DOCUMENT ME! @@ -51,16 +52,15 @@ public class MSFfile extends AlignFile * * @param inFile * DOCUMENT ME! - * @param sourceType + * @param type * DOCUMENT ME! * * @throws IOException * DOCUMENT ME! */ - public MSFfile(String inFile, DataSourceType sourceType) - throws IOException + public MSFfile(String inFile, DataSourceType type) throws IOException { - super(inFile, sourceType); + super(inFile, type); } public MSFfile(FileParse source) throws IOException @@ -69,24 +69,23 @@ public class MSFfile extends AlignFile } /** - * DOCUMENT ME! + * Read and parse MSF sequence data */ @Override public void parse() throws IOException { - int i = 0; boolean seqFlag = false; - String key = new String(); - Vector headers = new Vector(); - Hashtable seqhash = new Hashtable(); - String line; + List headers = new ArrayList(); + Hashtable seqhash = new Hashtable(); try { + String line; while ((line = nextLine()) != null) { StringTokenizer str = new StringTokenizer(line); + String key = null; while (str.hasMoreTokens()) { String inStr = str.nextToken(); @@ -95,31 +94,31 @@ public class MSFfile extends AlignFile if (inStr.indexOf("Name:") != -1) { key = str.nextToken(); - headers.addElement(key); + headers.add(key); } - // if line has // set SeqFlag to 1 so we know sequences are coming + // if line has // set SeqFlag 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)) + if ((inStr.indexOf("//") == -1) && seqFlag) { - // seqeunce id is the first field + // sequence id is the first field key = inStr; - StringBuffer tempseq; + StringBuilder tempseq; // Get sequence from hash if it exists if (seqhash.containsKey(key)) { - tempseq = (StringBuffer) seqhash.get(key); + tempseq = seqhash.get(key); } else { - tempseq = new StringBuffer(); + tempseq = new StringBuilder(64); seqhash.put(key, tempseq); } @@ -127,7 +126,8 @@ public class MSFfile extends AlignFile while (str.hasMoreTokens()) { // append the word to the sequence - tempseq.append(str.nextToken()); + String sequenceBlock = str.nextToken(); + tempseq.append(sequenceBlock); } } } @@ -141,11 +141,11 @@ public class MSFfile extends AlignFile this.noSeqs = headers.size(); // Add sequences to the hash - for (i = 0; i < headers.size(); i++) + for (int i = 0; i < headers.size(); i++) { - if (seqhash.get(headers.elementAt(i)) != null) + if (seqhash.get(headers.get(i)) != null) { - String head = headers.elementAt(i).toString(); + String head = headers.get(i); String seq = seqhash.get(head).toString(); if (maxLength < head.length()) @@ -153,8 +153,11 @@ public class MSFfile extends AlignFile maxLength = head.length(); } - // Replace ~ with a sensible gap character - seq = seq.replace('~', '-'); + /* + * replace ~ (leading/trailing positions) with the gap character; + * use '.' as this is the internal gap character required by MSF + */ + seq = seq.replace('~', '.'); Sequence newSeq = parseId(head); @@ -165,7 +168,7 @@ public class MSFfile extends AlignFile else { System.err.println("MSFFile Parser: Can't find sequence for " - + headers.elementAt(i)); + + headers.get(i)); } } } @@ -203,16 +206,27 @@ public class MSFfile extends AlignFile return check % 10000; } + /** + * DOCUMENT ME! + * + * @param s + * DOCUMENT ME! + * @param is_NA + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ @Override - public String print(SequenceI[] sqs, boolean jvsuffix) + public String print(SequenceI[] sqs, boolean jvSuffix) { boolean is_NA = Comparison.isNucleotide(sqs); SequenceI[] s = new SequenceI[sqs.length]; - StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") - + "_MULTIPLE_ALIGNMENT 1.0"); + StringBuilder out = new StringBuilder(256); + out.append("!!").append(is_NA ? "NA" : "AA") + .append("_MULTIPLE_ALIGNMENT 1.0"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet. out.append(newline); out.append(newline); @@ -222,12 +236,14 @@ public class MSFfile extends AlignFile while ((i < sqs.length) && (sqs[i] != null)) { - // Replace all internal gaps with . and external spaces with ~ - s[i] = new Sequence(sqs[i].getName(), sqs[i].getSequenceAsString() - .replace('-', '.'), sqs[i].getStart(), sqs[i].getEnd()); + /* + * modify to MSF format: uses '.' for internal gaps, + * and '~' for leading or trailing gaps + */ + String seqString = sqs[i].getSequenceAsString() + .replace('-', '.'); - StringBuffer sb = new StringBuffer(); - sb.append(s[i].getSequence()); + StringBuilder sb = new StringBuilder(seqString); for (int ii = 0; ii < sb.length(); ii++) { @@ -252,12 +268,12 @@ public class MSFfile extends AlignFile break; } } + s[i] = new Sequence(sqs[i].getName(), sb.toString(), + sqs[i].getStart(), sqs[i].getEnd()); - s[i].setSequence(sb.toString()); - - if (s[i].getSequence().length > max) + if (sb.length() > max) { - max = s[i].getSequence().length; + max = sb.length(); } i++; @@ -293,7 +309,7 @@ public class MSFfile extends AlignFile while ((i < s.length) && (s[i] != null)) { - nameBlock[i] = new String(" Name: " + printId(s[i], jvsuffix) + " "); + nameBlock[i] = new String(" Name: " + printId(s[i], jvSuffix) + " "); idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length) + " Check: " @@ -345,7 +361,7 @@ public class MSFfile extends AlignFile while ((j < s.length) && (s[j] != null)) { - String name = printId(s[j], jvsuffix); + String name = printId(s[j], jvSuffix); out.append(new Format("%-" + maxid + "s").form(name + " "));