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 java.io.*; - -import jalview.datamodel.*; -import jalview.util.*; - -public class PileUpfile - extends MSFfile + *+ * 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.SequenceI; +import jalview.util.Format; + +import java.io.IOException; + +public class PileUpfile extends MSFfile { /** @@ -47,34 +52,32 @@ public class PileUpfile /** * Creates a new MSFfile object. - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! + * + * @param inFile + * DOCUMENT ME! + * @param sourceType + * DOCUMENT ME! + * + * @throws IOException + * DOCUMENT ME! */ - public PileUpfile(String inFile, String type) - throws IOException + public PileUpfile(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } + public PileUpfile(FileParse source) throws IOException { super(source); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String print() - { - return print(getSeqsAsArray()); - } - public String print(SequenceI[] s) + @Override + public String print(SequenceI[] s, boolean jvsuffix) { - StringBuffer out = new StringBuffer("PileUp\n\n"); + StringBuffer out = new StringBuffer("PileUp"); + out.append(newline); + out.append(newline); int max = 0; int maxid = 0; @@ -89,17 +92,20 @@ public class PileUpfile i++; } - out.append(" MSF: " + s[0].getSequence().length + - " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n"); + out.append(" MSF: " + s[0].getLength() + + " Type: P Check: " + bigChecksum % 10000 + " .."); + out.append(newline); + out.append(newline); + out.append(newline); i = 0; - while ( (i < s.length) && (s[i] != null)) + 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\n"); + out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: " + + seq.length() + " Check: " + checksums[i] + + " Weight: 1.00"); + out.append(newline); if (seq.length() > max) { @@ -120,24 +126,23 @@ public class PileUpfile } maxid++; - out.append("\n\n//\n\n"); + 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--; - } + int nochunks = (max / len) + (max % len > 0 ? 1 : 0); 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 = printId(s[j]); + String name = printId(s[j], jvsuffix); out.append(new Format("%-" + maxid + "s").form(name + " ")); @@ -146,8 +151,8 @@ public class PileUpfile int start = (i * 50) + (k * 10); int end = start + 10; - if ( (end < s[j].getSequence().length) && - (start < s[j].getSequence().length)) + int length = s[j].getLength(); + if ((end < length) && (start < length)) { out.append(s[j].getSequence(start, end)); @@ -157,21 +162,21 @@ public class PileUpfile } else { - out.append("\n"); + out.append(newline); } } else { - if (start < s[j].getSequence().length) + if (start < length) { out.append(s[j].getSequenceAsString().substring(start)); - out.append("\n"); + out.append(newline); } else { if (k == 0) { - out.append("\n"); + out.append(newline); } } } @@ -180,7 +185,7 @@ public class PileUpfile j++; } - out.append("\n"); + out.append(newline); } return out.toString();