X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=adfc1cbdd8173d6e31c73a5f357b48c72c011040;hb=0b5e12b6e86604263fe6b45814b50d7ccc60d1ee;hp=8402d2476aa4962c40ff3e8ad9af4f1648d882de;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 8402d24..adfc1cb 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -22,6 +22,7 @@ package jalview.io; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.util.Comparison; import java.io.IOException; import java.util.Vector; @@ -58,7 +59,7 @@ public class PIRFile extends AlignFile { if (line.length() == 0) { - // System.out.println("blank line"); + // jalview.bin.Console.outPrintln("blank line"); continue; } if (line.indexOf("C;") == 0 || line.indexOf("#") == 0) @@ -103,14 +104,9 @@ public class PIRFile extends AlignFile } @Override - public String print() + public String print(SequenceI[] s, boolean jvsuffix) { - return print(getSeqsAsArray()); - } - - public String print(SequenceI[] s) - { - boolean is_NA = jalview.util.Comparison.isNucleotide(s); + boolean is_NA = Comparison.isNucleotide(s); int len = 72; StringBuffer out = new StringBuffer(); int i = 0; @@ -162,7 +158,7 @@ public class PIRFile extends AlignFile } else { - out.append(">P1;" + printId(s[i])); + out.append(">P1;" + printId(s[i], jvsuffix)); out.append(newline); if (s[i].getDescription() != null) {