X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=ea870582e3f3f5eef6c3e8a3a39e1f90b20b6791;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=8fa76ecca3ec5346855f9e36bb7293b20f16130c;hpb=c945c9641de88cad01b09b3db19e45667dfe751e;p=jalview.git diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 8fa76ec..ea87058 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -22,6 +22,9 @@ package jalview.io; import java.io.File; import java.io.IOException; +import java.util.Locale; + +import jalview.bin.Console; /** * DOCUMENT ME! @@ -31,12 +34,14 @@ import java.io.IOException; */ public class IdentifyFile { - - public FileFormatI identify(Object file, DataSourceType protocol) throws FileFormatException + + public FileFormatI identify(Object file, DataSourceType protocol) + throws FileFormatException { // BH 2018 - return (file instanceof File ? identify((File) file, protocol) : identify((String) file, protocol)); - + return (file instanceof File ? identify((File) file, protocol) + : identify((String) file, protocol)); + } public FileFormatI identify(File file, DataSourceType sourceType) @@ -54,8 +59,7 @@ public class IdentifyFile } } catch (Exception e) { - System.err.println("Error whilst identifying " + file); - e.printStackTrace(System.err); + Console.error("Error whilst identifying " + file, e); emessage = e.getMessage(); } if (parser != null) @@ -90,8 +94,7 @@ public class IdentifyFile } } catch (Exception e) { - System.err.println("Error whilst identifying " + file); - e.printStackTrace(System.err); + Console.error("Error whilst identifying " + file, e); emessage = e.getMessage(); } if (parser != null) @@ -165,26 +168,39 @@ public class IdentifyFile if (source.inFile != null) { String fileStr = source.inFile.getName(); - // possibly a Jalview archive. - if (fileStr.lastIndexOf(".jar") > -1 - || fileStr.lastIndexOf(".zip") > -1) + if (fileStr.contains(".jar") || fileStr.contains(".zip") + || fileStr.contains(".jvp")) { + // possibly a Jalview archive (but check further) reply = FileFormat.Jalview; } } if (!lineswereskipped && data.startsWith("PK")) { - reply = FileFormat.Jalview; // archive. + reply = FileFormat.Jalview; // archive break; } } - data = data.toUpperCase(); + data = data.toUpperCase(Locale.ROOT); if (data.startsWith(ScoreMatrixFile.SCOREMATRIX)) { reply = FileFormat.ScoreMatrix; break; } + if (data.startsWith("LOCUS")) + { + reply = FileFormat.GenBank; + break; + } + if (data.startsWith("ID ")) + { + if (data.substring(2).trim().split(";").length == 7) + { + reply = FileFormat.Embl; + break; + } + } if (data.startsWith("H ") && !aaIndexHeaderRead) { aaIndexHeaderRead = true; @@ -319,7 +335,7 @@ public class IdentifyFile if ((lessThan > -1)) // possible Markup Language data i.e HTML, // RNAML, XML { - String upper = data.toUpperCase(); + String upper = data.toUpperCase(Locale.ROOT); if (upper.substring(lessThan).startsWith(" [ ...]"); + Console.error("Usage: [ ...]"); } } - }