X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=591c37cf12038e289f304ebbca60d07cf7b063a0;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=af8c949db48c581dd3eb0f59c75227b87de30e8f;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index af8c949..591c37c 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -25,12 +25,17 @@ */ package jalview.io; -import java.io.*; -import java.util.*; - -import jalview.datamodel.*; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; import jalview.util.MessageManager; +import java.io.IOException; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; + /** * Parser for the JPred/JNet concise format. This is a series of CSV lines, each * line is either a sequence (QUERY), a sequence profile (align;), or jnet @@ -294,7 +299,11 @@ public class JPredFile extends AlignFile if (maxLength != seq_entries.elementAt(i).toString().length()) { - throw new IOException(MessageManager.formatMessage("exception.jpredconcide_entry_has_unexpected_number_of_columns", new String[]{ids.elementAt(i).toString()})); + throw new IOException( + MessageManager + .formatMessage( + "exception.jpredconcide_entry_has_unexpected_number_of_columns", + new String[] { ids.elementAt(i).toString() })); } if ((newSeq.getName().startsWith("QUERY") || newSeq.getName() @@ -318,7 +327,11 @@ public class JPredFile extends AlignFile } catch (Exception e) { tal = null; - IOException ex = new IOException(MessageManager.formatMessage("exception.couldnt_parse_concise_annotation_for_prediction", new String[]{e.getMessage()})); + IOException ex = new IOException( + MessageManager + .formatMessage( + "exception.couldnt_parse_concise_annotation_for_prediction", + new String[] { e.getMessage() })); e.printStackTrace(); // java 1.1 does not have : // ex.setStackTrace(e.getStackTrace()); throw ex;