/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
int maxLength = 0;
/**
- * Sequences to be added to form a new alignment.
+ * Sequences to be added to form a new alignment. TODO: remove vector in this
+ * class
*/
protected Vector<SequenceI> seqs;
/**
* Constructor which parses the data from a file of some specified type.
*
- * @param inFile
- * Filename to read from.
+ * @param dataObject
+ * Filename, URL or Pasted String to read from.
* @param type
- * What type of file to read from (File, URL)
+ * What type of file to read from (File, URL, Pasted String)
*/
- public AlignFile(String inFile, String type) throws IOException
+ public AlignFile(String dataObject, String type) throws IOException
{
- this(true, inFile, type);
+ this(true, dataObject, type);
}
/**
*
* @param parseImmediately
* if false, need to call 'doParse()' to begin parsing data
- * @param inFile
- * Filename to read from.
+ * @param dataObject
+ * Filename, URL or Pasted String to read from.
* @param type
* What type of file to read from (File, URL)
* @throws IOException
*/
- public AlignFile(boolean parseImmediately, String inFile, String type)
+ public AlignFile(boolean parseImmediately, String dataObject, String type)
throws IOException
{
- super(inFile, type);
+ super(dataObject, type);
initData();
if (parseImmediately)
{
if (space > -1)
{
seq = new Sequence(id.substring(0, space), "");
- seq.setDescription(id.substring(space + 1));
+ String desc = id.substring(space + 1);
+ seq.setDescription(desc);
+
+ /*
+ * it is tempting to parse Ensembl style gene description e.g.
+ * chromosome:GRCh38:7:140696688:140721955:1 and set the
+ * start position of the sequence, but this causes much confusion
+ * for reverse strand feature locations
+ */
}
else
{