From 81d824a66c486fb52ebb1b7b6b778758b289d4f8 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 10 Oct 2014 16:17:01 +0100 Subject: [PATCH] JAL-674 change jalview.io.AlignFile to allow parsing to be deferred till after the parser class has been fully initialised/configured --- src/jalview/io/AlignFile.java | 56 ++++++++++++++++++++++++++++++++++++----- 1 file changed, 50 insertions(+), 6 deletions(-) diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index f73e250..2962cb2 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -64,6 +64,8 @@ public abstract class AlignFile extends FileParse boolean jvSuffix = true; + private boolean parseCalled; + /** * Creates a new AlignFile object. */ @@ -85,16 +87,28 @@ public abstract class AlignFile extends FileParse */ public AlignFile(String inFile, String type) throws IOException { + this(true, inFile, type); + } + + /** + * Constructor which (optionally delays) parsing of data from a file of some specified type. + * + * @param parseImmediately + * if false, need to call 'doParse()' to begin parsing data + * @param inFile + * Filename to read from. + * @param type + * What type of file to read from (File, URL) + * @throws IOException + */ + public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException + { super(inFile, type); initData(); - parse(); - // sets the index of each sequence in the alignment - for (int i = 0, c = seqs.size(); i < c; i++) - { - seqs.get(i).setIndex(i); + if (parseImmediately) { + doParse(); } } - /** * Attempt to read from the position where some other parsing process left * off. @@ -104,8 +118,36 @@ public abstract class AlignFile extends FileParse */ public AlignFile(FileParse source) throws IOException { + this(true,source); + } + /** + * Construct a new parser to read from the position where some other parsing process left + * + * @param parseImmediately + * if false, need to call 'doParse()' to begin parsing data + * @param source + */ + public AlignFile(boolean parseImmediately, FileParse source) throws IOException + { super(source); initData(); + if (parseImmediately) { + doParse(); + } + } + /** + * called if parsing was delayed till after parser was constructed + * @throws IOException + */ + public void doParse() throws IOException + { + if (parseCalled) + { + throw new IOException( + "Implementation error: Parser called twice for same data.\n" + + "Need to call initData() again before parsing can be reattempted."); + } + parseCalled=true; parse(); // sets the index of each sequence in the alignment for (int i = 0, c = seqs.size(); i < c; i++) @@ -114,6 +156,7 @@ public abstract class AlignFile extends FileParse } } + /** * Return the seqs Vector */ @@ -226,6 +269,7 @@ public abstract class AlignFile extends FileParse { seqs = new Vector(); annotations = new Vector(); + parseCalled=false; } /** -- 1.7.10.2