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JAL-674 change jalview.io.AlignFile to allow parsing to be deferred till after the...
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Oct 2014 15:17:01 +0000
(16:17 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Oct 2014 15:17:01 +0000
(16:17 +0100)
src/jalview/io/AlignFile.java
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diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
f73e250
..
2962cb2
100755
(executable)
--- 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;
boolean jvSuffix = true;
+ private boolean parseCalled;
+
/**
* Creates a new AlignFile object.
*/
/**
* Creates a new AlignFile object.
*/
@@
-85,16
+87,28
@@
public abstract class AlignFile extends FileParse
*/
public AlignFile(String inFile, String type) throws IOException
{
*/
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();
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.
/**
* 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
{
*/
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();
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++)
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
*/
/**
* Return the seqs Vector
*/
@@
-226,6
+269,7
@@
public abstract class AlignFile extends FileParse
{
seqs = new Vector();
annotations = new Vector();
{
seqs = new Vector();
annotations = new Vector();
+ parseCalled=false;
}
/**
}
/**