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JAL-2321 isParseImmediately() allows the parse() method to determine if it was called...
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
d36a588
..
7b1e84a
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-40,7
+40,8
@@
import java.util.Vector;
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile extends FileParse implements AlignmentFileI
+public abstract class AlignFile extends FileParse
+ implements AlignmentFileReaderI, AlignmentFileWriterI
{
int noSeqs = 0;
{
int noSeqs = 0;
@@
-65,14
+66,27
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
/**
* Properties to be added to generated alignment object
*/
/**
* Properties to be added to generated alignment object
*/
- protected Hashtable properties;
+ private Hashtable properties;
long start;
long end;
long start;
long end;
+ /**
+ * true if parse() has been called
+ */
private boolean parseCalled;
private boolean parseCalled;
+ private boolean parseImmediately;
+
+ /**
+ * @return if doParse() was called at construction time
+ */
+ protected boolean isParseImmediately()
+ {
+ return parseImmediately;
+ }
+
/**
* Creates a new AlignFile object.
*/
/**
* Creates a new AlignFile object.
*/
@@
-117,8
+131,7
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
* @throws IOException
*/
public AlignFile(boolean parseImmediately, String dataObject,
* @throws IOException
*/
public AlignFile(boolean parseImmediately, String dataObject,
- DataSourceType sourceType)
- throws IOException
+ DataSourceType sourceType) throws IOException
{
super(dataObject, sourceType);
initData();
{
super(dataObject, sourceType);
initData();
@@
-153,6
+166,11
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
{
super(source);
initData();
{
super(source);
initData();
+
+ // stash flag in case parse needs to know if it has to autoconfigure or was
+ // configured after construction
+ this.parseImmediately = parseImmediately;
+
if (parseImmediately)
{
doParse();
if (parseImmediately)
{
doParse();
@@
-174,11
+192,6
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
}
parseCalled = true;
parse();
}
parseCalled = true;
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);
- }
}
/**
}
/**
@@
-281,9
+294,8
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
{
if (key == null)
{
{
if (key == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
}
if (value == null)
{
@@
-370,8
+382,8
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
}
/**
}
/**
- * Creates the output id. Adds prefix Uniprot format source|id And suffix
- * Jalview /start-end
+ * Creates the output id. Adds prefix Uniprot format source|id and optionally
+ * suffix Jalview /start-end
*
* @param jvsuffix
*
*
* @param jvsuffix
*
@@
-382,6
+394,11
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
return seq.getDisplayId(jvsuffix);
}
return seq.getDisplayId(jvsuffix);
}
+ String printId(SequenceI seq)
+ {
+ return printId(seq, true);
+ }
+
/**
* vector of String[] treeName, newickString pairs
*/
/**
* vector of String[] treeName, newickString pairs
*/
@@
-411,4
+428,8
@@
public abstract class AlignFile extends FileParse implements AlignmentFileI
}
}
}
}
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
}
}