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JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
1233940
..
b2cf262
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-82,6
+82,8
@@
public abstract class AlignFile extends FileParse
private boolean dataClosed = false;
private boolean dataClosed = false;
+ private boolean doXferSettings = true;
+
/**
* @return if doParse() was called at construction time
*/
/**
* @return if doParse() was called at construction time
*/
@@
-152,6
+154,12
@@
public abstract class AlignFile extends FileParse
* @param source
* @throws IOException
*/
* @param source
* @throws IOException
*/
+ public AlignFile(FileParse source, boolean doXferSettings)
+ throws IOException
+ {
+ this(true, source, true, doXferSettings);
+ }
+
public AlignFile(FileParse source) throws IOException
{
this(true, source);
public AlignFile(FileParse source) throws IOException
{
this(true, source);
@@
-174,12
+182,19
@@
public abstract class AlignFile extends FileParse
public AlignFile(boolean parseImmediately, FileParse source,
boolean closeData) throws IOException
{
public AlignFile(boolean parseImmediately, FileParse source,
boolean closeData) throws IOException
{
+ this(parseImmediately, source, closeData, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData, boolean doXferSettings) throws IOException
+ {
super(source);
initData();
// stash flag in case parse needs to know if it has to autoconfigure or was
// configured after construction
this.parseImmediately = parseImmediately;
super(source);
initData();
// stash flag in case parse needs to know if it has to autoconfigure or was
// configured after construction
this.parseImmediately = parseImmediately;
+ this.doXferSettings = doXferSettings;
if (parseImmediately)
{
if (parseImmediately)
{
@@
-206,7
+221,7
@@
public abstract class AlignFile extends FileParse
+ "Need to call initData() again before parsing can be reattempted.");
}
parseCalled = true;
+ "Need to call initData() again before parsing can be reattempted.");
}
parseCalled = true;
- parse();
+ parse(this.doXferSettings);
if (closeData && !dataClosed)
{
dataIn.close();
if (closeData && !dataClosed)
{
dataIn.close();
@@
-371,6
+386,18
@@
public abstract class AlignFile extends FileParse
public abstract void parse() throws IOException;
/**
public abstract void parse() throws IOException;
/**
+ * This method is only overridden by JmolParser because of its use in
+ * StructureFile to parse annotations
+ *
+ * @param doXferSettings
+ * @throws IOException
+ */
+ public void parse(boolean doXferSettings) throws IOException
+ {
+ parse();
+ }
+
+ /**
* A general parser for ids.
*
* @String id Id to be parsed
* A general parser for ids.
*
* @String id Id to be parsed
@@
-452,4
+479,14
@@
public abstract class AlignFile extends FileParse
{
seqs.add(seq);
}
{
seqs.add(seq);
}
+
+ public void setDoXferSettings(boolean b)
+ {
+ doXferSettings = b;
+ }
+
+ public boolean getDoXferSettings()
+ {
+ return doXferSettings;
+ }
}
}