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JAL-629 implementation of --tempfac options
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
3202ac9
..
889d72e
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-28,6
+28,7
@@
import java.util.List;
import java.util.Vector;
import jalview.datamodel.AlignmentAnnotation;
import java.util.Vector;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
@@
-81,6
+82,13
@@
public abstract class AlignFile extends FileParse
private boolean dataClosed = false;
private boolean dataClosed = false;
+ private AlignmentAnnotation.TFType temperatureFactorType = null;
+
+ public AlignmentAnnotation.TFType getTemperatureFactorType()
+ {
+ return this.temperatureFactorType;
+ }
+
/**
* @return if doParse() was called at construction time
*/
/**
* @return if doParse() was called at construction time
*/
@@
-117,7
+125,13
@@
public abstract class AlignFile extends FileParse
public AlignFile(Object dataObject, DataSourceType sourceType)
throws IOException
{
public AlignFile(Object dataObject, DataSourceType sourceType)
throws IOException
{
- this(true, dataObject, sourceType);
+ this(dataObject, sourceType, null);
+ }
+
+ public AlignFile(Object dataObject, DataSourceType sourceType,
+ AlignmentAnnotation.TFType tempfacType) throws IOException
+ {
+ this(true, dataObject, sourceType, tempfacType);
}
/**
}
/**
@@
-135,9
+149,16
@@
public abstract class AlignFile extends FileParse
public AlignFile(boolean parseImmediately, Object dataObject,
DataSourceType sourceType) throws IOException
{
public AlignFile(boolean parseImmediately, Object dataObject,
DataSourceType sourceType) throws IOException
{
+ this(parseImmediately, dataObject, sourceType, null);
+ }
+
+ public AlignFile(boolean parseImmediately, Object dataObject,
+ DataSourceType sourceType, AlignmentAnnotation.TFType tempfacType) throws IOException
+ {
// BH allows File or String
super(dataObject, sourceType);
initData();
// BH allows File or String
super(dataObject, sourceType);
initData();
+ this.temperatureFactorType = tempfacType;
if (parseImmediately)
{
doParse();
if (parseImmediately)
{
doParse();