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JAL-629 stash some TFType and PAEFile info into a PDBEntry
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
889d72e
..
1233940
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-28,12
+28,12
@@
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.SequenceI;
import jalview.util.MessageManager;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-82,13
+82,6
@@
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
*/
@@
-125,13
+118,7
@@
public abstract class AlignFile extends FileParse
public AlignFile(Object dataObject, DataSourceType sourceType)
throws IOException
{
public AlignFile(Object dataObject, DataSourceType sourceType)
throws IOException
{
- this(dataObject, sourceType, null);
- }
-
- public AlignFile(Object dataObject, DataSourceType sourceType,
- AlignmentAnnotation.TFType tempfacType) throws IOException
- {
- this(true, dataObject, sourceType, tempfacType);
+ this(true, dataObject, sourceType);
}
/**
}
/**
@@
-149,16
+136,9
@@
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();
@@
-399,7
+379,7
@@
public abstract class AlignFile extends FileParse
{
Sequence seq = null;
id = id.trim();
{
Sequence seq = null;
id = id.trim();
- int space = id.indexOf(" ");
+ int space = StringUtils.indexOfFirstWhitespace(id);
if (space > -1)
{
seq = new Sequence(id.substring(0, space), "");
if (space > -1)
{
seq = new Sequence(id.substring(0, space), "");