JAL-4150 test and quick patch copying code from AlignFrame.paste() to Desktop.paste...

[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 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.util.StringUtils;
 
 /**
  * DOCUMENT ME!
@@ -82,13 +82,6 @@ public abstract class AlignFile extends FileParse
 
   private boolean dataClosed = false;
 
-  private AlignmentAnnotation.TFType temperatureFactorType = null;
-
-  public AlignmentAnnotation.TFType getTemperatureFactorType()
-  {
-    return this.temperatureFactorType;
-  }
-
   /**
    * @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
   {
-    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
   {
-    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();
-    this.temperatureFactorType = tempfacType;
     if (parseImmediately)
     {
       doParse();
@@ -399,7 +379,7 @@ public abstract class AlignFile extends FileParse
   {
     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), "");