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 jalview.datamodel.AlignmentAnnotation.TFType;
 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 AlignmentAnnotation.TFType temperatureFactorType = null;
+
+  public AlignmentAnnotation.TFType getTemperatureFactorType()
+  {
+    return this.temperatureFactorType;
+  }
+
   /**
    * @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
   {
-    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
   {
+    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();