X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FStructureFile.java;h=f498c1ee5c13b5915cabec4a1e56a8a7da55e466;hb=49ff0aa506eb0b2e031fa3e8d16337e0c8cf2508;hp=c816f6dac80251297c0d0b4fd772322d3f83f991;hpb=892e857760e779796e156b4fa36d97d8d31e73e1;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index c816f6d..f498c1e 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -30,7 +30,6 @@ import jalview.analysis.AlignSeq;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentAnnotation.TFType;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -38,6 +37,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
 import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
@@ -68,6 +68,47 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
+  private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT;
+
+  private String paeMatrix = null;
+
+  private boolean alphaFoldModel;
+
+  public void setPAEMatrix(String paeFilename)
+  {
+    paeMatrix = paeFilename;
+  }
+
+  public String getPAEMatrix()
+  {
+    return paeMatrix;
+  }
+
+  public boolean hasPAEMatrix()
+  {
+    return paeMatrix != null;
+  }
+
+  public void setTemperatureFactorType(StructureImportSettings.TFType t)
+  {
+    this.temperatureFactorType = t;
+  }
+
+  public StructureImportSettings.TFType getTemperatureFactorType()
+  {
+    return temperatureFactorType;
+  }
+
+  public void setAlphafoldModel(boolean afm)
+  {
+    alphaFoldModel = afm;
+  }
+
+  public boolean isAlphafoldModel()
+  {
+    return alphaFoldModel;
+  }
+
   public StructureFile(Object inFile, DataSourceType sourceType)
           throws IOException
   {
@@ -75,9 +116,11 @@ public abstract class StructureFile extends AlignFile
   }
 
   public StructureFile(Object inFile, DataSourceType sourceType,
-          AlignmentAnnotation.TFType tempfacType) throws IOException
+          StructureImportSettings.TFType tempfacType) throws IOException
   {
-    super(inFile, sourceType, tempfacType);
+    super(false, inFile, sourceType);
+    this.setTemperatureFactorType(tempfacType);
+    doParse();
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -101,7 +144,8 @@ public abstract class StructureFile extends AlignFile
             .isProcessSecondaryStructure();
     this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
-
+    this.temperatureFactorType = StructureImportSettings
+            .getTemperatureFactorType();
   }
 
   public StructureFile(boolean parseImmediately, Object dataObject,
@@ -325,6 +369,8 @@ public abstract class StructureFile extends AlignFile
                 .setProcessSecondaryStructure(predictSecondaryStructure);
         StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
+        StructureImportSettings
+                .setTemperatureFactorType(temperatureFactorType);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl
                 .getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));