From c4ac1df8d2ee8e02ad8f571e250aa0f3e1d8dbed Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 24 Mar 2016 15:55:28 +0000
Subject: [PATCH] JAL-1919 Added ability to generate temprature factor
 annotation via JmolParser

---
 src/jalview/ext/jmol/JmolParser.java |   16 +++++++++++++---
 src/jalview/io/StructureFile.java    |   23 ++++++++++++++++++++---
 2 files changed, 33 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index c9243ed..3280471 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -64,14 +64,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           throws IOException
   {
     super(inFile, type);
-    // addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
   }
 
   public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
           boolean externalSecStr, FileParse fp) throws IOException
   {
     super(fp);
-    // addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
   }
 
   public JmolParser()
@@ -167,6 +165,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
+      xferSettings();
+
       makeResidueList();
       makeCaBondList();
 
@@ -220,7 +220,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
                 .getIndex()] : Float.valueOf(atom.getOccupancy100());
         curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
-        // curAtom.tfactor = atom.group.;
+        curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
         significantAtoms.add(curAtom);
       }
@@ -560,4 +560,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     this.predictSecondaryStructure = predictSecondaryStructure;
   }
 
+  public boolean isVisibleChainAnnotation()
+  {
+    return visibleChainAnnotation;
+  }
+
+  public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
+  {
+    this.visibleChainAnnotation = visibleChainAnnotation;
+  }
+
 }
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index fd488f0..9efaaac 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -63,6 +63,18 @@ public abstract class StructureFile extends AlignFile
     this.predictSecondaryStructure = predictSecondaryStructure;
     this.externalSecondaryStructure = externalSecStr;
   }
+
+  public void xferSettings()
+  {
+    this.visibleChainAnnotation = StructureViewSettings
+            .isVisibleChainAnnotation();
+    this.predictSecondaryStructure = StructureViewSettings
+            .isPredictSecondaryStructure();
+    this.externalSecondaryStructure = StructureViewSettings
+            .isExternalSecondaryStructure();
+
+  }
+
   public StructureFile(boolean parseImmediately, String inFile, String type)
           throws IOException
   {
@@ -259,12 +271,17 @@ public abstract class StructureFile extends AlignFile
         final Constructor constructor = cl
 .getConstructor(new Class[] {
             boolean.class, boolean.class, boolean.class, FileParse.class });
-        final Object[] args = new Object[] { true, true, true,
+        final Object[] args = new Object[] { visibleChainAnnotation,
+            predictSecondaryStructure, externalSecondaryStructure,
             new FileParse(getDataName(),
                 type) };
 
-        StructureViewSettings.setShowSeqFeatures(false);
-        StructureViewSettings.setPredictSecondaryStructure(true);
+        StructureViewSettings.setShowSeqFeatures(true);
+        StructureViewSettings.setVisibleChainAnnotation(false);
+        StructureViewSettings
+                .setPredictSecondaryStructure(predictSecondaryStructure);
+        StructureViewSettings
+                .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
                 "getSeqsAsArray", new Class[] {}).invoke(jmf));
-- 
1.7.10.2