Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / io / StructureFile.java

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index f498c1e..df384a6 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -23,6 +23,7 @@ package jalview.io;
 import java.awt.Color;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
+import java.net.MalformedURLException;
 import java.util.List;
 import java.util.Vector;
 
@@ -36,6 +37,7 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.TFType;
 import mc_view.PDBChain;
@@ -68,7 +70,7 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
-  private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT;
+  private TFType temperatureFactorType = TFType.DEFAULT;
 
   private String paeMatrix = null;
 
@@ -89,12 +91,12 @@ public abstract class StructureFile extends AlignFile
     return paeMatrix != null;
   }
 
-  public void setTemperatureFactorType(StructureImportSettings.TFType t)
+  public void setTemperatureFactorType(TFType t)
   {
     this.temperatureFactorType = t;
   }
 
-  public StructureImportSettings.TFType getTemperatureFactorType()
+  public TFType getTemperatureFactorType()
   {
     return temperatureFactorType;
   }
@@ -116,7 +118,7 @@ public abstract class StructureFile extends AlignFile
   }
 
   public StructureFile(Object inFile, DataSourceType sourceType,
-          StructureImportSettings.TFType tempfacType) throws IOException
+          TFType tempfacType) throws IOException
   {
     super(false, inFile, sourceType);
     this.setTemperatureFactorType(tempfacType);
@@ -125,7 +127,13 @@ public abstract class StructureFile extends AlignFile
 
   public StructureFile(FileParse fp) throws IOException
   {
-    super(fp);
+    this(fp, true);
+  }
+
+  public StructureFile(FileParse fp, boolean doXferSettings)
+          throws IOException
+  {
+    super(fp, doXferSettings);
   }
 
   public void addSettings(boolean addAlignmentAnnotations,
@@ -138,14 +146,17 @@ public abstract class StructureFile extends AlignFile
 
   public void xferSettings()
   {
-    this.visibleChainAnnotation = StructureImportSettings
-            .isVisibleChainAnnotation();
-    this.predictSecondaryStructure = StructureImportSettings
-            .isProcessSecondaryStructure();
-    this.externalSecondaryStructure = StructureImportSettings
-            .isExternalSecondaryStructure();
-    this.temperatureFactorType = StructureImportSettings
-            .getTemperatureFactorType();
+    if (this.getDoXferSettings())
+    {
+      this.visibleChainAnnotation = StructureImportSettings
+              .isVisibleChainAnnotation();
+      this.predictSecondaryStructure = StructureImportSettings
+              .isProcessSecondaryStructure();
+      this.externalSecondaryStructure = StructureImportSettings
+              .isExternalSecondaryStructure();
+      this.temperatureFactorType = StructureImportSettings
+              .getTemperatureFactorType();
+    }
   }
 
   public StructureFile(boolean parseImmediately, Object dataObject,
@@ -231,7 +242,7 @@ public abstract class StructureFile extends AlignFile
   protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
           throws Exception
   {
-    // System.out.println("this is a PDB format and RNA sequence");
+    // jalview.bin.Console.outPrintln("this is a PDB format and RNA sequence");
     // note: we use reflection here so that the applet can compile and run
     // without the HTTPClient bits and pieces needed for accessing Annotate3D
     // web service
@@ -325,7 +336,7 @@ public abstract class StructureFile extends AlignFile
         processPdbFileWithAnnotate3d(rnaSequences);
       } catch (Exception x)
       {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
+        jalview.bin.Console.errPrintln("Exceptions when dealing with RNA in pdb file");
         x.printStackTrace();
 
       }
@@ -338,60 +349,43 @@ public abstract class StructureFile extends AlignFile
     {
       try
       {
-        processWithJmolParser(proteinSequences);
+        processWithJmolParser(proteinSequences, true);
       } catch (Exception x)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Exceptions from Jmol when processing data in pdb file");
         x.printStackTrace();
       }
     }
   }
 
-  @SuppressWarnings({ "unchecked", "rawtypes" })
-  private void processWithJmolParser(List<SequenceI> prot) throws Exception
+  private void processWithJmolParser(List<SequenceI> prot,
+          boolean doXferSettings) throws MalformedURLException, IOException
   {
-    try
-    {
+    FileParse fp = new FileParse(getDataName(), dataSourceType);
 
-      Class cl = Class.forName("jalview.ext.jmol.JmolParser");
-      if (cl != null)
+    StructureImportSettings.setShowSeqFeatures(false);
+    StructureImportSettings.setVisibleChainAnnotation(false);
+    StructureImportSettings
+            .setProcessSecondaryStructure(predictSecondaryStructure);
+    StructureImportSettings
+            .setExternalSecondaryStructure(externalSecondaryStructure);
+    StructureImportSettings.setTemperatureFactorType(temperatureFactorType);
+    JmolParser jmf = new JmolParser(fp, doXferSettings);
+    AlignmentI al = new Alignment((SequenceI[]) jmf.getSeqsAsArray());
+    jmf.addAnnotations(al);
+    for (SequenceI sq : al.getSequences())
+    {
+      if (sq.getDatasetSequence() != null)
       {
-        final Constructor constructor = cl
-                .getConstructor(new Class[]
-                { FileParse.class });
-        final Object[] args = new Object[] {
-            new FileParse(getDataName(), dataSourceType) };
-
-        StructureImportSettings.setShowSeqFeatures(false);
-        StructureImportSettings.setVisibleChainAnnotation(false);
-        StructureImportSettings
-                .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));
-        cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
-                .invoke(jmf, al);
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            sq.getDatasetSequence().getAllPDBEntries().clear();
-          }
-          else
-          {
-            sq.getAllPDBEntries().clear();
-          }
-        }
-        replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
+        sq.getDatasetSequence().getAllPDBEntries().clear();
+      }
+      else
+      {
+        sq.getAllPDBEntries().clear();
       }
-    } catch (ClassNotFoundException q)
-    {
     }
+    replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
     StructureImportSettings.setShowSeqFeatures(true);
   }