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 61b3d1d..df384a6 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -242,7 +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
@@ -336,7 +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();
 
       }
@@ -352,61 +352,13 @@ public abstract class StructureFile extends AlignFile
         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 NOTprocessWithJmolParser(List<SequenceI> prot)
-          throws Exception
-  {
-    try
-    {
-
-      Class cl = Class.forName("jalview.ext.jmol.JmolParser");
-      if (cl != 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);
-      }
-    } catch (ClassNotFoundException q)
-    {
-    }
-    StructureImportSettings.setShowSeqFeatures(true);
-  }
-
   private void processWithJmolParser(List<SequenceI> prot,
           boolean doXferSettings) throws MalformedURLException, IOException
   {