Merge branch 'apifix/JAL-1926_JAL-2106' into develop

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 3a7419c..fc0e207 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -8,8 +8,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -25,7 +26,8 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
-  private String dbRefType;
+  private PDBEntry.Type dbRefType;
+
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
@@ -66,19 +68,19 @@ public abstract class StructureFile extends AlignFile
 
   public void xferSettings()
   {
-    this.visibleChainAnnotation = StructureViewSettings
+    this.visibleChainAnnotation = StructureImportSettings
             .isVisibleChainAnnotation();
-    this.predictSecondaryStructure = StructureViewSettings
-            .isPredictSecondaryStructure();
-    this.externalSecondaryStructure = StructureViewSettings
+    this.predictSecondaryStructure = StructureImportSettings
+            .isProcessSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
 
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
+  public StructureFile(boolean parseImmediately, String dataObject, String type)
           throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, type);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -115,16 +117,11 @@ public abstract class StructureFile extends AlignFile
     DBRefEntry sourceDBRef = new DBRefEntry();
     sourceDBRef.setAccessionId(getId());
     sourceDBRef.setSource(DBRefSource.PDB);
-    sourceDBRef.setStartRes(pdbSequence.getStart());
-    sourceDBRef.setEndRes(pdbSequence.getEnd());
-
-    SequenceI chainseq = pdbSequence.deriveSequence();
-    chainseq.setSourceDBRef(sourceDBRef);
-    chainseq.addPDBId(entry);
-    chainseq.addDBRef(sourceDBRef);
-
+    pdbSequence.setSourceDBRef(sourceDBRef);
+    pdbSequence.addPDBId(entry);
+    pdbSequence.addDBRef(sourceDBRef);
+    SequenceI chainseq = pdbSequence;
     seqs.addElement(chainseq);
-
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
 
     if (chainannot != null && visibleChainAnnotation)
@@ -185,8 +182,7 @@ public abstract class StructureFile extends AlignFile
 
   @SuppressWarnings("unchecked")
   protected void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al,
-          String pep, boolean b)
+          AlignmentI al, String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
             .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
@@ -259,8 +255,7 @@ public abstract class StructureFile extends AlignFile
   }
 
   @SuppressWarnings({ "unchecked", "rawtypes" })
-  private void processWithJmolParser(List<SequenceI> prot)
-          throws Exception
+  private void processWithJmolParser(List<SequenceI> prot) throws Exception
   {
     try
     {
@@ -268,19 +263,17 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
-        final Constructor constructor = cl
-.getConstructor(new Class[] {
+        final Constructor constructor = cl.getConstructor(new Class[] {
             boolean.class, boolean.class, boolean.class, FileParse.class });
         final Object[] args = new Object[] { visibleChainAnnotation,
             predictSecondaryStructure, externalSecondaryStructure,
-            new FileParse(getDataName(),
-                type) };
-
-        StructureViewSettings.setShowSeqFeatures(false);
-        StructureViewSettings.setVisibleChainAnnotation(false);
-        StructureViewSettings
-                .setPredictSecondaryStructure(predictSecondaryStructure);
-        StructureViewSettings
+            new FileParse(getDataName(), type) };
+
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
+                .setProcessSecondaryStructure(predictSecondaryStructure);
+        StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
@@ -303,13 +296,14 @@ public abstract class StructureFile extends AlignFile
     } catch (ClassNotFoundException q)
     {
     }
+    StructureImportSettings.setShowSeqFeatures(true);
   }
 
   public PDBChain findChain(String id) throws Exception
   {
     for (PDBChain chain : getChains())
     {
-      if (chain.id.equalsIgnoreCase(id))
+      if (chain.id.equals(id))
       {
         return chain;
       }
@@ -406,13 +400,18 @@ public abstract class StructureFile extends AlignFile
     this.chains = chains;
   }
 
-  public String getDbRefType()
+  public Type getDbRefType()
   {
     return dbRefType;
   }
 
   public void setDbRefType(String dbRefType)
   {
+    this.dbRefType = Type.valueOf(dbRefType);
+  }
+
+  public void setDbRefType(Type dbRefType)
+  {
     this.dbRefType = dbRefType;
   }