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 e2b73d1..fc0e207 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,13 +1,16 @@
 package jalview.io;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 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.StructureImportSettings;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -23,19 +26,21 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
+  private PDBEntry.Type dbRefType;
+
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
    */
   protected boolean visibleChainAnnotation = false;
 
-  /*
+  /**
    * Set true to predict secondary structure (using JMol for protein, Annotate3D
    * for RNA)
    */
-  protected boolean predictSecondaryStructure = true;
+  protected boolean predictSecondaryStructure = false;
 
-  /*
+  /**
    * Set true (with predictSecondaryStructure=true) to predict secondary
    * structure using an external service (currently Annotate3D for RNA only)
    */
@@ -53,10 +58,29 @@ public abstract class StructureFile extends AlignFile
     super(fp);
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
+  public void addSettings(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
+  {
+    this.visibleChainAnnotation = addAlignmentAnnotations;
+    this.predictSecondaryStructure = predictSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
+  }
+
+  public void xferSettings()
+  {
+    this.visibleChainAnnotation = StructureImportSettings
+            .isVisibleChainAnnotation();
+    this.predictSecondaryStructure = StructureImportSettings
+            .isProcessSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
+            .isExternalSecondaryStructure();
+
+  }
+
+  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
@@ -75,7 +99,7 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
-    entry.setType(PDBEntry.Type.PDB);
+    entry.setType(this.dbRefType);
     entry.setProperty(new Hashtable());
     if (chain.id != null)
     {
@@ -93,21 +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());
-
-    // PDBChain objects maintain reference to dataset
-
-    // SequenceI chainseq = pdbSequence.deriveSequence();
-    // chainseq.setSourceDBRef(sourceDBRef);
-    // chainseq.addPDBId(entry);
-    // chainseq.addDBRef(sourceDBRef);
-    SequenceI chainseq = chain.sequence;
-    chainseq.addPDBId(entry);
-    chainseq.setSourceDBRef(sourceDBRef);
-    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)
@@ -168,8 +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,
@@ -242,8 +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
     {
@@ -251,10 +263,18 @@ public abstract class StructureFile extends AlignFile
       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(),
-                type) };
+        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) };
+
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
+                .setProcessSecondaryStructure(predictSecondaryStructure);
+        StructureImportSettings
+                .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
                 "getSeqsAsArray", new Class[] {}).invoke(jmf));
@@ -276,13 +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;
       }
@@ -378,4 +399,34 @@ public abstract class StructureFile extends AlignFile
   {
     this.chains = chains;
   }
+
+  public Type getDbRefType()
+  {
+    return dbRefType;
+  }
+
+  public void setDbRefType(String dbRefType)
+  {
+    this.dbRefType = Type.valueOf(dbRefType);
+  }
+
+  public void setDbRefType(Type dbRefType)
+  {
+    this.dbRefType = dbRefType;
+  }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }