JAL-1919 house-keeping

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 7262443..97e11eb 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -8,7 +9,7 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -25,6 +26,7 @@ public abstract class StructureFile extends AlignFile
   private String id;
 
   private String dbRefType;
+
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
@@ -62,10 +64,22 @@ public abstract class StructureFile extends AlignFile
     this.predictSecondaryStructure = predictSecondaryStructure;
     this.externalSecondaryStructure = externalSecStr;
   }
-  public StructureFile(boolean parseImmediately, String inFile, String type)
+
+  public void xferSettings()
+  {
+    this.visibleChainAnnotation = StructureImportSettings
+            .isVisibleChainAnnotation();
+    this.predictSecondaryStructure = StructureImportSettings
+            .isPredictSecondaryStructure();
+    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
@@ -104,14 +118,11 @@ public abstract class StructureFile extends AlignFile
     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)
@@ -172,8 +183,7 @@ 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,
@@ -246,8 +256,7 @@ 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
     {
@@ -255,15 +264,18 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
-        final Constructor constructor = cl
-.getConstructor(new Class[] {
+        final Constructor constructor = cl.getConstructor(new Class[] {
             boolean.class, boolean.class, boolean.class, FileParse.class });
-        final Object[] args = new Object[] { true, true, true,
-            new FileParse(getDataName(),
-                type) };
-
-        StructureViewSettings.setShowSeqFeatures(false);
-        StructureViewSettings.setPredictSecondaryStructure(true);
+        final Object[] args = new Object[] { visibleChainAnnotation,
+            predictSecondaryStructure, externalSecondaryStructure,
+            new FileParse(getDataName(), type) };
+
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
+                .setPredictSecondaryStructure(predictSecondaryStructure);
+        StructureImportSettings
+                .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
                 "getSeqsAsArray", new Class[] {}).invoke(jmf));
@@ -285,13 +297,14 @@ 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;
       }
@@ -397,4 +410,19 @@ public abstract class StructureFile extends AlignFile
   {
     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();
+  }
 }