JAL-1911 bugfix - do not save i18n text in preference file

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 4a50196..f41d86a 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -27,9 +28,9 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
+import jalview.io.PDBFeatureSettings;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -41,19 +42,25 @@ import com.stevesoft.pat.Regex;
  * @author JimP
  * 
  */
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+public class Pdb extends EbiFileRetrievedProxy
 {
   public Pdb()
   {
     super();
-    addDbSourceProperty(DBRefSource.PROTSEQDB);
   }
 
+  public static final String FEATURE_INSERTION = "INSERTION";
+
+  public static final String FEATURE_RES_NUM = "RESNUM";
+
+  private static String currentDefaultFomart = DBRefSource.PDB;
+
   /*
    * (non-Javadoc)
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
     // TODO Auto-generated method stub
@@ -65,6 +72,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
     return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
@@ -75,6 +83,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.PDB;
@@ -85,6 +94,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
+  @Override
   public String getDbVersion()
   {
     return "0";
@@ -95,9 +105,10 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    AlignmentI pdbfile = null;
+    AlignmentI pdbAlignment = null;
     Vector result = new Vector();
     String chain = null;
     String id = null;
@@ -121,8 +132,12 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
       stopQuery();
       return null;
     }
+    String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
+            : ".xml";
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    file = ebi.fetchDataAsFile("pdb:" + id,
+            getCurrentDefaultFormat().toLowerCase(), "raw", ext)
+            .getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -131,12 +146,13 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     try
     {
 
-      pdbfile = new FormatAdapter().readFile(file,
-              jalview.io.AppletFormatAdapter.FILE, "PDB");
-      if (pdbfile != null)
+      pdbAlignment = new FormatAdapter().readFile(file,
+              jalview.io.AppletFormatAdapter.FILE,
+              getCurrentDefaultFormat());
+      if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
-        for (SequenceI pdbcs : pdbfile.getSequences())
+        for (SequenceI pdbcs : pdbAlignment.getSequences())
         {
           String chid = null;
           // Mapping map=null;
@@ -188,18 +204,18 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         // now remove marked sequences
         for (SequenceI pdbcs : toremove)
         {
-          pdbfile.deleteSequence(pdbcs);
+          pdbAlignment.deleteSequence(pdbcs);
           if (pdbcs.getAnnotation() != null)
           {
             for (AlignmentAnnotation aa : pdbcs.getAnnotation())
             {
-              pdbfile.deleteAnnotation(aa);
+              pdbAlignment.deleteAnnotation(aa);
             }
           }
         }
       }
 
-      if (pdbfile == null || pdbfile.getHeight() < 1)
+      if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
       {
         throw new Exception(MessageManager.formatMessage(
                 "exception.no_pdb_records_for_chain", new String[] { id,
@@ -211,7 +227,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
       stopQuery();
       throw (ex);
     }
-    return pdbfile;
+    return pdbAlignment;
   }
 
   /*
@@ -219,6 +235,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     Regex r = getAccessionValidator();
@@ -228,11 +245,13 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
   /**
    * obtain human glyoxalase chain A sequence
    */
+  @Override
   public String getTestQuery()
   {
     return "1QIPA";
   }
 
+  @Override
   public String getDbName()
   {
     return "PDB"; // getDbSource();
@@ -243,4 +262,29 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
   {
     return 0;
   }
+
+  public static String getCurrentDefaultFormat()
+  {
+    return currentDefaultFomart;
+  }
+
+  public static void setCurrentDefaultFormat(String currentDefaultFomart)
+  {
+    Pdb.currentDefaultFomart = currentDefaultFomart;
+  }
+
+  /**
+   * 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();
+  }
 }