JAL-1919 code improvement to make PDB sequence fetcher file format configurable....

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 74bec63..df98833 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -26,6 +26,7 @@ import jalview.appletgui.FeatureRenderer;
 import jalview.appletgui.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -67,7 +68,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   int my = 0;
 
-  public PDBfile pdb;
+  public StructureFile pdb;
 
   PDBEntry pdbentry;
 
@@ -204,11 +205,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
       {
+        @Override
         public void print(String x)
         {
           mappingDetails.append(x);
         }
 
+        @Override
         public void println()
         {
           mappingDetails.append("\n");
@@ -267,6 +270,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         doKeyPressed(evt);
@@ -470,6 +474,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paint(Graphics g)
   {
 
@@ -774,6 +779,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -818,6 +824,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -860,18 +867,22 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     int x = evt.getX();
@@ -921,6 +932,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -1037,6 +1049,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     return fatom;
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
@@ -1108,6 +1121,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
+  @Override
   public String[] getPdbFile()
   {
     return new String[] { pdbentry.getFile() };
@@ -1210,6 +1224,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index dfe7c8f..1c7a1f7 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -26,6 +26,7 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.FeatureRenderer;
 import jalview.gui.SequenceRenderer;
+import jalview.io.StructureFile;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -65,7 +66,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   int my = 0;
 
-  public PDBfile pdb;
+  public StructureFile pdb;
 
   PDBEntry pdbentry;
 
@@ -201,11 +202,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
       {
+        @Override
         public void print(String x)
         {
           mappingDetails.append(x);
         }
 
+        @Override
         public void println()
         {
           mappingDetails.append("\n");
@@ -245,6 +248,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         keyPressed(evt);
@@ -452,6 +456,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paintComponent(Graphics g)
   {
     super.paintComponent(g);
@@ -745,6 +750,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -789,6 +795,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -824,18 +831,22 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     int x = evt.getX();
@@ -885,6 +896,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -1065,6 +1077,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
+  @Override
   public String[] getPdbFile()
   {
     return new String[] { pdbentry.getFile() };
@@ -1169,6 +1182,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 309a0e1..da744a4 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -152,7 +152,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     {
       EBIFetchClient ebi = new EBIFetchClient();
       String query = "pdb:" + pdbentry.getId();
-      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw", ".xml")
               .getAbsolutePath());
 
       if (pdbentry.getFile() != null)

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index b9acac0..8374721 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -25,6 +25,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
+import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
@@ -204,7 +205,7 @@ public class AppletJmol extends EmbmenuFrame implements
     String alreadyMapped = StructureSelectionManager
             .getStructureSelectionManager(ap.av.applet)
             .alreadyMappedToFile(pdbentry.getId());
-    MCview.PDBfile reader = null;
+    StructureFile reader = null;
     if (alreadyMapped != null)
     {
       reader = StructureSelectionManager.getStructureSelectionManager(
@@ -283,6 +284,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
     this.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         closeViewer();
@@ -415,6 +417,7 @@ public class AppletJmol extends EmbmenuFrame implements
     this.setVisible(false);
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == mappingMenuItem)
@@ -535,6 +538,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.setColourBySequence(itm == seqColour);
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == jmolColour)
@@ -553,6 +557,7 @@ public class AppletJmol extends EmbmenuFrame implements
     }
   }
 
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
@@ -564,10 +569,12 @@ public class AppletJmol extends EmbmenuFrame implements
 
   }
 
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
@@ -641,11 +648,13 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     Dimension currentSize = new Dimension();
 
+    @Override
     public void update(Graphics g)
     {
       paint(g);
     }
 
+    @Override
     public void paint(Graphics g)
     {
       currentSize = this.getSize();

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f9480ab..ebc2c21 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,6 +20,8 @@
  */
 package jalview.bin;
 
+import jalview.datamodel.DBRefSource;
+import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
 import jalview.ws.sifts.SiftsSettings;
@@ -226,6 +228,8 @@ public class Cache
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
 
+  private final static String DEFAULT_STRUCTURE_FOMART = DBRefSource.MMCIF;
+
   /**
    * Initialises the Jalview Application Log
    */
@@ -422,6 +426,8 @@ public class Cache
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
+    Pdb.setCurrentDefaultFomart(jalview.bin.Cache.getDefault(
+            "DEFAULT_STRUCTURE_FOMART", DEFAULT_STRUCTURE_FOMART));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 7c3d192..3f0847b 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -28,6 +28,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
@@ -1121,7 +1122,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       String fileName = modelfilenames[modelnum];
       boolean foundEntry = false;
-      MCview.PDBfile pdb = null;
+      StructureFile pdb = null;
       String pdbfile = null;
       // model was probably loaded inline - so check the pdb file hashcode
       if (loadedInline)

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 1247ace..e2637a9 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
@@ -48,7 +49,7 @@ public class AssociatePdbFileWithSeq
           StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
-    MCview.PDBfile pdbfile = null;
+    StructureFile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[] { sequence }, null, choice,
                     protocol);

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2e396aa..89ba84b 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -44,6 +44,7 @@ import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Objects;
+import java.util.Vector;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
@@ -740,7 +741,12 @@ public class StructureChooser extends GStructureChooser implements
         SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
                 refSeqColIndex);
         selectedSeqsToView.add(selectedSeq);
-        PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+            PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+            if (pdbEntry == null)
+            {
+              pdbEntry = getFindEntry(pdbIdStr,
+                      selectedSeq.getAllPDBEntries());
+            }
         if (pdbEntry == null)
         {
           pdbEntry = new PDBEntry();
@@ -821,6 +827,21 @@ public class StructureChooser extends GStructureChooser implements
     }).start();
   }
 
+  private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+  {
+    Objects.requireNonNull(id);
+    Objects.requireNonNull(pdbEntries);
+    PDBEntry foundEntry = null;
+    for (PDBEntry entry : pdbEntries)
+    {
+      if (entry.getId().equalsIgnoreCase(id))
+      {
+        return entry;
+      }
+    }
+    return foundEntry;
+  }
+
   private void launchStructureViewer(StructureSelectionManager ssm,
           final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 00b3143..6bb04ab 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -34,6 +34,7 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.sifts.SiftsClient;
@@ -319,12 +320,13 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public PDBfile setMapping(SequenceI[] sequence,
+  synchronized public StructureFile setMapping(SequenceI[] sequence,
           String[] targetChains, String pdbFile, String protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
+
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -343,7 +345,7 @@ public class StructureSelectionManager
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
-  synchronized public PDBfile setMapping(boolean forStructureView,
+  synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile,
           String protocol)
@@ -378,12 +380,21 @@ public class StructureSelectionManager
         }
       }
     }
-    PDBfile pdb = null;
+    StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
-              pdbFile, protocol);
+
+      if (pdbFile != null && isCIFFile(pdbFile))
+      {
+        pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
+                secStructServices, pdbFile, protocol);
+      }
+      else
+      {
+        pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+                pdbFile, protocol);
+      }
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
@@ -525,8 +536,15 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  private boolean isCIFFile(String filename)
+  {
+    String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+            filename.length());
+    return "cif".equalsIgnoreCase(fileExt);
+  }
+
   private StructureMapping getStructureMapping(SequenceI seq,
-          String pdbFile, String targetChainId, PDBfile pdb,
+          String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
           AlignSeq maxAlignseq)
   {
@@ -560,7 +578,7 @@ public class StructureSelectionManager
 
   private StructureMapping getNWMappings(SequenceI seq,
           String pdbFile,
-          String maxChainId, PDBChain maxChain, PDBfile pdb,
+          String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {
     final StringBuilder mappingDetails = new StringBuilder(128);

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 66ebe1b..d063247 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -62,7 +62,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
+              emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null,
+              ".xml");
     } catch (Exception e)
     {
       stopQuery();

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 3fd7541..358c838 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -47,6 +47,8 @@ public class Pdb extends EbiFileRetrievedProxy
     super();
   }
 
+  private static String currentDefaultFomart = DBRefSource.MMCIF;
+
   /*
    * (non-Javadoc)
    * 
@@ -124,8 +126,12 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
+    String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
+            : ".xml";
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    file = ebi.fetchDataAsFile("pdb:" + id,
+            getCurrentDefaultFomart().toLowerCase(), "raw", ext)
+            .getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -135,7 +141,8 @@ public class Pdb extends EbiFileRetrievedProxy
     {
 
       pdbAlignment = new FormatAdapter().readFile(file,
-              jalview.io.AppletFormatAdapter.FILE, "PDB");
+              jalview.io.AppletFormatAdapter.FILE,
+              getCurrentDefaultFomart());
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -249,4 +256,14 @@ public class Pdb extends EbiFileRetrievedProxy
   {
     return 0;
   }
+
+  public static String getCurrentDefaultFomart()
+  {
+    return currentDefaultFomart;
+  }
+
+  public static void setCurrentDefaultFomart(String currentDefaultFomart)
+  {
+    Pdb.currentDefaultFomart = currentDefaultFomart;
+  }
 }

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 12ebe90..17f1842 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -165,7 +165,7 @@ public class Uniprot extends DbSourceProxyImpl
       // uniprotxml parameter required since december 2007
       // uniprotkb dbname changed introduced december 2008
       File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
-              null);
+              null, ".xml");
       Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
 
       if (entries != null)

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index c33871d..468b7f0 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -97,13 +97,13 @@ public class EBIFetchClient
    * @return the file holding the response
    * @throws OutOfMemoryError
    */
-  public File fetchDataAsFile(String ids, String f, String s)
+  public File fetchDataAsFile(String ids, String f, String s, String ext)
           throws OutOfMemoryError
   {
     File outFile = null;
     try
     {
-      outFile = File.createTempFile("jalview", ".xml");
+      outFile = File.createTempFile("jalview", ext);
       outFile.deleteOnExit();
       fetchData(ids, f, s, outFile);
       if (outFile.length() == 0)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index d30482f..ef6df43 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -26,6 +26,7 @@ import jalview.api.SiftsClientI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
 import jalview.util.Format;
@@ -77,7 +78,7 @@ public class SiftsClient implements SiftsClientI
 {
   private Entry siftsEntry;
 
-  private PDBfile pdb;
+  private StructureFile pdb;
 
   private String pdbId;
 
@@ -147,7 +148,7 @@ public class SiftsClient implements SiftsClientI
    * @param pdbId
    * @throws SiftsException
    */
-  public SiftsClient(PDBfile pdb) throws SiftsException
+  public SiftsClient(StructureFile pdb) throws SiftsException
   {
     this.pdb = pdb;
     this.pdbId = pdb.getId();

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index cbdbc40..1630110 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -30,13 +30,12 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
-
 public class Mapping
 {
 
@@ -67,7 +66,7 @@ public class Mapping
       { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
 
       StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-      PDBfile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+      StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
               new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
               jalview.io.FormatAdapter.FILE);
       assertTrue(pmap != null);
@@ -138,7 +137,8 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
-    PDBfile pde = ssm.setMapping(true, new SequenceI[] { sq }, new String[]
+    StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
+            new String[]
     { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
@@ -234,7 +234,7 @@ public class Mapping
                     FormatAdapter.PASTE, "FASTA");
     SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+    StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "examples/3W5V.pdb",
             jalview.io.FormatAdapter.FILE);
     if (pmap == null)
@@ -262,7 +262,7 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     ssm.setProcessSecondaryStructure(true);
     ssm.setAddTempFacAnnot(true);
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+    StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
             jalview.io.FormatAdapter.FILE);
     assertTrue(pmap != null);

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index ddee3ac..3529375 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -28,6 +28,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -35,8 +36,6 @@ import java.util.List;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
-
 public class StructureSelectionManagerTest
 {
   private StructureSelectionManager ssm;
@@ -112,7 +111,7 @@ public class StructureSelectionManagerTest
     StructureSelectionManager sm = new StructureSelectionManager();
     sm.setProcessSecondaryStructure(true);
     sm.setAddTempFacAnnot(true);
-    PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
+    StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
             new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
     assertTrue(pmap != null);