JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 3ae0650..277b84d 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1119,7 +1119,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 08bca8c..3b47d94 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -1075,7 +1075,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 94df99a..0122802 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -164,7 +164,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void closeViewer()
   {
     // remove listeners for all structures in viewer
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     viewer.dispose();
     lastCommand = null;
     viewer = null;
@@ -250,7 +250,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
      * get the distinct structure files modelled
      * (a file with multiple chains may map to multiple sequences)
      */
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (!waitForFileLoad(files))
     {
       return null;
@@ -577,7 +577,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private int getModelNum(String modelFileName)
   {
-    String[] mfn = getPdbFile();
+    String[] mfn = getStructureFiles();
     if (mfn == null)
     {
       return -1;
@@ -601,8 +601,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   // ////////////////////////////////
   // /StructureListener
-  @Override
-  public synchronized String[] getPdbFile()
+  // @Override
+  public synchronized String[] getPdbFilex()
   {
     if (viewer == null)
     {
@@ -667,6 +667,32 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return modelFileNames;
   }
 
+  @Override
+  public synchronized String[] getStructureFiles()
+  {
+    List<String> mset = new ArrayList<String>();
+    if (viewer == null)
+    {
+      return new String[0];
+    }
+
+    if (modelFileNames == null)
+    {
+      int modelCount = viewer.ms.mc;
+      String filePath = null;
+      for (int i = 0; i < modelCount; ++i)
+      {
+        filePath = viewer.ms.getModelFileName(i);
+        if (!mset.contains(filePath))
+        {
+          mset.add(filePath);
+        }
+      }
+      modelFileNames = mset.toArray(new String[mset.size()]);
+    }
+
+    return modelFileNames;
+  }
   /**
    * map from string to applet
    */
@@ -1035,7 +1061,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     chainNames = new ArrayList<String>();
     chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
-    String[] modelfilenames = getPdbFile();
+    String[] modelfilenames = getStructureFiles();
     // first check if we've lost any structures
     if (oldmodels != null && oldmodels.length > 0)
     {

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index ffce90c..daf6131 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -289,7 +289,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void closeViewer(boolean closeChimera)
   {
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     if (closeChimera)
     {
       viewer.exitChimera();
@@ -340,7 +340,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
     StringBuilder allComs = new StringBuilder(128);
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
 
     if (!waitForFileLoad(files))
     {
@@ -577,7 +577,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * to the Chimera command 'list models type molecule', see
      * ChimeraManager.getModelList().
      */
-    List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+    List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
     boolean hasSubModels = maps != null && maps.size() > 1;
     return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
   }
@@ -745,7 +745,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public synchronized String[] getPdbFile()
+  public synchronized String[] getStructureFiles()
   {
     if (viewer == null)
     {
@@ -1100,7 +1100,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     // TODO refactor as required to pull up to an interface
     AlignmentI alignment = avp.getAlignment();
 
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return 0;

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5d23f49..68a847e 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -410,8 +410,8 @@ public class AppJmol extends StructureViewerBase
     int waitFor = 35;
     int waitTotal = 0;
     while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
-            : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
-                    .getPdbFile().length == files.size()))
+            : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null && jmb
+                    .getStructureFiles().length == files.size()))
     {
       try
       {
@@ -429,7 +429,7 @@ public class AppJmol extends StructureViewerBase
 //        System.err.println("finished: " + jmb.isFinishedInit()
 //                + "; loaded: " + Arrays.toString(jmb.getPdbFile())
 //                + "; files: " + files.toString());
-        jmb.getPdbFile();
+        jmb.getStructureFiles();
         break;
       }
     }
@@ -494,7 +494,7 @@ public class AppJmol extends StructureViewerBase
     String pdbid = "";
     try
     {
-      String[] filesInViewer = jmb.getPdbFile();
+      String[] filesInViewer = jmb.getStructureFiles();
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       Pdb pdbclient = new Pdb();

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index d7f7c31..c52be92 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -919,7 +919,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         // TODO: cope with multiple PDB files in view
         in = new BufferedReader(
-                new FileReader(getBinding().getPdbFile()[0]));
+                new FileReader(getBinding().getStructureFiles()[0]));
         File outFile = chooser.getSelectedFile();
   
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -991,7 +991,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * enable 'Superpose with' if more than one mapped structure
      */
     viewSelectionMenu.setEnabled(false);
-    if (getBinding().getPdbFile().length > 1
+    if (getBinding().getStructureFiles().length > 1
             && getBinding().getSequence().length > 1)
     {
       viewSelectionMenu.setEnabled(true);

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 7580222..c390b17 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -126,7 +126,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return modelSet;
   }

diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index e5c5d04..9fde3f1 100644 (file)
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -31,7 +31,7 @@ public interface StructureListener
    * handles messages for, or null if generic listener (only used by
    * removeListener method)
    */
-  public String[] getPdbFile();
+  public String[] getStructureFiles();
 
   /**
    * Called by StructureSelectionManager to inform viewer to highlight given

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 3ab642f..6930161 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -739,7 +739,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        for (String pdbfile : sl.getPdbFile())
+        for (String pdbfile : sl.getStructureFiles())
         {
           pdbs.remove(pdbfile);
         }

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 84475fe..d9e8c95 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -532,7 +532,7 @@ public abstract class AAStructureBindingModel extends
           BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return -1;
@@ -756,7 +756,7 @@ public abstract class AAStructureBindingModel extends
     {
       return;
     }
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
   
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index d85bb10..29fd092 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -217,7 +217,7 @@ public class JalviewChimeraView
      * (or possibly 52-145 to 1-94 - see JAL-2319)
      */
     StructureSelectionManager ssm = binding.getSsm();
-    String pdbFile = binding.getPdbFile()[0];
+    String pdbFile = binding.getStructureFiles()[0];
     StructureMapping[] mappings = ssm.getMapping(pdbFile);
     assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
             "Failed to perform SIFTS mapping");

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 7ba22b4..dc096ed 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -138,7 +138,7 @@ public class AAStructureBindingModelTest
     testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
     {
       @Override
-      public String[] getPdbFile()
+      public String[] getStructureFiles()
       {
         return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
       }
@@ -230,7 +230,7 @@ public class AAStructureBindingModelTest
     /*
      * create a data bean to hold data per structure file
      */
-    SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
+    SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().length];
     for (int i = 0; i < structs.length; i++)
     {
       structs[i] = testee.new SuperposeData(al.getWidth());