JAL-3400 include sequence name in View | Show Chain menu

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index d820273..c727baf 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -77,8 +77,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   Vector<String> atomsPicked = new Vector<>();
 
-  private List<String> chainNames;
-
   Hashtable<String, String> chainFile;
 
   /*
@@ -1196,12 +1194,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setLoadingFromArchive(false);
   }
 
-  @Override
-  public List<String> getChainNames()
-  {
-    return chainNames;
-  }
-
   protected IProgressIndicator getIProgressIndicator()
   {
     return null;

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 381bbea..a5273f5 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -76,8 +76,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private static final String ALPHACARBON = "CA";
 
-  private List<String> chainNames = new ArrayList<>();
-
   private Hashtable<String, String> chainFile = new Hashtable<>();
 
   /*
@@ -1021,18 +1019,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Returns a list of chains mapped in this viewer. Note this list is not
-   * currently scoped per structure.
-   * 
-   * @return
-   */
-  @Override
-  public List<String> getChainNames()
-  {
-    return chainNames;
-  }
-
-  /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
   public void focusView()

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index d04d1d6..853ecc1 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -53,6 +53,7 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
 
@@ -515,6 +516,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     {
       return;
     }
+
+    /*
+     * add the 'All' menu item
+     */
     JMenuItem menuItem = new JMenuItem(
             MessageManager.getString("label.all"));
     menuItem.addActionListener(new ActionListener()
@@ -534,12 +539,29 @@ public abstract class StructureViewerBase extends GStructureViewer
         allChainsSelected = false;
       }
     });
-
     chainMenu.add(menuItem);
 
+    /*
+     * add a menu item for each structure and chain
+     */
+    Collections.sort(chainNames);
+    String lastSeqName = "";
     for (String chain : chainNames)
     {
-      menuItem = new JCheckBoxMenuItem(chain, true);
+      String seqName = getSequenceNameForChain(chain);
+      int nameLength = seqName.length();
+      if (nameLength > 16)
+      {
+        seqName = seqName.substring(0, 8) + "..."
+                + seqName.substring(nameLength - 8, nameLength);
+      }
+      String text = chain;
+      if (!lastSeqName.equals(seqName))
+      {
+        text = text + " " + seqName;
+      }
+      lastSeqName = seqName;
+      menuItem = new JCheckBoxMenuItem(text, true);
       menuItem.addItemListener(new ItemListener()
       {
         @Override
@@ -557,6 +579,26 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
+   * Answers the name of the sequence mapped to the given chain (formatted as
+   * pdbId:chainId, e.g. 1A70:A). Answers null if no mapped sequence is found. If
+   * more than one sequence is matched, just answers the name of the first one
+   * found.
+   * 
+   * @param chain
+   * @return
+   */
+  private String getSequenceNameForChain(String chain)
+  {
+    String[] tokens = chain.split(":");
+    String pdbId = tokens[0];
+    String chainId = tokens[1];
+    List<StructureMapping> mappings = getBinding().getSsm()
+            .getMappingForChain(pdbId, chainId);
+    return mappings.isEmpty() ? null
+            : mappings.get(0).getSequence().getName();
+  }
+
+  /**
    * Action on selecting one of Jalview's registered colour schemes
    */
   @Override

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 66cd8f2..a7a970f 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -291,7 +291,7 @@ public abstract class GStructureViewer extends JInternalFrame
         JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuItem;
         if (item.isSelected())
         {
-          chains.add(item.getText());
+          chains.add(item.getText().split(" ")[0]);
         }
       }
     }

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 054ed2f..e1045c0 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1161,6 +1161,28 @@ public class StructureSelectionManager
   }
 
   /**
+   * Answers a (possibly empty) list of structure to sequence mappings matching
+   * the given pdb and chain ids
+   * 
+   * @param pdbId
+   * @param chain
+   * @return
+   */
+  public List<StructureMapping> getMappingForChain(String pdbId,
+          String chain)
+  {
+    List<StructureMapping> result = new ArrayList<>();
+    for (StructureMapping sm : mappings)
+    {
+      if (sm.pdbid.equals(pdbId) && sm.pdbchain.equals(chain))
+      {
+        result.add(sm);
+      }
+    }
+    return result;
+  }
+
+  /**
    * Returns a readable description of all mappings for the given pdbfile to any
    * of the given sequences
    * 

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 8a7c355..b55885d 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -113,6 +113,8 @@ public abstract class AAStructureBindingModel
 
   private boolean hideHiddenRegions;
 
+  protected List<String> chainNames = new ArrayList<>();
+
   /**
    * Data bean class to simplify parameterisation in superposeStructures
    */
@@ -754,13 +756,6 @@ public abstract class AAStructureBindingModel
   }
 
   /**
-   * Returns a list of chains mapped in this viewer.
-   * 
-   * @return
-   */
-  public abstract List<String> getChainNames();
-
-  /**
    * Returns the Jalview panel hosting the structure viewer (if any)
    * 
    * @return
@@ -1175,4 +1170,15 @@ public abstract class AAStructureBindingModel
     }
     return colourMap;
   }
+
+  /**
+   * Returns a list of chains mapped in this viewer. Note this list is not
+   * currently scoped per structure.
+   * 
+   * @return
+   */
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
 }

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 1d620c4..18c4a14 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -72,12 +72,6 @@ public class ChimeraCommandsTest
     }
 
     @Override
-    public List<String> getChainNames()
-    {
-      return null;
-    }
-
-    @Override
     public void setJalviewColourScheme(ColourSchemeI cs)
     {
     }

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index ee155ac..3992746 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -208,13 +208,6 @@ public class AAStructureBindingModelTest
       }
       
       @Override
-      public List<String> getChainNames()
-      {
-        // TODO Auto-generated method stub
-        return null;
-      }
-      
-      @Override
       protected void colourBySequence(String[] colourBySequenceCommands)
       {
         // TODO Auto-generated method stub
@@ -303,12 +296,6 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      public List<String> getChainNames()
-      {
-        return null;
-      }
-
-      @Override
       public void setJalviewColourScheme(ColourSchemeI cs)
       {
       }