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

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index ec51943..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
@@ -556,7 +578,25 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  abstract void showSelectedChains();
+  /**
+   * 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
@@ -779,12 +819,6 @@ public abstract class StructureViewerBase extends GStructureViewer
     buildColourMenu();
   }
 
-  @Override
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    getBinding().setJalviewColourScheme(cs);
-  }
-
   /**
    * Sends commands to the structure viewer to superimpose structures based on
    * currently associated alignments. May optionally return an error message for
@@ -902,7 +936,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       // Set the colour using the current view for the associated alignframe
       for (AlignmentViewPanel avp : _colourwith)
       {
-        binding.colourBySequence(avp);
+        binding.updateStructureColours(avp);
       }
       seqColoursApplied = true;
     }
@@ -1075,4 +1109,21 @@ public abstract class StructureViewerBase extends GStructureViewer
     toFront();
   }
 
+  @Override
+  public abstract AAStructureBindingModel getBinding();
+
+  /**
+   * Show only the selected chain(s) in the viewer
+   */
+  protected void showSelectedChains()
+  {
+    setSelectedChains();
+  
+    /*
+     * refresh display without resizing - easier to see what changed
+     */
+    getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+            false);
+  }
+
 }