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 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