JAL-3030 try to open a split frame if file and file2 are supplied

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index 1187bcf..18be43b 100644 (file)
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -1,20 +1,24 @@
 package jalview.bin;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
+import jalview.gui.SplitFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
 import jalview.io.IdentifyFile;
+import jalview.structure.StructureSelectionManager;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Objects;
 
 import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
 
 /**
  * Entry point for Jalview as Javascript. Expects parameter names as for the
@@ -55,7 +59,7 @@ public class JalviewJS
     try
     {
       new JalviewJS().doMain(args);
-    } catch (FileFormatException e)
+    } catch (Throwable e)
     {
       e.printStackTrace();
     }
@@ -95,7 +99,8 @@ public class JalviewJS
    */
   private void usage()
   {
-    System.err.println("Usage: JalviewJS file <alignmentFile>");
+    System.err.println(
+            "Usage: JalviewJS file <alignmentFile> [features <featuresFile>]");
     System.err.println("See documentation for full parameter list");
   }
 
@@ -178,28 +183,94 @@ public class JalviewJS
     frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 
     /*
-     * construct an AlignFrame and extract its contents and menu bar
+     * construct an AlignFrame (optionally with features)
+     */
+    AlignFrame alignFrame = createAlignFrame(PARAM_FILE);
+    loadFeatures(alignFrame, getParameter(PARAM_FEATURES));
+
+    JInternalFrame internalFrame = alignFrame;
+
+    /*
+     * convert to SplitFrame if a valid file2 is supplied
+     */
+    AlignFrame alignFrame2 = createAlignFrame(PARAM_FILE2);
+    if (alignFrame2 != null)
+    {
+      SplitFrame splitFrame = loadSplitFrame(alignFrame, alignFrame2);
+      if (splitFrame != null)
+      {
+        internalFrame = splitFrame;
+      }
+    }
+
+    /*
+     * move AlignFrame (or SplitFrame) menu bar and content pane to our frame
      * TODO there may be a less obscure way to do this
      */
-    AlignFrame alignFrame = createAlignFrame();
-    frame.setContentPane(alignFrame.getContentPane());
-    frame.setJMenuBar(alignFrame.getJMenuBar());
+    frame.setContentPane(internalFrame.getContentPane());
+    frame.setJMenuBar(internalFrame.getJMenuBar());
 
     // fudge so that dialogs can be opened with this frame as parent
+    // todo JAL-3031 also override Desktop.addInternalFrame etc
     // Desktop.parent = frame.getContentPane();
 
-    loadFeatures(alignFrame, getParameter(PARAM_FEATURES));
-
     frame.pack();
     frame.setSize(AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     frame.setVisible(true);
   }
 
   /**
-   * Load on a features file if one was specified as a parameter
+   * Constructs a SplitFrame if cdna-protein mappings can be made between the
+   * given alignment frames, else returns null. Any mappings made are registered
+   * with StructureSelectionManager to enable broadcast to listeners.
    * 
    * @param alignFrame
+   * @param alignFrame2
+   * @return
+   */
+  protected SplitFrame loadSplitFrame(AlignFrame alignFrame,
+          AlignFrame alignFrame2)
+  {
+    // code borrowed from AlignViewport.openLinkedAlignment
+    AlignmentI al1 = alignFrame.getViewport().getAlignment();
+    AlignmentI al2 = alignFrame2.getViewport().getAlignment();
+    boolean al1Nuc = al1.isNucleotide();
+    if (al1Nuc == al2.isNucleotide())
+    {
+      System.err.println("Can't make split frame as alignments are both "
+              + (al1Nuc ? "nucleotide" : "protein"));
+      return null;
+    }
+    AlignmentI protein = al1Nuc ? al2 : al1;
+    AlignmentI cdna = al1Nuc ? al1 : al2;
+    boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein,
+            cdna);
+    if (!mapped)
+    {
+      System.err.println("Can't make any mappings for split frame");
+      return null;
+    }
+
+    /*
+     * register sequence mappings
+     */
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
+    ssm.registerMappings(protein.getCodonFrames());
+
+    cdna.alignAs(protein);
+
+    SplitFrame splitFrame = new SplitFrame(
+            al1Nuc ? alignFrame : alignFrame2,
+            al1Nuc ? alignFrame2 : alignFrame);
+
+    return splitFrame;
+  }
+
+  /**
+   * Loads on a features file if one was specified as a parameter
    * 
+   * @param alignFrame
    * @param featureFile
    */
   protected void loadFeatures(AlignFrame alignFrame, String featureFile)
@@ -216,21 +287,24 @@ public class JalviewJS
 
   /**
    * Constructs and returns the frame containing the alignment and its
-   * annotations
+   * annotations. Returns null if the specified parameter value is not set.
+   * 
+   * @param fileParam
    * 
    * @return
    * @throws FileFormatException
    */
-  AlignFrame createAlignFrame() throws FileFormatException
+  AlignFrame createAlignFrame(String fileParam) throws FileFormatException
   {
-    String file = getParameter(PARAM_FILE);
-    Objects.requireNonNull(file);
-
-    DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
-    FileFormatI format = new IdentifyFile().identify(file, protocol);
-    FileLoader fileLoader = new FileLoader(false);
-    AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
-            format);
+    AlignFrame af = null;
+    String file = getParameter(fileParam);
+    if (file != null)
+    {
+      DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+      FileFormatI format = new IdentifyFile().identify(file, protocol);
+      FileLoader fileLoader = new FileLoader(false);
+      af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+    }
 
     return af;
   }