From c544a7491c89cc4bb1ea1533940b3b325f4c35ec Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 19 Jun 2018 12:02:52 +0100
Subject: [PATCH] JAL-3030 first cut of JalviewJS.main entry point accepting
 'file' parameter

---
 src/jalview/bin/JalviewJS.java |  190 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 190 insertions(+)
 create mode 100644 src/jalview/bin/JalviewJS.java

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
new file mode 100644
index 0000000..c20e47b
--- /dev/null
+++ b/src/jalview/bin/JalviewJS.java
@@ -0,0 +1,190 @@
+package jalview.bin;
+
+import jalview.gui.AlignFrame;
+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 java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+
+/**
+ * Entry point for Jalview as Javascript. Expects parameter names as for the
+ * JalviewLite applet, formatted as for the Jalview application, for example
+ * 
+ * <pre>
+ *   JalviewJS file /examples/uniref50.fa features /examples/exampleFeatures.txt \
+ *       PDBFile "/examples/pdb1.txt seq1"
+ * </pre>
+ * 
+ * Note that (unlike the applet) parameter names are case sensitive
+ */
+// TODO or format as file=/examples/uniref50.fa (etc)?
+public class JalviewJS
+{
+  private static final String PARAM_FILE = "file";
+
+  private static final String PARAM_FILE2 = "file2";
+
+  private static final String PARAM_TREE = "tree";
+
+  private static final String PARAM_FEATURES = "features";
+
+  private static final String PARAM_ANNOTATIONS = "annotations";
+
+  private static final String PARAM_SHOW_ANNOTATION = "showAnnotation";
+
+  private static final String PARAM_PDBFILE = "PDBFile";
+
+  public static void main(String[] args)
+  {
+    try
+    {
+      new JalviewJS().doMain(args);
+    } catch (FileFormatException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  private String paramFile;
+
+  private String paramFile2;
+
+  private String paramTree;
+
+  private String paramFeatures;
+
+  private String paramAnnotations;
+
+  private String paramShowAnnotation;
+
+  private List<String> paramPdbFile;
+
+  /**
+   * Parses parameters and shows the frame and any loaded panels
+   * 
+   * @throws FileFormatException
+   */
+  void doMain(String[] args) throws FileFormatException
+  {
+    loadParameters(args);
+    if (paramFile == null)
+    {
+      usage();
+    }
+    else
+    {
+      showFrame();
+    }
+  }
+
+  /**
+   * Prints a chastising, yet helpful, error message on syserr
+   */
+  private void usage()
+  {
+    System.err.println("Usage: JalviewJS file <alignmentFileName>");
+    System.err.println("See documentation for full parameter list");
+  }
+
+  /**
+   * Parses any supplied parameters. Note that (unlike for the applet),
+   * parameter names are case sensitive.
+   * 
+   * @param args
+   * 
+   * @see http://www.jalview.org/examples/index.html#appletParameters
+   */
+  void loadParameters(String[] args)
+  {
+    ArgsParser parser = new ArgsParser(args);
+    paramFile = parser.getValue(PARAM_FILE);
+    paramFile2 = parser.getValue(PARAM_FILE2);
+    paramTree = parser.getValue(PARAM_TREE);
+    paramFeatures = parser.getValue(PARAM_FEATURES);
+    paramAnnotations = parser.getValue(PARAM_ANNOTATIONS);
+    paramShowAnnotation = parser.getValue(PARAM_SHOW_ANNOTATION);
+    paramPdbFile = loadPdbParameters(parser);
+  }
+
+  /**
+   * Reads parameter PDBFile, PDBFile1, PDFile2, ... and saves the value(s) (if
+   * any)
+   * 
+   * @param parser
+   * @return
+   */
+  List<String> loadPdbParameters(ArgsParser parser)
+  {
+    List<String> values = new ArrayList<>();
+    String value = parser.getValue(PARAM_PDBFILE);
+    if (value != null)
+    {
+      values.add(value);
+    }
+    int i = 1;
+    while (true)
+    {
+      value = parser.getValue(PARAM_PDBFILE + String.valueOf(i));
+      if (value != null)
+      {
+        values.add(value);
+      }
+      else
+      {
+        break;
+      }
+    }
+    return values;
+  }
+
+  /**
+   * Constructs and displays a JFrame containing an alignment panel (and any
+   * additional panels depending on parameters supplied)
+   * 
+   * @throws FileFormatException
+   */
+  void showFrame() throws FileFormatException
+  {
+    JFrame frame = new JFrame(this.paramFile);
+    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+    JInternalFrame alignFrame = createAlignFrame();
+    frame.setContentPane(alignFrame.getContentPane());
+
+    frame.pack();
+    frame.setSize(AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+    frame.setVisible(true);
+  }
+
+  /**
+   * Constructs and returns the frame containing the alignment and its
+   * annotations
+   * 
+   * @return
+   * @throws FileFormatException
+   */
+  JInternalFrame createAlignFrame() throws FileFormatException
+  {
+    Objects.requireNonNull(this.paramFile);
+
+    DataSourceType protocol = AppletFormatAdapter
+            .checkProtocol(this.paramFile);
+    FileFormatI format = new IdentifyFile().identify(this.paramFile,
+            protocol);
+    FileLoader fileLoader = new FileLoader(false);
+    AlignFrame af = fileLoader.LoadFileWaitTillLoaded(this.paramFile,
+            protocol, format);
+
+    return af;
+  }
+
+}
-- 
1.7.10.2