JAL-3030 reads features file, properties file

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index d161d1d..4e24354 100644 (file)
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -1,6 +1,7 @@
 package jalview.bin;
 
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -9,11 +10,12 @@ import jalview.io.FileLoader;
 import jalview.io.IdentifyFile;
 
 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
@@ -43,6 +45,12 @@ public class JalviewJS
 
   private static final String PARAM_PDBFILE = "PDBFile";
 
+  private static final String PARAM_PROPS = "props";
+
+  private Map<String, String> params;
+
+  private List<String> pdbFileParams;
+
   public static void main(String[] args)
   {
     try
@@ -54,20 +62,6 @@ public class JalviewJS
     }
   }
 
-  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
    * 
@@ -76,7 +70,7 @@ public class JalviewJS
   void doMain(String[] args) throws FileFormatException
   {
     loadParameters(args);
-    if (paramFile == null)
+    if (getParameter(PARAM_FILE) == null)
     {
       usage();
     }
@@ -87,11 +81,22 @@ public class JalviewJS
   }
 
   /**
+   * Answers the value of the given runtime parameter, or null if not provided
+   * 
+   * @param paramName
+   * @return
+   */
+  private String getParameter(String paramName)
+  {
+    return params.get(paramName);
+  }
+
+  /**
    * Prints a chastising, yet helpful, error message on syserr
    */
   private void usage()
   {
-    System.err.println("Usage: JalviewJS file <alignmentFileName>");
+    System.err.println("Usage: JalviewJS file <alignmentFile>");
     System.err.println("See documentation for full parameter list");
   }
 
@@ -106,13 +111,29 @@ public class JalviewJS
   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);
+    params = new HashMap<>();
+
+    // TODO javascript-friendly source of properties
+    Cache.loadProperties(parser.getValue(PARAM_PROPS));
+    loadParameter(parser, PARAM_FILE);
+    loadParameter(parser, PARAM_FILE2);
+    loadParameter(parser, PARAM_TREE);
+    loadParameter(parser, PARAM_FEATURES);
+    loadParameter(parser, PARAM_ANNOTATIONS);
+    loadParameter(parser, PARAM_SHOW_ANNOTATION);
+    pdbFileParams = loadPdbParameters(parser);
+  }
+
+  /**
+   * Reads one command line parameter value and saves it against the parameter
+   * name. Note the saved value is null if the parameter is not present.
+   * 
+   * @param parser
+   * @param param
+   */
+  protected void loadParameter(ArgsParser parser, String param)
+  {
+    params.put(param, parser.getValue(param));
   }
 
   /**
@@ -154,36 +175,63 @@ public class JalviewJS
    */
   void showFrame() throws FileFormatException
   {
-    JFrame frame = new JFrame(this.paramFile);
+    JFrame frame = new JFrame(getParameter(PARAM_FILE));
     frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 
-    JInternalFrame alignFrame = createAlignFrame();
+    /*
+     * construct an AlignFrame and extract its contents and menu bar
+     * TODO there may be a less obscure way to do this
+     */
+    AlignFrame alignFrame = createAlignFrame();
     frame.setContentPane(alignFrame.getContentPane());
     frame.setJMenuBar(alignFrame.getJMenuBar());
 
+    // fudge so that dialogs can be opened with this frame as parent
+    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
+   * 
+   * @param alignFrame
+   * 
+   * @param featureFile
+   */
+  protected void loadFeatures(AlignFrame alignFrame, String featureFile)
+  {
+    if (featureFile != null)
+    {
+      // todo extract helper for protocol resolution from JalviewLite
+      DataSourceType sourceType = featureFile.startsWith("http")
+              ? DataSourceType.URL
+              : DataSourceType.FILE;
+      alignFrame.parseFeaturesFile(featureFile, sourceType);
+    }
+  }
+
+  /**
    * Constructs and returns the frame containing the alignment and its
    * annotations
    * 
    * @return
    * @throws FileFormatException
    */
-  JInternalFrame createAlignFrame() throws FileFormatException
+  AlignFrame createAlignFrame() throws FileFormatException
   {
-    Objects.requireNonNull(this.paramFile);
+    String file = getParameter(PARAM_FILE);
+    Objects.requireNonNull(file);
 
-    DataSourceType protocol = AppletFormatAdapter
-            .checkProtocol(this.paramFile);
-    FileFormatI format = new IdentifyFile().identify(this.paramFile,
-            protocol);
+    DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+    FileFormatI format = new IdentifyFile().identify(file, protocol);
     FileLoader fileLoader = new FileLoader(false);
-    AlignFrame af = fileLoader.LoadFileWaitTillLoaded(this.paramFile,
-            protocol, format);
+    AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+            format);
 
     return af;
   }