X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=unused%2FJalviewJS.java;fp=unused%2FJalviewJS.java;h=1218c891eb0cf57259ac1027faf8e897e231f9ac;hp=0000000000000000000000000000000000000000;hb=65740880573a48adc758bec3939ece9d9ae104dd;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477

diff --git a/unused/JalviewJS.java b/unused/JalviewJS.java
new file mode 100644
index 0000000..1218c89
--- /dev/null
+++ b/unused/JalviewJS.java
@@ -0,0 +1,324 @@
+package jalview.bin;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.SplitFrame;
+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 javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+
+/**
+ * 
+ * early work -- deprecated
+ * 
+ * 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
+{
+
+  static
+  {
+    /**
+     * @j2sNative
+     * 
+     *            thisApplet.__Info.args =
+     *            ["file","examples/uniref50.fa","features",
+     *            "examples/exampleFeatures.txt",
+     *            "props","/Users/gmcarstairs/.jalview_properties"];
+     */
+
+  }
+
+  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";
+
+  private static final String PARAM_PROPS = "props";
+
+  private Map<String, String> params;
+
+  private List<String> pdbFileParams;
+
+  public static void main(String[] args) throws Exception
+  {
+    new JalviewJS().doMain(args);
+  }
+
+  /**
+   * Parses parameters and shows the frame and any loaded panels
+   * 
+   * @throws FileFormatException
+   */
+  void doMain(String[] args) throws FileFormatException
+  {
+    loadParameters(args);
+    if (getParameter(PARAM_FILE) == null)
+    {
+      usage();
+    }
+    else
+    {
+      showFrame();
+    }
+  }
+
+  /**
+   * 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 <alignmentFile> [features <featuresFile>]");
+    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);
+    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));
+  }
+
+  /**
+   * 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(getParameter(PARAM_FILE));
+    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+    /*
+     * 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
+     */
+    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();
+
+    frame.pack();
+    frame.setSize(AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+    frame.setVisible(true);
+  }
+
+  /**
+   * 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)
+  {
+    if (featureFile != null)
+    {
+      // todo extract helper for protocol resolution from JalviewLite
+      DataSourceType sourceType = featureFile.startsWith("http")
+              ? DataSourceType.URL
+              : DataSourceType.RELATIVE_URL;
+      alignFrame.parseFeaturesFile(featureFile, sourceType);
+    }
+  }
+
+  /**
+   * Constructs and returns the frame containing the alignment and its
+   * annotations. Returns null if the specified parameter value is not set.
+   * 
+   * @param fileParam
+   * 
+   * @return
+   * @throws FileFormatException
+   */
+  AlignFrame createAlignFrame(String fileParam) throws FileFormatException
+  {
+    AlignFrame af = null;
+    String file = getParameter(fileParam);
+    if (file != null)
+    {
+      DataSourceType protocol = file.startsWith("http") ? DataSourceType.URL
+              : DataSourceType.RELATIVE_URL;
+      // 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;
+  }
+
+}