X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=25c907d9424f72c20ade33153ec242589d50e329;hb=f149a335b5467a4802eded5da0ca2fc732d7caf7;hp=9a4d9e20000558bf10ab90982e5c7da8f29a0e02;hpb=aaf78c2f304b237a9c800137126967ace9437c99;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 9a4d9e2..25c907d 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -53,6 +53,7 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
+import java.net.URL;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -68,6 +69,10 @@ import netscape.javascript.JSObject;
 public class JalviewLite extends Applet implements StructureSelectionManagerProvider, JalviewLiteJsApi
 {
 
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager.getStructureSelectionManager(this);
+  }
   // /////////////////////////////////////////
   // The following public methods maybe called
   // externally, eg via javascript in HTML page
@@ -933,11 +938,44 @@ public class JalviewLite extends Applet implements StructureSelectionManagerProv
       
     } catch (Exception ex)
     {
-      System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"' and leftHandColumn='"+leftHandColumn+"'");
+      System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"' and leftHandColumn='"+leftHandColumn+"')");
       ex.printStackTrace();
     }
   }
 
+  /* (non-Javadoc)
+   * @see jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui.AlignFrame, java.lang.String)
+   */
+  @Override
+  public void scrollViewToRowIn(AlignFrame alf, String topRow)
+  {
+    try {
+      alf.scrollToRow(new Integer(topRow).intValue());
+      
+    } catch (Exception ex)
+    {
+      System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"')");
+      ex.printStackTrace();
+    }
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui.AlignFrame, java.lang.String)
+   */
+  @Override
+  public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
+  {
+
+    try {
+      alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+      
+    } catch (Exception ex)
+    {
+      System.err.println("Couldn't parse integer arguments (leftHandColumn='"+leftHandColumn+"')");
+      ex.printStackTrace();
+    } 
+  }
+
   // //////////////////////////////////////////////
   // //////////////////////////////////////////////
 
@@ -1864,7 +1902,7 @@ public class JalviewLite extends Applet implements StructureSelectionManagerProv
     {
       if (file.indexOf("://") == -1)
       {
-        String fl = applet.getDocumentBase() + file;
+        String fl = applet.resolveUrlForLocalOrAbsolute(file, getDocumentBase());
         try
         {
           if (new java.net.URL(fl).openStream() != null)
@@ -1880,20 +1918,17 @@ public class JalviewLite extends Applet implements StructureSelectionManagerProv
         {
         }
         ;
-        fl = applet.getCodeBase() + file;
+        fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
         try
         {
           if (new java.net.URL(fl).openStream() != null)
           {
             if (debug)
             {
-              if (debug)
-              {
-                System.err.println("Prepended codebase for resource: '"
-                        + file + "'");
-              }
-              return fl;
+              System.err.println("Prepended codebase for resource: '"
+                      + file + "'");
             }
+            return fl;
           }
         } catch (Exception x)
         {
@@ -2271,6 +2306,81 @@ public class JalviewLite extends Applet implements StructureSelectionManagerProv
 
   }
 
+  public void openJalviewHelpUrl()
+  {
+    String helpUrl=getParameter("jalviewhelpurl");
+    if (helpUrl==null || helpUrl.trim().length()<5)
+    {
+      helpUrl="http://www.jalview.org/help.html";
+    }
+    showURL(helpUrl, "HELP");    
+  }
+  
+  /**
+   * form a complete URL given a path to a resource and a reference location on the same server
+   * @param url - an absolute path on the same server as localref or a document located relative to localref
+   * @param localref - a URL on the same server as url
+   * @return a complete URL for the resource located by url
+   */
+  private String resolveUrlForLocalOrAbsolute(String url, URL localref)
+  {
+    String codebase = localref.toString();
+    if (url.indexOf("/") == 0)
+    {
+      url = codebase.substring(0, codebase.length()
+              - localref.getFile().length())
+              + url;
+    }
+    else
+    {
+      url = localref + url;
+    }
+    return url;
+  }
+
+  /**
+   * open a URL in the browser - resolving it according to relative refs and coping with javascript: protocol if necessary.
+   * @param url
+   * @param target
+   */
+  public void showURL(String url, String target)
+  {
+    try
+    {
+      if (url.indexOf(":") == -1)
+      {
+        // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+        // form valid URL
+        // Should really use docbase, not codebase.
+        URL prepend;
+        url = resolveUrlForLocalOrAbsolute(url, prepend=getDefaultParameter("resolvetocodebase", false) ? getDocumentBase() : getCodeBase());
+        if (debug) {
+          System.err.println("Show url (prepended "+prepend+" - toggle resolvetocodebase if code/docbase resolution is wrong): " + url);
+        }
+      }
+      else
+      {
+        if (debug) {
+          System.err.println("Show url: " + url);
+        }
+      }
+      if (url.indexOf("javascript:") == 0)
+      {
+        // no target for the javascript context
+        getAppletContext().showDocument(
+                new java.net.URL(url));
+      }
+      else
+      {
+        getAppletContext().showDocument(
+                new java.net.URL(url), target);
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
   /**
    * bind structures in a viewer to any matching sequences in an alignFrame (use
    * sequenceIds to limit scope of search to specific sequences)