X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=9104ac14e1cff0a368b25fe95219e82fa89560b9;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c1d3a402deb39cd02dff981c906f119db8266229;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index c1d3a40..9104ac1 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,264 +1,321 @@
-package jalview.javascript;
-
-import java.awt.Color;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.appletgui.AlignFrame;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.SequenceI;
-import jalview.ext.jmol.JmolCommands;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-public class MouseOverStructureListener extends JSFunctionExec implements
-        JsCallBack, StructureListener
-{
-
-  String _listenerfn;
-
-  String[] modelSet;
-
-  public MouseOverStructureListener(JalviewLite jalviewLite,
-          String listener, String[] modelList)
-  {
-    super(jalviewLite);
-    _listenerfn = listener;
-    modelSet = modelList;
-    if (modelSet != null)
-    {
-      for (int i = 0; i < modelSet.length; i++)
-      {
-        // resolve a real filename
-        try
-        {
-          if (new java.net.URL(modelSet[i]).openConnection() != null)
-          {
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-        try
-        {
-          String db = jvlite.getDocumentBase().toString();
-          db = db.substring(0, db.lastIndexOf("/"));
-          if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
-          {
-            modelSet[i] = db + "/" + modelSet[i];
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-        try
-        {
-          if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
-                  .openConnection() != null)
-          {
-            modelSet[i] = jvlite.getCodeBase() + modelSet[i];
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-
-      }
-    }
-  }
-
-  @Override
-  public String[] getPdbFile()
-  {
-    return modelSet;
-  }
-
-  @Override
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-
-    // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
-    // chain, pdbfile)
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    String[] st = new String[0];
-    try
-    {
-      executeJavascriptFunction(_listenerfn, st = new String[]
-      { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
-          "" + atomIndex });
-    } catch (Exception ex)
-    {
-      System.err.println("Couldn't execute callback with " + _listenerfn
-              + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
-              + "," + st[3] + "\n");
-      ex.printStackTrace();
-
-    }
-
-  }
-
-  @Override
- public synchronized void updateColours(Object srce)
-  {
-    final Object source = srce;
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(jvlite);
-    // if (jvlite.debug)
-    // {
-    // ssm.reportMapping();
-    // }
-    if (source instanceof jalview.api.AlignmentViewPanel)
-    {
-      SequenceI[][] sequence = new SequenceI[modelSet.length][];
-      for (int m = 0; m < modelSet.length; m++)
-      {
-        StructureMapping[] sm = ssm.getMapping(modelSet[m]);
-        if (sm != null && sm.length > 0)
-        {
-          sequence[m] = new SequenceI[sm.length];
-          for (int i = 0; i < sm.length; i++)
-          {
-            sequence[m][i] = sm[i].getSequence();
-          }
-        }
-        else
-        {
-          sequence[m] = new SequenceI[0];
-        }
-        // if (jvlite.debug)
-        // {
-        // System.err.println("Mapped '" + modelSet[m] + "' to "
-        // + sequence[m].length + " sequences.");
-        // }
-      }
-
-      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
-              .getSequenceRenderer();
-      FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
-              .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
-              ((jalview.appletgui.AlignmentPanel) source).av) : null;
-      if (fr != null)
-      {
-        ((jalview.appletgui.FeatureRenderer) fr)
-                .transferSettings(((jalview.appletgui.AlignmentPanel) source)
-                        .getFeatureRenderer());
-      }
-      ;
-
-      // Form a colour command for the given alignment panel
-      final String[] colcommands = JmolCommands.getColourBySequenceCommand(
-              ssm, modelSet, sequence, sr, fr,
-              ((AlignmentViewPanel) source).getAlignment());
-      if (colcommands==null)
-      {
-        // 
-        return;
-      }
-      String mclass,mhandle;
-      if (jvlite.isJsMessageSetChanged(mclass="colourstruct",mhandle=((jalview.appletgui.AlignmentPanel) source).av
-              .getViewId(), colcommands)) {
-      jvlite.setJsMessageSet(mclass, mhandle , colcommands);
-      // and notify javascript handler
-      String st[] = new String[]
-                                                  {
-              "colourstruct",
-              ""
-                      + ((jalview.appletgui.AlignmentPanel) source).av
-                              .getViewId(), ""+colcommands.length, ""+(colcommands[0]!=null ? colcommands[0].length() : 0)};
-      try
-      {
-        executeJavascriptFunction(
-                true,
-                _listenerfn,st
-);
-      } catch (Exception ex)
-      {
-        System.err.println("Couldn't execute callback with "
-                + _listenerfn + " using args { " + st[0] + ", "
-                + st[1] + ", " + st[2] + "," + st[3] + "\n");
-        ex.printStackTrace();
-
-      }
-      }
-/*      new Thread(new Runnable()
-      {
-        public void run()
-        {
-          // and send to javascript handler
-          String st[] = new String[0];
-          int i = 0;
-          for (String colcommand : colcommands)
-          {
-            // do sync execution for each chunk
-            try
-            {
-              executeJavascriptFunction(
-                      false,
-                      _listenerfn,
-                      st = new String[]
-                      {
-                          "colourstruct",
-                          ""
-                                  + ((jalview.appletgui.AlignmentPanel) source).av
-                                          .getViewId(), handle, "" });
-            } catch (Exception ex)
-            {
-              System.err.println("Couldn't execute callback with "
-                      + _listenerfn + " using args { " + st[0] + ", "
-                      + st[1] + ", " + st[2] + "," + st[3] + "\n");
-              ex.printStackTrace();
-
-            }
-          }
-        }
-      }).start();
-  */
-    }
-
-  }
-
-  @Override
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    return null;
-  }
-
-  @Override
-  public AlignFrame getAlignFrame()
-  {
-    // associated with all alignframes, always.
-    return null;
-  }
-
-  @Override
-  public String getListenerFunction()
-  {
-    return _listenerfn;
-  }
-
-  public void finalise()
-  {
-    jvlite=null;
-    super.finalize();
-  }
-  @Override
-  public void releaseReferences(Object svl)
-  {
-    
-    // TODO Auto-generated method stub
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.javascript;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.appletgui.AlignFrame;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolCommands;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Propagate events involving PDB structures associated with sequences to a
+ * javascript function. Generally, the javascript handler is called with a
+ * series of arguments like (eventname, ... ). As of Jalview 2.7, the following
+ * different types of events are supported:
+ * <ul>
+ * <li>mouseover: javascript function called with arguments
+ * 
+ * <pre>
+ * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue
+ * number moused over), String(atom index corresponding to residue)]
+ * </pre>
+ * 
+ * </li>
+ * <li>colourstruct: javascript function called with arguments
+ * 
+ * <pre>
+ * ['colourstruct',String(alignment view id),String(number of javascript message
+ * chunks to collect),String(length of first chunk in set of messages - or zero
+ * for null message)]
+ * </pre>
+ * 
+ * <br>
+ * The message contains a series of Jmol script commands that will colour
+ * structures according to their associated sequences in the current view. Use
+ * jalview
+ * .javascript.JalviewLiteJsApi.getJsMessage('colourstruct',String(alignment
+ * view id)) to retrieve successive chunks of the message.</li>
+ * </ul>
+ * 
+ * @author Jim Procter (jprocter)
+ * 
+ */
+public class MouseOverStructureListener extends JSFunctionExec implements
+        JsCallBack, StructureListener
+{
+
+  String _listenerfn;
+
+  String[] modelSet;
+
+  public MouseOverStructureListener(JalviewLite jalviewLite,
+          String listener, String[] modelList)
+  {
+    super(jalviewLite);
+    _listenerfn = listener;
+    modelSet = modelList;
+    if (modelSet != null)
+    {
+      for (int i = 0; i < modelSet.length; i++)
+      {
+        modelSet[i] = resolveModelFile(modelSet[i]);
+      }
+    }
+  }
+
+  /**
+   * Returns the first out of: file, file prefixed by document base, or file
+   * prefixed by codebase which can be resolved to a valid URL. If none can,
+   * returns the input parameter value.
+   * 
+   * @param file
+   */
+  public String resolveModelFile(String file)
+  {
+    // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+    if (HttpUtils.isValidUrl(file))
+    {
+      return file;
+    }
+
+    String db = jvlite.getDocumentBase().toString();
+    db = db.substring(0, db.lastIndexOf("/"));
+    String docBaseFile = db + "/" + file;
+    if (HttpUtils.isValidUrl(docBaseFile))
+    {
+      return docBaseFile;
+    }
+
+    String cb = jvlite.getCodeBase() + file;
+    if (HttpUtils.isValidUrl(cb))
+    {
+      return cb;
+    }
+
+    return file;
+  }
+
+  @Override
+  public String[] getPdbFile()
+  {
+    return modelSet;
+  }
+
+  public void mouseOverStructure(int atomIndex, String strInfo)
+  {
+
+    // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
+    // chain, pdbfile)
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void highlightAtoms(List<AtomSpec> atoms)
+  {
+    for (AtomSpec atom : atoms)
+    {
+      try
+      {
+        // TODO is this right? StructureSelectionManager passes pdbFile as the
+        // field that is interpreted (in 2.8.2) as pdbId?
+        // JBPComment: yep - this is right! the Javascript harness uses the
+        // absolute pdbFile URI to locate the PDB file in the external viewer
+        executeJavascriptFunction(_listenerfn,
+                new String[] { "mouseover", "" + atom.getPdbFile(),
+                    "" + atom.getChain(), "" + (atom.getPdbResNum()),
+                    "" + atom.getAtomIndex() });
+      } catch (Exception ex)
+      {
+        System.err.println("Couldn't execute callback with " + _listenerfn
+                + " for atomSpec: " + atom);
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  @Override
+  public synchronized void updateColours(Object srce)
+  {
+    final Object source = srce;
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(jvlite);
+
+    if (JalviewLite.debug)
+    {
+      System.err.println(this.getClass().getName() + " modelSet[0]: "
+              + modelSet[0]);
+      ssm.reportMapping();
+    }
+
+    if (source instanceof jalview.api.AlignmentViewPanel)
+    {
+      SequenceI[][] sequence = new SequenceI[modelSet.length][];
+      for (int m = 0; m < modelSet.length; m++)
+      {
+        StructureMapping[] sm = ssm.getMapping(modelSet[m]);
+        if (sm != null && sm.length > 0)
+        {
+          sequence[m] = new SequenceI[sm.length];
+          for (int i = 0; i < sm.length; i++)
+          {
+            sequence[m][i] = sm[i].getSequence();
+          }
+        }
+        else
+        {
+          sequence[m] = new SequenceI[0];
+        }
+        // if (jvlite.debug)
+        // {
+        // System.err.println("Mapped '" + modelSet[m] + "' to "
+        // + sequence[m].length + " sequences.");
+        // }
+      }
+
+      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
+              .getSequenceRenderer();
+      FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
+              .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
+              ((jalview.appletgui.AlignmentPanel) source).av) : null;
+      if (fr != null)
+      {
+        ((jalview.appletgui.FeatureRenderer) fr)
+                .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+                        .getFeatureRenderer());
+      }
+      ;
+
+      // Form a colour command from the given alignment panel for each distinct
+      // structure
+      ArrayList<String[]> ccomands = new ArrayList<String[]>();
+      ArrayList<String> pdbfn = new ArrayList<String>();
+      StructureMappingcommandSet[] colcommands = JmolCommands
+              .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
+                      ((AlignmentViewPanel) source).getAlignment());
+      if (colcommands == null)
+      {
+        return;
+      }
+      int sz = 0;
+      for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      {
+        sz += ccset.commands.length;
+        ccomands.add(ccset.commands);
+        pdbfn.add(ccset.mapping);
+      }
+
+      String mclass, mhandle;
+      String ccomandset[] = new String[sz];
+      sz = 0;
+      for (String[] ccset : ccomands)
+      {
+        System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
+        sz += ccset.length;
+      }
+      if (jvlite.isJsMessageSetChanged(
+              mclass = "colourstruct",
+              mhandle = ((jalview.appletgui.AlignmentPanel) source).av
+                      .getViewId(), ccomandset))
+      {
+        jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
+        // and notify javascript handler
+        String st[] = new String[] {
+            "colourstruct",
+            "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
+            "" + ccomandset.length,
+            jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
+                    .size()])) };
+        try
+        {
+          executeJavascriptFunction(true, _listenerfn, st);
+        } catch (Exception ex)
+        {
+          System.err.println("Couldn't execute callback with "
+                  + _listenerfn + " using args { " + st[0] + ", " + st[1]
+                  + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
+          ex.printStackTrace();
+
+        }
+      }
+      /*
+       * new Thread(new Runnable() { public void run() { // and send to
+       * javascript handler String st[] = new String[0]; int i = 0; for (String
+       * colcommand : colcommands) { // do sync execution for each chunk try {
+       * executeJavascriptFunction( false, _listenerfn, st = new String[] {
+       * "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
+       * .getViewId(), handle, "" }); } catch (Exception ex) {
+       * System.err.println("Couldn't execute callback with " + _listenerfn +
+       * " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
+       * "\n"); ex.printStackTrace();
+       * 
+       * } } } }).start();
+       */
+    }
+
+  }
+
+  @Override
+  public AlignFrame getAlignFrame()
+  {
+    // associated with all alignframes, always.
+    return null;
+  }
+
+  @Override
+  public String getListenerFunction()
+  {
+    return _listenerfn;
+  }
+
+  public void finalise()
+  {
+    jvlite = null;
+    super.finalize();
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    return true;
+  }
+
+}