X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=1f39b545bbc3f73e42ef2cc0526c9ca1511b4ab6;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=6ebbf89425d532d017d9159a0fa05ac43f66ce7a;hpb=9ffbc78ef4639f680f304758c88d4e1d98c13859;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 6ebbf89..1f39b54 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -35,6 +35,7 @@ import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 import java.util.Random;
 import java.util.Vector;
 
@@ -47,6 +48,7 @@ import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
@@ -64,6 +66,8 @@ import jalview.schemes.ColourSchemes;
 import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
@@ -87,12 +91,21 @@ public abstract class StructureViewerBase extends GStructureViewer
     BySequence, ByChain, ChargeCysteine, ByViewer
   }
 
-  private static List<StructureViewerBase> svbs = new ArrayList<>();
+  /**
+   * Singleton list of all (open) instances of structureViewerBase TODO:
+   * JAL-3362 - review and adopt the swingJS-safe singleton pattern so each
+   * structure viewer base instance is kept to its own JalviewJS parent
+   */
+  private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
 
-  public static List<StructureViewerBase> getAllStructureViewerBases()
+  /**
+   * 
+   * @return list with all existing StructureViewers instance
+   */
+  public static List<JalviewStructureDisplayI> getAllStructureViewerBases()
   {
-    List<StructureViewerBase> goodSvbs = new ArrayList<>();
-    for (StructureViewerBase s : svbs)
+    List<JalviewStructureDisplayI> goodSvbs = new ArrayList<>();
+    for (JalviewStructureDisplayI s : svbs)
     {
       if (s != null && !goodSvbs.contains(s))
       {
@@ -132,6 +145,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected boolean allChainsSelected = false;
 
+  protected boolean allHetatmBeingSelected = false;
+
   protected JMenu viewSelectionMenu;
 
   /**
@@ -196,6 +211,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     return _aps.contains(ap2.av.getSequenceSetId());
   }
 
+  @Override
   public boolean isUsedforaligment(AlignmentViewPanel ap2)
   {
 
@@ -212,11 +228,13 @@ public abstract class StructureViewerBase extends GStructureViewer
    * 
    * @return TRUE if the view is NOT being coloured by the alignment colours.
    */
+  @Override
   public boolean isColouredByViewer()
   {
     return !getBinding().isColourBySequence();
   }
 
+  @Override
   public String getViewId()
   {
     if (viewId == null)
@@ -379,6 +397,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
+  @Override
   public abstract ViewerType getViewerType();
 
   /**
@@ -595,6 +614,88 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
+  void setHetatmMenuItems(Map<String, String> hetatmNames)
+  {
+    hetatmMenu.removeAll();
+    if (hetatmNames == null || hetatmNames.isEmpty())
+    {
+      hetatmMenu.setVisible(false);
+      return;
+    }
+    hetatmMenu.setVisible(true);
+    allHetatmBeingSelected = false;
+    JMenuItem allMenuItem = new JMenuItem(
+            MessageManager.getString("label.all"));
+    JMenuItem noneMenuItem = new JMenuItem(
+            MessageManager.getString("label.none"));
+    allMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        {
+          allHetatmBeingSelected = true;
+          // Toggle state of everything - on
+          for (int i = 0; i < hetatmMenu.getItemCount(); i++)
+          {
+            if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            {
+              ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+            }
+          }
+          allHetatmBeingSelected = false;
+          showSelectedHetatms();
+        }
+      }
+    });
+
+    noneMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        {
+          allHetatmBeingSelected = true;
+          // Toggle state of everything off
+          for (int i = 0; i < hetatmMenu.getItemCount(); i++)
+          {
+            if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            {
+              ((JCheckBoxMenuItem) hetatmMenu.getItem(i))
+                      .setSelected(false);
+            }
+          }
+          allHetatmBeingSelected = false;
+          showSelectedHetatms();
+        }
+      }
+    });
+    hetatmMenu.add(noneMenuItem);
+    hetatmMenu.add(allMenuItem);
+
+    for (Map.Entry<String, String> chain : hetatmNames.entrySet())
+    {
+      JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(),
+              false);
+      menuItem.setToolTipText(chain.getValue());
+      menuItem.addItemListener(new ItemListener()
+      {
+        @Override
+        public void itemStateChanged(ItemEvent evt)
+        {
+          if (!allHetatmBeingSelected)
+          {
+            // update viewer only when we were clicked, not programmatically
+            // checked/unchecked
+            showSelectedHetatms();
+          }
+        }
+      });
+
+      hetatmMenu.add(menuItem);
+    }
+  }
+
   /**
    * Action on selecting one of Jalview's registered colour schemes
    */
@@ -999,6 +1100,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       return;
     }
     setChainMenuItems(binding.getChainNames());
+    setHetatmMenuItems(binding.getHetatmNames());
 
     this.setTitle(binding.getViewerTitle(getViewerName(), true));
 
@@ -1088,7 +1190,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     // TODO would rather have startProgress/stopProgress as the
     // IProgressIndicator interface
-    long tm = random.nextLong();
+    long tm = IdUtils.newId(IdType.PROGRESS);
     if (progressBar != null)
     {
       progressBar.setProgressBar(msg, tm);
@@ -1150,6 +1252,26 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
+   * Display selected hetatms in viewer
+   */
+  protected void showSelectedHetatms()
+  {
+    List<String> toshow = new ArrayList<>();
+    for (int i = 0; i < hetatmMenu.getItemCount(); i++)
+    {
+      if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+      {
+        JCheckBoxMenuItem item = (JCheckBoxMenuItem) hetatmMenu.getItem(i);
+        if (item.isSelected())
+        {
+          toshow.add(item.getText());
+        }
+      }
+    }
+    getBinding().showHetatms(toshow);
+  }
+
+  /**
    * Tries to fetch a PDB file and save to a temporary local file. Returns the
    * saved file path if successful, or null if not.
    * 
@@ -1163,8 +1285,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     EBIAlfaFold afclient = new EBIAlfaFold();
     AlignmentI pdbseq = null;
     String pdbid = processingEntry.getId();
-    long handle = System.currentTimeMillis()
-            + Thread.currentThread().hashCode();
+    long handle = IdUtils.newId(IdType.PROGRESS);
 
     /*
      * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
@@ -1241,6 +1362,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    * 
    * @return
    */
+  @Override
   public File saveSession()
   {
     if (getBinding() == null)
@@ -1352,6 +1474,16 @@ public abstract class StructureViewerBase extends GStructureViewer
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     // jmb = null;
+
+    try
+    {
+      svbs.remove(this);
+    } catch (Throwable t)
+    {
+      Console.info(
+              "Unexpected exception when deregistering structure viewer",
+              t);
+    }
     dispose();
   }