Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 01a3c2d..085be71 100644 (file)
--- 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;
@@ -88,6 +90,29 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
+   * 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<>();
+
+  /**
+   * 
+   * @return list with all existing StructureViewers instance
+   */
+  public static List<JalviewStructureDisplayI> getAllStructureViewerBases()
+  {
+    List<JalviewStructureDisplayI> goodSvbs = new ArrayList<>();
+    for (JalviewStructureDisplayI s : svbs)
+    {
+      if (s != null && !goodSvbs.contains(s))
+      {
+        goodSvbs.add(s);
+      }
+    }
+    return goodSvbs;
+  }
+
+  /**
    * list of sequenceSet ids associated with the view
    */
   protected List<String> _aps = new ArrayList<>();
@@ -117,6 +142,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected boolean allChainsSelected = false;
 
+  protected boolean allHetatmBeingSelected = false;
+
   protected JMenu viewSelectionMenu;
 
   /**
@@ -137,6 +164,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     super();
     setFrameIcon(null);
+    svbs.add(this);
   }
 
   /**
@@ -180,6 +208,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     return _aps.contains(ap2.av.getSequenceSetId());
   }
 
+  @Override
   public boolean isUsedforaligment(AlignmentViewPanel ap2)
   {
 
@@ -578,6 +607,81 @@ public abstract class StructureViewerBase extends GStructureViewer
       chainMenu.add(menuItem);
     }
   }
+  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
@@ -983,6 +1087,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       return;
     }
     setChainMenuItems(binding.getChainNames());
+    setHetatmMenuItems(binding.getHetatmNames());
 
     this.setTitle(binding.getViewerTitle(getViewerName(), true));
 
@@ -1132,7 +1237,25 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
     getBinding().showChains(toshow);
   }
-
+  /**
+   * 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.
@@ -1197,7 +1320,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       }
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
     } finally
     {
@@ -1336,6 +1459,13 @@ 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();
   }