JAL-2422 JAL-3551 viewer text/variables generalised, Pymol paths added

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index aa39ee7..1bbc397 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -20,25 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.DataSourceType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.structure.StructureMapping;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.event.ActionEvent;
@@ -65,6 +46,24 @@ import javax.swing.JRadioButtonMenuItem;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.DataSourceType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
+
 /**
  * Base class with common functionality for JMol, Chimera or other structure
  * viewers.
@@ -199,8 +198,6 @@ public abstract class StructureViewerBase extends GStructureViewer
     this.viewId = viewId;
   }
 
-  public abstract String getStateInfo();
-
   protected void buildActionMenu()
   {
     if (_alignwith == null)
@@ -680,7 +677,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     });
 
     viewerColour = new JRadioButtonMenuItem();
-    // text is set in overrides of this method
+    viewerColour
+            .setText(MessageManager.getString("label.colour_with_viewer"));
+    viewerColour.setToolTipText(MessageManager
+            .getString("label.let_viewer_manage_structure_colours"));
     viewerColour.setName(ViewerColour.ByViewer.name());
     viewerColour.setSelected(!binding.isColourBySequence());
 
@@ -718,10 +718,18 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void itemStateChanged(ItemEvent e)
       {
-        alignStructs.setEnabled(!_alignwith.isEmpty());
-        alignStructs.setToolTipText(MessageManager.formatMessage(
-                "label.align_structures_using_linked_alignment_views",
-                _alignwith.size()));
+        if (_alignwith.isEmpty())
+        {
+          alignStructs.setEnabled(false);
+          alignStructs.setToolTipText(null);
+        }
+        else
+        {
+          alignStructs.setEnabled(true);
+          alignStructs.setToolTipText(MessageManager.formatMessage(
+                  "label.align_structures_using_linked_alignment_views",
+                  _alignwith.size()));
+        }
       }
     };
     viewSelectionMenu = new ViewSelectionMenu(
@@ -772,19 +780,8 @@ public abstract class StructureViewerBase extends GStructureViewer
     String reply = null;
     try
     {
-      AlignmentI[] als = new Alignment[_alignwith.size()];
-      HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
-      int[] alm = new int[_alignwith.size()];
-      int a = 0;
-
-      for (AlignmentViewPanel alignPanel : _alignwith)
-      {
-        als[a] = alignPanel.getAlignment();
-        alm[a] = -1;
-        alc[a++] = alignPanel.getAlignment().getHiddenColumns();
-      }
-      reply = getBinding().superposeStructures(als, alm, alc);
-      if (reply != null)
+      reply = getBinding().superposeStructures(_alignwith);
+      if (reply != null && !reply.isEmpty())
       {
         String text = MessageManager
                 .formatMessage("error.superposition_failed", reply);
@@ -1100,4 +1097,69 @@ public abstract class StructureViewerBase extends GStructureViewer
     getBinding().showChains(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.
+   * 
+   * @param processingEntry
+   * @return
+   */
+  protected String fetchPdbFile(PDBEntry processingEntry)
+  {
+    String filePath = null;
+    Pdb pdbclient = new Pdb();
+    AlignmentI pdbseq = null;
+    String pdbid = processingEntry.getId();
+    long handle = System.currentTimeMillis()
+            + Thread.currentThread().hashCode();
+  
+    /*
+     * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
+     */
+    String msg = MessageManager.formatMessage("status.fetching_pdb",
+            new Object[]
+            { pdbid });
+    getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+    // long hdl = startProgressBar(MessageManager.formatMessage(
+    // "status.fetching_pdb", new Object[]
+    // { pdbid }));
+    try
+    {
+      pdbseq = pdbclient.getSequenceRecords(pdbid);
+    } catch (Exception e)
+    {
+      System.err.println(
+              "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
+    } finally
+    {
+      msg = pdbid + " " + MessageManager.getString("label.state_completed");
+      getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+      // stopProgressBar(msg, hdl);
+    }
+    /*
+     * If PDB data were saved and are not invalid (empty alignment), return the
+     * file path.
+     */
+    if (pdbseq != null && pdbseq.getHeight() > 0)
+    {
+      // just use the file name from the first sequence's first PDBEntry
+      filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+              .elementAt(0).getFile()).getAbsolutePath();
+      processingEntry.setFile(filePath);
+    }
+    return filePath;
+  }
+
+  /**
+   * If supported, saves the state of the structure viewer to a temporary file
+   * and returns the file, else returns null
+   * 
+   * @return
+   */
+  public File saveSession()
+  {
+    // TODO: a wait loop to ensure the file is written fully before returning?
+    return getBinding() == null ? null : getBinding().saveSession();
+  }
+
 }