JAL-3829 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with...

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 4058cda..9280caa 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -25,10 +25,10 @@ import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Graphics;
-import java.awt.Rectangle;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
@@ -41,6 +41,9 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.fts.service.alphafold.AlphafoldRestClient;
 import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structure.StructureCommand;
@@ -49,7 +52,9 @@ import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
 
 public class AppJmol extends StructureViewerBase
 {
@@ -87,48 +92,55 @@ public class AppJmol extends StructureViewerBase
    * @param bounds
    * @param viewid
    */
-  public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
-          AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
-          boolean leaveColouringToJmol, String loadStatus, Rectangle bounds,
-          String viewid)
+  public AppJmol(StructureViewerModel viewerModel, AlignmentPanel ap,
+          String sessionFile, String viewid)
   {
-    PDBEntry[] pdbentrys = new PDBEntry[files.length];
-    for (int i = 0; i < pdbentrys.length; i++)
+    Map<File, StructureData> pdbData = viewerModel.getFileData();
+    PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()];
+    SequenceI[][] seqs = new SequenceI[pdbData.size()][];
+    int i = 0;
+    for (StructureData data : pdbData.values())
     {
-      // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
-      PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
-              files[i]);
+      PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+              PDBEntry.Type.PDB, data.getFilePath());
       pdbentrys[i] = pdbentry;
+      List<SequenceI> sequencesForPdb = data.getSeqList();
+      seqs[i] = sequencesForPdb
+              .toArray(new SequenceI[sequencesForPdb.size()]);
+      i++;
     }
-    // / TODO: check if protocol is needed to be set, and if chains are
+
+    // TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
             pdbentrys, seqs, null);
 
     jmb.setLoadingFromArchive(true);
     addAlignmentPanel(ap);
-    if (useToAlign)
+    if (viewerModel.isAlignWithPanel())
     {
       useAlignmentPanelForSuperposition(ap);
     }
     initMenus();
-    if (leaveColouringToJmol || !usetoColour)
+    boolean useToColour = viewerModel.isColourWithAlignPanel();
+    boolean leaveColouringToJmol = viewerModel.isColourByViewer();
+    if (leaveColouringToJmol || !useToColour)
     {
       jmb.setColourBySequence(false);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    else if (usetoColour)
+    else if (useToColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
       seqColour.setSelected(true);
       viewerColour.setSelected(false);
     }
-    this.setBounds(bounds);
+
+    this.setBounds(viewerModel.getX(), viewerModel.getY(),
+            viewerModel.getWidth(), viewerModel.getHeight());
     setViewId(viewid);
-    // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
-    // bounds.width,bounds.height);
 
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
@@ -139,7 +151,10 @@ public class AppJmol extends StructureViewerBase
         closeViewer(false);
       }
     });
-    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+    StringBuilder cmd = new StringBuilder();
+    cmd.append("load FILES ").append(QUOTE)
+            .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE);
+    initJmol(cmd.toString());
   }
 
   @Override
@@ -147,8 +162,6 @@ public class AppJmol extends StructureViewerBase
   {
     super.initMenus();
 
-    viewerActionMenu.setText(MessageManager.getString("label.jmol"));
-
     viewerColour
             .setText(MessageManager.getString("label.colour_with_jmol"));
     viewerColour.setToolTipText(MessageManager
@@ -344,8 +357,10 @@ public class AppJmol extends StructureViewerBase
       try
       {
         Cache.log.debug("Waiting around for jmb notify.");
-        Thread.sleep(waitFor);
         waitTotal += waitFor;
+
+        // Thread.sleep() throws an exception in JS
+        Thread.sleep(waitFor);
       } catch (Exception e)
       {
       }
@@ -425,6 +440,8 @@ public class AppJmol extends StructureViewerBase
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       Pdb pdbclient = new Pdb();
+      EBIAlfaFold afclient = new EBIAlfaFold();
+      
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
       {
         String file = jmb.getPdbEntry(pi).getFile();
@@ -433,14 +450,34 @@ public class AppJmol extends StructureViewerBase
           // todo: extract block as method and pull up (also ChimeraViewFrame)
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
-          pdbid = jmb.getPdbEntry(pi).getId();
+          PDBEntry strucEntry = jmb.getPdbEntry(pi);
+          pdbid = strucEntry.getId();
           long hdl = pdbid.hashCode() - System.currentTimeMillis();
           setProgressMessage(MessageManager
                   .formatMessage("status.fetching_pdb", new String[]
                   { pdbid }), hdl);
           try
           {
-            pdbseq = pdbclient.getSequenceRecords(pdbid);
+            if (afclient.isValidReference(pdbid))
+            {
+              pdbseq = afclient.getSequenceRecords(pdbid);
+            } else {
+              if (strucEntry.hasRetrievalUrl())
+              {
+                File tmpFile = File.createTempFile(pdbid, "cif");
+                String fromUrl = strucEntry.getRetrievalUrl();
+                UrlDownloadClient.download(fromUrl, tmpFile);
+                
+                // may not need this check ?
+                file = tmpFile.getAbsolutePath();
+                if (file != null)
+                {
+                  pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
+                }
+              } else {
+                pdbseq = pdbclient.getSequenceRecords(pdbid);
+              }
+            }
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning("Retrieving PDB id " + pdbid, oomerror);