JAL-1761 pattern for structure viewer construction from project file

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 87fb1b4..7cf10e7 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 +41,8 @@ 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.gui.ImageExporter.ImageWriterI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structure.StructureCommand;
@@ -87,48 +89,55 @@ 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 +148,10 @@ 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