JAL-1761 pattern for structure viewer construction from project file

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 65b002b..0e5675c 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -28,6 +28,7 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
@@ -40,6 +41,8 @@ import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -240,22 +243,34 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param colourBySequence
    * @param newViewId
    */
-  public ChimeraViewFrame(String chimeraSessionFile,
-          AlignmentPanel alignPanel, PDBEntry[] pdbArray,
-          SequenceI[][] seqsArray, boolean colourByChimera,
-          boolean colourBySequence, String newViewId)
+  public ChimeraViewFrame(StructureViewerModel viewerData,
+          AlignmentPanel alignPanel, String sessionFile, String vid)
   {
     this();
-    setViewId(newViewId);
-    this.chimeraSessionFile = chimeraSessionFile;
+    setViewId(vid);
+    this.chimeraSessionFile = sessionFile;
+    Map<File, StructureData> pdbData = viewerData.getFileData();
+    PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
+    SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
+    int i = 0;
+    for (StructureData data : pdbData.values())
+    {
+      PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+              PDBEntry.Type.PDB, data.getFilePath());
+      pdbArray[i] = pdbentry;
+      List<SequenceI> sequencesForPdb = data.getSeqList();
+      seqsArray[i] = sequencesForPdb
+              .toArray(new SequenceI[sequencesForPdb.size()]);
+      i++;
+    }
     openNewChimera(alignPanel, pdbArray, seqsArray);
-    if (colourByChimera)
+    if (viewerData.isColourByViewer())
     {
       jmb.setColourBySequence(false);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    else if (colourBySequence)
+    else if (viewerData.isColourWithAlignPanel())
     {
       jmb.setColourBySequence(true);
       seqColour.setSelected(true);