X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=bf80831a32e4d19a5e01d93578d8333d0bc075e7;hb=51728d3951398f9c12d7017c776953f17322cc68;hp=abebcf7a7bff935aab5241092b81c4afdf90de72;hpb=c3b8fbc19c04c2daec702a2bffdfab5d10555143;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index abebcf7..bf80831 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,14 +20,13 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
@@ -49,8 +48,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -78,8 +75,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   Hashtable<String, String> chainFile;
 
-  public String fileLoadingError;
-
   /*
    * the default or current model displayed if the model cannot be identified
    * from the selection message
@@ -100,7 +95,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
-          String protocol)
+          DataSourceType protocol)
   {
     super(ssm, pdbentry, sequenceIs, protocol);
     /*
@@ -173,6 +168,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     releaseUIResources();
   }
 
+  @Override
   public void colourByChain()
   {
     colourBySequence = false;
@@ -182,6 +178,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     evalStateCommand("select *;color chain");
   }
 
+  @Override
   public void colourByCharge()
   {
     colourBySequence = false;
@@ -243,6 +240,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param _hiddenCols
    *          an array of corresponding hidden columns for each alignment
    */
+  @Override
   public void superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
@@ -489,35 +487,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * colour any structures associated with sequences in the given alignment
-   * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
-   * if colourBySequence is enabled.
+   * Sends a set of colour commands to the structure viewer
+   * 
+   * @param colourBySequenceCommands
    */
-  public void colourBySequence(AlignmentViewPanel alignmentv)
+  @Override
+  protected void colourBySequence(
+          StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
-    if (!colourBySequence || !isLoadingFinished())
-    {
-      return;
-    }
-    if (getSsm() == null)
-    {
-      return;
-    }
-    String[] files = getPdbFile();
-
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
-            files, sr, fr, alignment))
+    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
     {
       for (String cbyseq : cpdbbyseq.commands)
       {
@@ -533,6 +511,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param alignment
    * @return
    */
+  @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
@@ -600,17 +579,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment);
-
-  /**
    * instruct the Jalview binding to update the pdbentries vector if necessary
    * prior to matching the jmol view's contents to the list of structure files
    * Jalview knows about.
@@ -719,16 +687,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
-  /**
-   * returns the current sequenceRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment);
+  
 
   // ///////////////////////////////
   // JmolStatusListener
@@ -1143,13 +1102,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
+        addSequence(pe, getSequence()[pe]);
         if (fileName == null)
         {
           if (false)
           // see JAL-623 - need method of matching pasted data up
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, AppletFormatAdapter.PASTE);
+                    pdbfile, DataSourceType.PASTE);
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -1167,12 +1127,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             // needs
             // to be tested. See mantis bug
             // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-            String protocol = AppletFormatAdapter.URL;
+            DataSourceType protocol = DataSourceType.URL;
             try
             {
               if (fl.exists())
               {
-                protocol = AppletFormatAdapter.FILE;
+                protocol = DataSourceType.FILE;
               }
             } catch (Exception e)
             {
@@ -1287,6 +1247,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI cs)
   {
     colourBySequence = false;
@@ -1301,10 +1262,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     command.append("select *;color white;");
     List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
             false);
-    for (String res : residueSet)
+    for (String resName : residueSet)
     {
-      Color col = cs.findColour(res.charAt(0));
-      command.append("select " + res + ";color[" + col.getRed() + ","
+      char res = resName.length() == 3 ? ResidueProperties
+              .getSingleCharacterCode(resName) : resName.charAt(0);
+      Color col = cs.findColour(res, 0, null, null, 0f);
+      command.append("select " + resName + ";color[" + col.getRed() + ","
               + col.getGreen() + "," + col.getBlue() + "];");
     }
 
@@ -1401,6 +1364,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
+  @Override
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);
@@ -1410,7 +1374,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // Jalview doesn't honour resize panel requests
     return null;