JAL-4366 allow a 3di alignment to be loaded and shown as a split frame with existing...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index e7c237e..d56764b 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -25,6 +25,7 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
+import java.io.File;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -46,11 +47,19 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -719,12 +728,62 @@ public class AlignViewport extends AlignmentViewport
         al.addSequence(seq);
       }
     }
-
+    for (ContactMatrixI cm : toAdd.getContactMaps())
+    {
+      al.addContactList(cm);
+    }
     ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
   /**
+   * Load a File into this AlignViewport attempting to detect format if not
+   * given or given as null.
+   * 
+   * @param file
+   * @param format
+   */
+  public void addFile(File file, FileFormatI format)
+  {
+    addFile(file, format, true);
+  }
+
+  public void addFile(File file, FileFormatI format, boolean async)
+  {
+    DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+
+    if (format == null)
+    {
+      try
+      {
+        format = new IdentifyFile().identify(file, protocol);
+      } catch (FileFormatException e1)
+      {
+        jalview.bin.Console.error("Unknown file format for '" + file + "'");
+      }
+    }
+    else if (FileFormats.getInstance().isIdentifiable(format))
+    {
+      try
+      {
+        format = new IdentifyFile().identify(file, protocol);
+      } catch (FileFormatException e)
+      {
+        jalview.bin.Console.error("Unknown file format for '" + file + "'",
+                e);
+      }
+    }
+
+    new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
+            async);
+  }
+
+  public void addFile(File file)
+  {
+    addFile(file, null);
+  }
+
+  /**
    * Show a dialog with the option to open and link (cDNA <-> protein) as a new
    * alignment, either as a standalone alignment or in a split frame. Returns
    * true if the new alignment was opened, false if not, because the user
@@ -750,13 +809,10 @@ public class AlignViewport extends AlignmentViewport
     JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
             .setResponseHandler(0, () -> {
               addDataToAlignment(al);
-              return null;
             }).setResponseHandler(1, () -> {
               us.openLinkedAlignmentAs(al, title, true);
-              return null;
             }).setResponseHandler(2, () -> {
               us.openLinkedAlignmentAs(al, title, false);
-              return null;
             });
     dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
@@ -774,18 +830,31 @@ public class AlignViewport extends AlignmentViewport
     AlignmentI thisAlignment = newWindowOrSplitPane
             ? new Alignment(getAlignment())
             : getAlignment();
-    AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
-    final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
-
-    /*
-     * Map sequences. At least one should get mapped as we have already passed
-     * the test for 'mappability'. Any mappings made will be added to the
-     * protein alignment. Note creating dataset sequences on the new alignment
-     * is a pre-requisite for building mappings.
-     */
+    
+    // always create dataset for imported alignment before doing anything else..
     al.setDataset(null);
-    AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
+    
+    if (!al.isNucleotide() && !thisAlignment.isNucleotide())
+    {
+      // link AA to 3di or other kind of 'alternative' 1:1 mapping alignment
+      AlignmentUtils.map3diPeptideToProteinAligment(thisAlignment,al);
+
+    }
+    else
+    {
+      // link CODON triplets to Protein
+      AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+      final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
 
+      /*
+       * Map sequences. At least one should get mapped as we have already passed
+       * the test for 'mappability'. Any mappings made will be added to the
+       * protein alignment. Note creating dataset sequences on the new alignment
+       * is a pre-requisite for building mappings.
+       */
+      AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
+    }
+    
     /*
      * Create the AlignFrame for the added alignment. If it is protein, mappings
      * are registered with StructureSelectionManager as a side-effect.
@@ -820,7 +889,7 @@ public class AlignViewport extends AlignmentViewport
     if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
-      protein = openSplitFrame(newAlignFrame, thisAlignment);
+      AlignmentI mapped = openSplitFrame(newAlignFrame, thisAlignment);
     }
   }
 
@@ -941,7 +1010,7 @@ public class AlignViewport extends AlignmentViewport
    */
   protected boolean noReferencesTo(AlignedCodonFrame acf)
   {
-    AlignFrame[] frames = Desktop.getAlignFrames();
+    AlignFrame[] frames = Desktop.getDesktopAlignFrames();
     if (frames == null)
     {
       return true;
@@ -1102,4 +1171,5 @@ public class AlignViewport extends AlignmentViewport
   {
     this.viewName = viewName;
   }
+
 }