Merge branch 'develop' into features/JAL-1759jmolUpdate

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index c59d201..b275186 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -38,18 +38,6 @@
  */
 package jalview.gui;
 
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
@@ -76,6 +64,19 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
 
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
 /**
  * DOCUMENT ME!
  * 
@@ -83,7 +84,7 @@ import jalview.ws.params.AutoCalcSetting;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, AlignViewportI, CommandListener
+        SelectionSource, CommandListener
 {
   Font font;
 
@@ -656,35 +657,32 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * 
    * @param pdbEntries
-   * @return a series of SequenceI arrays, one for each PDBEntry, listing which
-   *         sequence in the alignment holds a reference to it
+   * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+   *         sequences in the alignment hold a reference to it
    */
   public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
   {
-    ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
     for (PDBEntry pdb : pdbEntries)
     {
-      ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
-      for (int i = 0; i < alignment.getHeight(); i++)
+      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      for (SequenceI sq : alignment.getSequences())
       {
-        Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
-                .getPDBId();
+        Vector<PDBEntry> pdbs = sq
+                .getDatasetSequence().getPDBId();
         if (pdbs == null)
         {
           continue;
         }
-        SequenceI sq;
-        for (int p = 0; p < pdbs.size(); p++)
+        for (PDBEntry p1 : pdbs)
         {
-          PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
           if (p1.getId().equals(pdb.getId()))
           {
-            if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+            if (!seqs.contains(sq))
             {
               seqs.add(sq);
+              continue;
             }
-
-            continue;
           }
         }
       }
@@ -801,7 +799,7 @@ public class AlignViewport extends AlignmentViewport implements
      * If any cDNA/protein mappings can be made between the alignments, offer to
      * open a linked alignment with split frame option.
      */
-    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
       if (AlignmentUtils.isMappable(al, getAlignment()))
       {
@@ -857,14 +855,6 @@ public class AlignViewport extends AlignmentViewport implements
     final boolean openInNewWindow = (response == 2);
 
     /*
-     * Create the AlignFrame first (which creates the new alignment's datasets),
-     * before attempting sequence mapping.
-     */
-    AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-            AlignFrame.DEFAULT_HEIGHT);
-    newAlignFrame.setTitle(title);
-
-    /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
@@ -873,6 +863,23 @@ public class AlignViewport extends AlignmentViewport implements
     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.
+     */
+    al.setDataset(null);
+    AlignmentUtils.mapProteinToCdna(protein, cdna);
+
+    /*
+     * Create the AlignFrame for the added alignment. Note this will include the
+     * cDNA consensus annotation if it is protein (because the alignment holds
+     * mappings to nucleotide)
+     */
+    AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+    newAlignFrame.setTitle(title);
     newAlignFrame.statusBar.setText(MessageManager.formatMessage(
             "label.successfully_loaded_file", new Object[]
             { title }));
@@ -891,13 +898,6 @@ public class AlignViewport extends AlignmentViewport implements
               AlignFrame.DEFAULT_HEIGHT);
     }
 
-    /*
-     * 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.
-     */
-    AlignmentUtils.mapProteinToCdna(protein, cdna);
-
     try
     {
       newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
@@ -939,7 +939,9 @@ public class AlignViewport extends AlignmentViewport implements
           AlignmentI complement, Set<AlignedCodonFrame> mappings)
   {
     /*
-     * Open in split pane. DNA sequence above, protein below.
+     * Make a new frame with a copy of the alignment we are adding to. If this
+     * is protein, the new frame will have a cDNA consensus annotation row
+     * added.
      */
     AlignFrame copyMe = new AlignFrame(complement,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -957,6 +959,10 @@ public class AlignViewport extends AlignmentViewport implements
     proteinFrame.setVisible(true);
     String linkedTitle = MessageManager
             .getString("label.linked_view_title");
+
+    /*
+     * Open in split pane. DNA sequence above, protein below.
+     */
     JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
     Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 
@@ -1030,4 +1036,5 @@ public class AlignViewport extends AlignmentViewport implements
       complementPanel.scrollToCentre(sr, seqOffset);
     }
   }
+
 }