Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5160a3a..d992233 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,6 +20,7 @@ package jalview.gui;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.analysis.CrossRef;
 import jalview.analysis.NJTree;
@@ -27,6 +28,7 @@ import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -72,7 +74,6 @@ import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
 import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -86,7 +87,6 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
-import java.awt.Color;
 import java.awt.Component;
 import java.awt.GridLayout;
 import java.awt.Rectangle;
@@ -118,6 +118,7 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
@@ -2062,7 +2063,59 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
   }
+  @Override
+  protected void expand_newalign(ActionEvent e)
+  {
+    try {
+    AlignmentI alignment = AlignmentUtils.expandContext(getViewport().getAlignment(), -1);
+    AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+            DEFAULT_HEIGHT);
+    String newtitle = new String("Flanking alignment");
+
+    if (Desktop.jalviewClipboard != null
+            && Desktop.jalviewClipboard[2] != null)
+    {
+      Vector hc = (Vector) Desktop.jalviewClipboard[2];
+      for (int i = 0; i < hc.size(); i++)
+      {
+        int[] region = (int[]) hc.elementAt(i);
+        af.viewport.hideColumns(region[0], region[1]);
+      }
+    }
+
+    // >>>This is a fix for the moment, until a better solution is
+    // found!!<<<
+    af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+            .transferSettings(
+                    alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
 
+    // TODO: maintain provenance of an alignment, rather than just make the
+    // title a concatenation of operations.
+    {
+      if (title.startsWith("Copied sequences"))
+      {
+        newtitle = title;
+      }
+      else
+      {
+        newtitle = newtitle.concat("- from " + title);
+      }
+    }
+
+    Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+            DEFAULT_HEIGHT);
+
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Exception whilst pasting: " + ex);
+      // could be anything being pasted in here
+    }
+    catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Viewing flanking region of alignment", oom);
+    }
+  }
   /**
    * DOCUMENT ME!
    * 
@@ -3182,10 +3235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-
         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
-        viewport.setGlobalColourScheme(cs);
       }
       else
       {
@@ -3892,23 +3942,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     calculateTree.removeAll();
     // build the calculate menu
+    
     for (final String type:new String[] {"NJ", "AV"})
     {
+      String treecalcnm = MessageManager.getString("label.tree_calc_"+type.toLowerCase());
       for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
       {
         JMenuItem tm = new JMenuItem();
-        ScoreMatrix sm = (ScoreMatrix) ResidueProperties.scoreMatrices.get(pwtype);
-        final String title="Calculate "+type+" using "+sm.getName();
-        tm.setText(title);// MessageManager.getString("label.neighbour_blosum62"));
-        tm
-                .addActionListener(new java.awt.event.ActionListener()
-                {
-                  public void actionPerformed(ActionEvent e)
-                  {
-                    NewTreePanel(type, (String) pwtype, title);
-                  }
-                });
-        calculateTree.add(tm);
+        ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
+        if (sm.isProtein()==!viewport.getAlignment().isNucleotide())
+        {
+          String smn = MessageManager.getStringOrReturn(
+                  "label.score_model_", sm.getName());
+          final String title = MessageManager.formatMessage(
+                  "label.treecalc_title", treecalcnm, smn);
+          tm.setText(title);//
+          tm.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              NewTreePanel(type, (String) pwtype, title);
+            }
+          });
+          calculateTree.add(tm);
+        }
 
       }
     }
@@ -4364,12 +4421,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
               this);
     }
-
-    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
-    {
-      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-              webService, this);
-    }
   }
 
   /*
@@ -5146,6 +5197,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
     webService.add(rfetch);
 
+    final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(MessageManager.getString("option.trim_retrieved_seqs"));
+    trimrs.setToolTipText(MessageManager.getString("label.trim_retrieved_sequences"));
+    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e) {
+      trimrs.setSelected(trimrs.isSelected());
+      Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", Boolean.valueOf(trimrs.isSelected()).toString());
+    };
+    });
+    rfetch.add(trimrs);
     JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
     fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
     fetchr.addActionListener(new ActionListener()