JAL-2446 merged to spike branch

[jalview.git] / src / jalview / appletgui / CutAndPasteTransfer.java

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 535dc62..1e806a5 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -22,17 +22,21 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesSourceI;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
-import jalview.io.FileParse;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
@@ -49,6 +53,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
+import java.io.IOException;
 
 public class CutAndPasteTransfer extends Panel implements ActionListener,
         MouseListener
@@ -63,7 +68,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   AlignFrame alignFrame;
 
-  FileParse source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
@@ -115,6 +120,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     addSequences.setVisible(false);
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == accept)
@@ -191,7 +197,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   {
     try
     {
-      NewickFile fin = new NewickFile(textarea.getText(), "Paste");
+      NewickFile fin = new NewickFile(textarea.getText(),
+              DataSourceType.PASTE);
 
       fin.parse();
       if (fin.getTree() != null)
@@ -204,8 +211,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       // TODO: JAL-1102 - should have a warning message in dialog, not simply
       // overwrite the broken input data with the exception
       textarea.setText(MessageManager.formatMessage(
-              "label.could_not_parse_newick_file", new Object[]
-              { ex.getMessage() }));
+              "label.could_not_parse_newick_file",
+              new Object[] { ex.getMessage() }));
       return false;
     }
     return false;
@@ -222,17 +229,14 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   {
     AlignmentI al = null;
 
-    String format = new IdentifyFile().Identify(text,
-            AppletFormatAdapter.PASTE);
-    AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
     try
     {
-      al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
+      FileFormatI format = new IdentifyFile().identify(text,
+              DataSourceType.PASTE);
+      AppletFormatAdapter afa = new AppletFormatAdapter(
+              alignFrame.alignPanel);
+      al = afa.readFile(text, DataSourceType.PASTE, format);
       source = afa.getAlignFile();
-    } catch (java.io.IOException ex)
-    {
-      ex.printStackTrace();
-    }
 
     if (al != null)
     {
@@ -253,23 +257,33 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
         if (source instanceof ComplexAlignFile)
         {
-          ColumnSelection colSel = ((ComplexAlignFile) source)
-                  .getColumnSelection();
+            HiddenColumns colSel = ((ComplexAlignFile) source)
+                    .getHiddenColumns();
           SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
-          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          String colourSchemeName = ((ComplexAlignFile) source)
+                  .getGlobalColourScheme();
           af = new AlignFrame(al, hiddenSeqs, colSel,
                   alignFrame.viewport.applet, "Cut & Paste input - "
                           + format, false);
           af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
-          af.changeColour(cs);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
+          if (cs != null)
+          {
+            af.changeColour(cs);
+          }
         }
         else
         {
           af = new AlignFrame(al, alignFrame.viewport.applet,
                   "Cut & Paste input - " + format, false);
+          if (source instanceof FeaturesSourceI)
+          {
+            af.getAlignViewport().setShowSequenceFeatures(true);
+          }
         }
 
         af.statusBar
@@ -283,6 +297,10 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
                 .getString("label.successfully_pasted_alignment_file"));
       }
     }
+    } catch (IOException ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
   /**
@@ -293,9 +311,10 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    * @param al
    * @return
    */
-  protected boolean openSplitFrame(AlignmentI al, String format)
+  protected boolean openSplitFrame(AlignmentI al, FileFormatI format)
   {
-    final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+    final AlignmentI thisAlignment = this.alignFrame.getAlignViewport()
+            .getAlignment();
     if (thisAlignment.isNucleotide() == al.isNucleotide())
     {
       // both nucleotide or both protein
@@ -303,7 +322,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     }
     AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
     AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
-    boolean mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
+    boolean mapped = AlignmentUtils.mapProteinAlignmentToCdna(protein, dna);
     if (!mapped)
     {
       return false;
@@ -324,13 +343,18 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     dialog.setMainPanel(question);
     dialog.setVisible(true);
     dialog.toFront();
-    
+
     if (!dialog.accept)
     {
       return false;
     }
 
     /*
+     * 'align' the added alignment to match the current one
+     */
+    al.alignAs(thisAlignment);
+
+    /*
      * Open SplitFrame with DNA above and protein below, including the alignment
      * from textbox and a copy of the original.
      */
@@ -341,8 +365,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
             "Cut & Paste input - " + format, false, false);
     AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
-    AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
-            : newFrame;
+    AlignFrame proteinFrame = al.isNucleotide() ? copyFrame : newFrame;
     SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
     sf.addToDisplay(false, applet);
     return true;
@@ -358,11 +381,10 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     try
     {
       tcf = new TCoffeeScoreFile(textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE);
+              jalview.io.DataSourceType.PASTE);
       if (tcf.isValid())
       {
-        if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
-                true))
+        if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true))
         {
           alignFrame.tcoffeeColour.setEnabled(true);
           alignFrame.alignPanel.fontChanged();
@@ -377,8 +399,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
           // file valid but didn't get added to alignment for some reason
           alignFrame.statusBar.setText(MessageManager.formatMessage(
                   "label.failed_add_tcoffee_scores",
-                  new Object[]
-                  { (tcf.getWarningMessage() != null ? tcf
+                  new Object[] { (tcf.getWarningMessage() != null ? tcf
                           .getWarningMessage() : "") }));
         }
       }
@@ -393,8 +414,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     if (tcf == null)
     {
       if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
-              textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE))
+              textarea.getText(), jalview.io.DataSourceType.PASTE))
       {
         alignFrame.alignPanel.fontChanged();
         alignFrame.alignPanel.setScrollValues(0, 0);
@@ -406,7 +426,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       else
       {
         if (!alignFrame.parseFeaturesFile(textarea.getText(),
-                jalview.io.AppletFormatAdapter.PASTE))
+                jalview.io.DataSourceType.PASTE))
         {
           alignFrame.statusBar
                   .setText(MessageManager
@@ -429,13 +449,13 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
     if (alignFrame.alignPanel.av.applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
-      { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null,
+              alignFrame.alignPanel, DataSourceType.PASTE);
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, new SequenceI[]
-      { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+              alignFrame.alignPanel, DataSourceType.PASTE);
     }
   }
 
@@ -481,6 +501,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     this.add(textarea, java.awt.BorderLayout.CENTER);
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     if (textarea.getText().startsWith(
@@ -490,18 +511,22 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     }
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }