Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 1e806a5..22a49cd 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -55,8 +55,8 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.io.IOException;
 
-public class CutAndPasteTransfer extends Panel implements ActionListener,
-        MouseListener
+public class CutAndPasteTransfer extends Panel
+        implements ActionListener, MouseListener
 {
   boolean pdbImport = false;
 
@@ -211,8 +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;
@@ -238,65 +238,64 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       al = afa.readFile(text, DataSourceType.PASTE, format);
       source = afa.getAlignFile();
 
-    if (al != null)
-    {
-      al.setDataset(null); // set dataset on alignment/sequences
-
-      /*
-       * SplitFrame option dependent on applet parameter for now.
-       */
-      boolean allowSplitFrame = alignFrame.viewport.applet
-              .getDefaultParameter("enableSplitFrame", false);
-      if (allowSplitFrame && openSplitFrame(al, format))
+      if (al != null)
       {
-        return;
-      }
-      if (newWindow)
-      {
-        AlignFrame af;
-
-        if (source instanceof ComplexAlignFile)
+        al.setDataset(null); // set dataset on alignment/sequences
+
+        /*
+         * SplitFrame option dependent on applet parameter for now.
+         */
+        boolean allowSplitFrame = alignFrame.viewport.applet
+                .getDefaultParameter("enableSplitFrame", false);
+        if (allowSplitFrame && openSplitFrame(al, format))
         {
+          return;
+        }
+        if (newWindow)
+        {
+          AlignFrame af;
+
+          if (source instanceof ComplexAlignFile)
+          {
             HiddenColumns colSel = ((ComplexAlignFile) source)
                     .getHiddenColumns();
-          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
-                  .getHiddenSequences();
-          boolean showSeqFeatures = ((ComplexAlignFile) source)
-                  .isShowSeqFeatures();
-          String colourSchemeName = ((ComplexAlignFile) source)
-                  .getGlobalColourScheme();
-          af = new AlignFrame(al, hiddenSeqs, colSel,
-                  alignFrame.viewport.applet, "Cut & Paste input - "
-                          + format, false);
-          af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
-          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
-                  colourSchemeName, al);
-          if (cs != null)
+            SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                    .getHiddenSequences();
+            boolean showSeqFeatures = ((ComplexAlignFile) source)
+                    .isShowSeqFeatures();
+            String colourSchemeName = ((ComplexAlignFile) source)
+                    .getGlobalColourScheme();
+            af = new AlignFrame(al, hiddenSeqs, colSel,
+                    alignFrame.viewport.applet,
+                    "Cut & Paste input - " + format, false);
+            af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+            ColourSchemeI cs = ColourSchemeMapper
+                    .getJalviewColourScheme(colourSchemeName, al);
+            if (cs != null)
+            {
+              af.changeColour(cs);
+            }
+          }
+          else
           {
-            af.changeColour(cs);
+            af = new AlignFrame(al, alignFrame.viewport.applet,
+                    "Cut & Paste input - " + format, false);
+            if (source instanceof FeaturesSourceI)
+            {
+              af.getAlignViewport().setShowSequenceFeatures(true);
+            }
           }
+
+          af.statusBar.setText(MessageManager.getString(
+                  "label.successfully_pasted_annotation_to_alignment"));
         }
         else
         {
-          af = new AlignFrame(al, alignFrame.viewport.applet,
-                  "Cut & Paste input - " + format, false);
-          if (source instanceof FeaturesSourceI)
-          {
-            af.getAlignViewport().setShowSequenceFeatures(true);
-          }
+          alignFrame.addSequences(al.getSequencesArray());
+          alignFrame.statusBar.setText(MessageManager
+                  .getString("label.successfully_pasted_alignment_file"));
         }
-
-        af.statusBar
-                .setText(MessageManager
-                        .getString("label.successfully_pasted_annotation_to_alignment"));
       }
-      else
-      {
-        alignFrame.addSequences(al.getSequencesArray());
-        alignFrame.statusBar.setText(MessageManager
-                .getString("label.successfully_pasted_alignment_file"));
-      }
-    }
     } catch (IOException ex)
     {
       ex.printStackTrace();
@@ -390,17 +389,17 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
           alignFrame.alignPanel.fontChanged();
           alignFrame.changeColour(new TCoffeeColourScheme(
                   alignFrame.viewport.getAlignment()));
-          alignFrame.statusBar
-                  .setText(MessageManager
-                          .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+          alignFrame.statusBar.setText(MessageManager.getString(
+                  "label.successfully_pasted_tcoffee_scores_to_alignment"));
         }
         else
         {
           // 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
-                          .getWarningMessage() : "") }));
+                  "label.failed_add_tcoffee_scores", new Object[]
+                  { (tcf.getWarningMessage() != null
+                          ? tcf.getWarningMessage()
+                          : "") }));
         }
       }
       else
@@ -418,9 +417,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       {
         alignFrame.alignPanel.fontChanged();
         alignFrame.alignPanel.setScrollValues(0, 0);
-        alignFrame.statusBar
-                .setText(MessageManager
-                        .getString("label.successfully_pasted_annotation_to_alignment"));
+        alignFrame.statusBar.setText(MessageManager.getString(
+                "label.successfully_pasted_annotation_to_alignment"));
 
       }
       else
@@ -428,9 +426,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
         if (!alignFrame.parseFeaturesFile(textarea.getText(),
                 jalview.io.DataSourceType.PASTE))
         {
-          alignFrame.statusBar
-                  .setText(MessageManager
-                          .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
+          alignFrame.statusBar.setText(MessageManager.getString(
+                  "label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
         }
       }
     }
@@ -487,8 +484,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   private void jbInit() throws Exception
   {
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-    textarea.setText(MessageManager
-            .getString("label.paste_your_alignment_file"));
+    textarea.setText(
+            MessageManager.getString("label.paste_your_alignment_file"));
     textarea.addMouseListener(this);
     this.setLayout(borderLayout1);
     accept.addActionListener(this);
@@ -504,8 +501,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    if (textarea.getText().startsWith(
-            MessageManager.getString("label.paste_your")))
+    if (textarea.getText()
+            .startsWith(MessageManager.getString("label.paste_your")))
     {
       textarea.setText("");
     }