moved to org.biojava

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 325a676..cc57961 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -37,7 +37,6 @@ import jalview.ws.*;
 import java.awt.dnd.*;\r
 import org.biojava.dasobert.eventmodel.*;\r
 \r
-\r
 /**\r
  * DOCUMENT ME!\r
  *\r
@@ -69,6 +68,7 @@ public class AlignFrame
    */\r
   public AlignFrame(AlignmentI al)\r
   {\r
+\r
     viewport = new AlignViewport(al);\r
 \r
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
@@ -359,16 +359,13 @@ public class AlignFrame
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
 \r
         if (reply == JOptionPane.YES_OPTION)\r
-          omitHidden = viewport.getSelectionAsString();\r
+          omitHidden = viewport.getViewAsString(false);\r
       }\r
 \r
       String output = new FormatAdapter().formatSequences(\r
           format,\r
           viewport.alignment.getSequencesArray(),\r
-          null);\r
-          //viewport.getSelectionAsNewSequence(),\r
-          //omitHidden) ;\r
-\r
+          omitHidden);\r
 \r
       if (output == null)\r
       {\r
@@ -400,12 +397,6 @@ public class AlignFrame
    */\r
   protected void outputText_actionPerformed(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-    Desktop.addInternalFrame(cap,\r
-                             "Alignment output - " + e.getActionCommand(), 600,\r
-                             500);\r
-\r
-\r
     String [] omitHidden = null;\r
 \r
     if(viewport.hasHiddenColumns)\r
@@ -417,12 +408,20 @@ public class AlignFrame
       JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
 \r
       if(reply==JOptionPane.YES_OPTION)\r
-       omitHidden = viewport.getSelectionAsString();\r
+      {\r
+        omitHidden = viewport.getViewAsString(false);\r
+      }\r
     }\r
 \r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+    Desktop.addInternalFrame(cap,\r
+                             "Alignment output - " + e.getActionCommand(), 600,\r
+                             500);\r
+\r
+\r
     cap.setText(new FormatAdapter().formatSequences(\r
         e.getActionCommand(),\r
-        viewport.getSelectionAsNewSequence(),\r
+        viewport.alignment.getSequencesArray(),\r
         omitHidden));\r
   }\r
 \r
@@ -480,6 +479,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);\r
   }\r
 \r
+\r
   public void exportAnnotations_actionPerformed(ActionEvent e)\r
   {\r
     new AnnotationExporter().exportAnnotations(\r
@@ -690,7 +690,7 @@ public class AlignFrame
 \r
     if (viewport.hasHiddenColumns)\r
     {\r
-      omitHidden = viewport.getSelectionAsString();\r
+      omitHidden = viewport.getViewAsString(true);\r
     }\r
 \r
     String output = new FormatAdapter().formatSequences(\r
@@ -768,6 +768,7 @@ public class AlignFrame
       String format = new IdentifyFile().Identify(str, "Paste");\r
       SequenceI[] sequences;\r
 \r
+\r
      if(Desktop.jalviewClipboard!=null)\r
      {\r
        // The clipboard was filled from within Jalview, we must use the sequences\r
@@ -783,32 +784,40 @@ public class AlignFrame
 \r
       if (newAlignment)\r
       {\r
+        System.out.println(format +" 2");\r
         alignment = new Alignment(sequences);\r
 \r
         if(Desktop.jalviewClipboard!=null)\r
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
         else\r
            alignment.setDataset( null );\r
+\r
       }\r
       else\r
       {\r
+        System.out.println(format +" 24");\r
         alignment = viewport.getAlignment();\r
 \r
         //!newAlignment\r
         for (int i = 0; i < sequences.length; i++)\r
         {\r
-\r
           Sequence newseq = new Sequence(sequences[i].getName(),\r
               sequences[i].getSequence(), sequences[i].getStart(),\r
               sequences[i].getEnd());\r
 \r
           alignment.addSequence(newseq);\r
         }\r
+\r
+\r
         viewport.setEndSeq(alignment.getHeight());\r
         alignment.getWidth();\r
         viewport.firePropertyChange("alignment", null, alignment.getSequences());\r
       }\r
 \r
+\r
+\r
+\r
+\r
       // Add any annotations attached to sequences\r
       for (int i = 0; i < sequences.length; i++)\r
      {\r
@@ -1407,7 +1416,7 @@ public class AlignFrame
 \r
   public void showAllColumns_actionPerformed(ActionEvent e)\r
   {\r
-    viewport.getColumnSelection().revealAllHiddenColumns(viewport);\r
+    viewport.showAllHiddenColumns();\r
   }\r
 \r
   public void hideSelSequences_actionPerformed(ActionEvent e)\r
@@ -1423,13 +1432,14 @@ public class AlignFrame
     {\r
       viewport.hideSequence(seqs[i]);\r
     }\r
-    repaint();\r
+\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void hideSelColumns_actionPerformed(ActionEvent e)\r
   {\r
     viewport.hideSelectedColumns();\r
-    repaint();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
@@ -2614,11 +2624,10 @@ public class AlignFrame
 \r
 \r
 \r
-\r
 public void showTranslation_actionPerformed(ActionEvent e)\r
 {\r
   SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
-  String [] seqstring = viewport.getSelectionAsString();\r
+  String [] seqstring = viewport.getViewAsString(true);\r
 \r
   int s, sSize = selection.length;\r
   SequenceI [] newSeq = new SequenceI[sSize];\r
@@ -2844,16 +2853,8 @@ public void drop(DropTargetDropEvent evt)
                                                 AppletFormatAdapter.FILE);\r
         if (!isGroupsFile)\r
         {\r
-          String protocol = "File";\r
-          String format = new IdentifyFile().Identify(file, protocol);\r
-          SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,\r
-              format);\r
-\r
-          FastaFile ff = new FastaFile();\r
-          Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
-          c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);\r
-\r
-          this.paste(false);\r
+          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);\r
+          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);\r
         }\r
       }\r
       else\r