Endres check for wrap alignment

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 325a676..14bf680 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
@@ -61,15 +60,14 @@ public class AlignFrame
   Stack redoList = new Stack();\r
   private int treeCount = 0;\r
 \r
-\r
   /**\r
-   * Creates a new AlignFrame object.\r
-   *\r
-   * @param al DOCUMENT ME!\r
+   * new alignment window with hidden columns\r
+   * @param al AlignmentI\r
+   * @param hiddenColumns ColumnSelection or null\r
    */\r
-  public AlignFrame(AlignmentI al)\r
-  {\r
-    viewport = new AlignViewport(al);\r
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {\r
+\r
+    viewport = new AlignViewport(al, hiddenColumns);\r
 \r
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
 \r
@@ -141,6 +139,17 @@ public class AlignFrame
 \r
   }\r
 \r
+\r
+  /**\r
+   * Creates a new AlignFrame object.\r
+   *\r
+   * @param al DOCUMENT ME!\r
+   */\r
+  public AlignFrame(AlignmentI al)\r
+  {\r
+    this(al, null);\r
+  }\r
+\r
   public AlignViewport getViewport()\r
   {\r
     return viewport;\r
@@ -359,16 +368,13 @@ 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 +406,6 @@ 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 +417,20 @@ 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 +488,7 @@ 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 +699,7 @@ 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 +777,7 @@ 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
@@ -789,6 +799,7 @@ public class AlignFrame
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
         else\r
            alignment.setDataset( null );\r
+\r
       }\r
       else\r
       {\r
@@ -797,18 +808,23 @@ public class AlignFrame
         //!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 +1423,7 @@ 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 +1439,14 @@ 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
@@ -2190,6 +2207,9 @@ public class AlignFrame
         return;\r
       }\r
 \r
+      if(viewport.alignment.getHeight()<2)\r
+        return;\r
+\r
       tp = new TreePanel(viewport, type, pwType);\r
     }\r
 \r
@@ -2278,27 +2298,28 @@ public class AlignFrame
    * or just the selected set will be submitted for multiple alignment.\r
    *\r
    */\r
-  private SequenceI[] gatherSequencesForAlignment()\r
+  private jalview.datamodel.AlignmentView gatherSequencesForAlignment()\r
   {\r
     // Now, check we have enough sequences\r
-    SequenceI[] msa = null;\r
+    AlignmentView msa = null;\r
 \r
     if ( (viewport.getSelectionGroup() != null) &&\r
         (viewport.getSelectionGroup().getSize(false) > 1))\r
     {\r
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
-      SequenceGroup seqs = viewport.getSelectionGroup();\r
+      /*SequenceGroup seqs = viewport.getSelectionGroup();\r
       int sz;\r
       msa = new SequenceI[sz = seqs.getSize(false)];\r
 \r
       for (int i = 0; i < sz; i++)\r
       {\r
         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
-      }\r
+      } */\r
+      msa = viewport.getAlignmentView(true);\r
     }\r
     else\r
     {\r
-      Vector seqs = viewport.getAlignment().getSequences();\r
+      /*Vector seqs = viewport.getAlignment().getSequences();\r
 \r
       if (seqs.size() > 1)\r
       {\r
@@ -2308,7 +2329,8 @@ public class AlignFrame
         {\r
           msa[i] = (SequenceI) seqs.elementAt(i);\r
         }\r
-      }\r
+      }*/\r
+      msa = viewport.getAlignmentView(false);\r
     }\r
     return msa;\r
   }\r
@@ -2512,7 +2534,7 @@ public class AlignFrame
           {\r
             public void actionPerformed(ActionEvent e)\r
             {\r
-              SequenceI[] msa = gatherSequencesForAlignment();\r
+              AlignmentView msa = gatherSequencesForAlignment();\r
               new jalview.ws.MsaWSClient(sh, title, msa,\r
                   false, true, viewport.getAlignment().getDataset(), af);\r
 \r
@@ -2529,7 +2551,7 @@ public class AlignFrame
             {\r
               public void actionPerformed(ActionEvent e)\r
               {\r
-                SequenceI[] msa = gatherSequencesForAlignment();\r
+                AlignmentView msa = gatherSequencesForAlignment();\r
                 new jalview.ws.MsaWSClient(sh, title, msa,\r
                     true, true, viewport.getAlignment().getDataset(), af);\r
 \r
@@ -2614,11 +2636,10 @@ 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 +2865,8 @@ 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