Only add 1 feature settings table

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9d1b8f1..9b3bd4a 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,16 +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
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {\r
 \r
-    viewport = new AlignViewport(al);\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
@@ -203,8 +212,6 @@ public class AlignFrame
     {\r
       alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
       alignPanel.repaint();\r
-      if(featureSettings!=null)\r
-        featureSettings.setTableData();\r
     }\r
   }\r
 \r
@@ -703,7 +710,7 @@ public class AlignFrame
         .setContents(new StringSelection(output), Desktop.instance);\r
 \r
     Vector hiddenColumns = null;\r
-    if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)\r
+    if(viewport.hasHiddenColumns)\r
     {\r
       hiddenColumns =new Vector();\r
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
@@ -784,7 +791,6 @@ 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
@@ -795,7 +801,6 @@ public class AlignFrame
       }\r
       else\r
       {\r
-        System.out.println(format +" 24");\r
         alignment = viewport.getAlignment();\r
 \r
         //!newAlignment\r
@@ -852,7 +857,7 @@ public class AlignFrame
        AlignFrame af = new AlignFrame(alignment);\r
        String newtitle = new String("Copied sequences");\r
 \r
-       if(Desktop.jalviewClipboard[2]!=null)\r
+       if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)\r
          {\r
            Vector hc = (Vector)Desktop.jalviewClipboard[2];\r
            for(int i=0; i<hc.size(); i++)\r
@@ -1075,6 +1080,13 @@ public class AlignFrame
     PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
+  public void invertColSel_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.invertColumnSelection();\r
+    alignPanel.repaint();\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -1515,7 +1527,7 @@ public class AlignFrame
   }\r
 \r
 \r
-  FeatureSettings featureSettings;\r
+  public FeatureSettings featureSettings;\r
   public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
     if(featureSettings !=null )\r
@@ -2291,27 +2303,28 @@ 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
@@ -2321,7 +2334,8 @@ public class AlignFrame
         {\r
           msa[i] = (SequenceI) seqs.elementAt(i);\r
         }\r
-      }\r
+      }*/\r
+      msa = viewport.getAlignmentView(false);\r
     }\r
     return msa;\r
   }\r
@@ -2525,7 +2539,7 @@ 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
@@ -2542,7 +2556,7 @@ 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