Set wrapped mode even if false

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5036a0b..14bf680 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,15 +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
@@ -140,6 +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
@@ -783,7 +793,6 @@ 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
@@ -794,7 +803,6 @@ public class AlignFrame
       }\r
       else\r
       {\r
-        System.out.println(format +" 24");\r
         alignment = viewport.getAlignment();\r
 \r
         //!newAlignment\r
@@ -857,7 +865,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)\r
            {\r
              int [] region = (int[]) hc.elementAt(i);\r
-             af.viewport.hideColumns(region[0], region[1]+1);\r
+             af.viewport.hideColumns(region[0], region[1]);\r
            }\r
          }\r
 \r
@@ -1415,7 +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
@@ -1431,13 +1439,14 @@ public class AlignFrame
     {\r
       viewport.hideSequence(seqs[i]);\r
     }\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
@@ -2198,6 +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
@@ -2286,27 +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
@@ -2316,7 +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
@@ -2520,7 +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
@@ -2537,7 +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