JAL-1628 wrappers for common checks on ColumnSelection

[jalview.git] / src / jalview / datamodel / ColumnSelection.java

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 0655660..97b7c67 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -6,21 +6,26 @@
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.util.ShiftList;
 
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * NOTE: Columns are zero based.
@@ -184,9 +189,9 @@ public class ColumnSelection
    * @param left
    *          shift in edit (+ve for removal, or -ve for inserts)
    */
-  public Vector compensateForEdit(int start, int change)
+  public List<int[]> compensateForEdit(int start, int change)
   {
-    Vector deletedHiddenColumns = null;
+    List<int[]> deletedHiddenColumns = null;
     for (int i = 0; i < size(); i++)
     {
       int temp = columnAt(i);
@@ -199,14 +204,14 @@ public class ColumnSelection
 
     if (hiddenColumns != null)
     {
-      deletedHiddenColumns = new Vector();
+      deletedHiddenColumns = new ArrayList<int[]>();
       int hSize = hiddenColumns.size();
       for (int i = 0; i < hSize; i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
-          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
+          deletedHiddenColumns.add(region);
 
           hiddenColumns.removeElementAt(i);
           i--;
@@ -750,6 +755,7 @@ public class ColumnSelection
   public boolean isVisible(int column)
   {
     if (hiddenColumns != null)
+    {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
         int[] region = (int[]) hiddenColumns.elementAt(i);
@@ -758,6 +764,7 @@ public class ColumnSelection
           return false;
         }
       }
+    }
 
     return true;
   }
@@ -1016,7 +1023,9 @@ public class ColumnSelection
         w += els.length;
       }
       if (w == 0)
+      {
         return;
+      }
       Enumeration e = annels.elements();
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;
@@ -1256,4 +1265,37 @@ public class ColumnSelection
       }
     }
   }
+
+  /**
+   * 
+   * @return true if there are columns marked
+   */
+  public boolean hasSelectedColumns()
+  {
+    return (selected != null && selected.size() > 0);
+  }
+
+  /**
+   * 
+   * @return true if there are columns hidden
+   */
+  public boolean hasHiddenColumns()
+  {
+    return hiddenColumns != null && hiddenColumns.size() > 0;
+  }
+
+  /**
+   * mark the columns corresponding to gap characters as hidden in the column
+   * selection
+   * 
+   * @param sr
+   */
+  public void hideInsertionsFor(SequenceI sr)
+  {
+    List<int[]> inserts = sr.getInsertions();
+    for (int[] r : inserts)
+    {
+      hideColumns(r[0], r[1]);
+    }
+  }
 }