X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=15bbffa1e8669610076b4d87363e14f55b33fef9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=93e03d13839ccec722b549f10ea4b60bf32f12d6;hpb=1d4b37e9bd54c095aa00e643b741c931eb61c58b;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 93e03d1..15bbffa 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,7 +25,7 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
 import java.util.ArrayList;
-import java.util.Enumeration;
+import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
 
@@ -34,10 +34,10 @@ import java.util.Vector;
  */
 public class ColumnSelection
 {
-  Vector selected = new Vector();
+  Vector<Integer> selected = new Vector<Integer>();
 
   // Vector of int [] {startCol, endCol}
-  Vector hiddenColumns;
+  Vector<int[]> hiddenColumns;
 
   /**
    * Add a column to the selection
@@ -63,7 +63,7 @@ public class ColumnSelection
   }
 
   /**
-   * removes col from selection
+   * Removes value 'col' from the selection (not the col'th item)
    * 
    * @param col
    *          index of column to be removed
@@ -74,6 +74,8 @@ public class ColumnSelection
 
     if (selected.contains(colInt))
     {
+      // if this ever changes to List.remove(), ensure Integer not int argument
+      // as List.remove(int i) removes the i'th item which is wrong
       selected.removeElement(colInt);
     }
   }
@@ -103,7 +105,7 @@ public class ColumnSelection
    * 
    * @return Vector containing selected columns as Integers
    */
-  public Vector getSelected()
+  public Vector<Integer> getSelected()
   {
     return selected;
   }
@@ -130,7 +132,7 @@ public class ColumnSelection
    */
   public int columnAt(int i)
   {
-    return ((Integer) selected.elementAt(i)).intValue();
+    return selected.elementAt(i).intValue();
   }
 
   /**
@@ -200,6 +202,7 @@ public class ColumnSelection
 
       if (temp >= start)
       {
+        // if this ever changes to List.set(), swap parameter order!!
         selected.setElementAt(new Integer(temp - change), i);
       }
     }
@@ -210,7 +213,7 @@ public class ColumnSelection
       int hSize = hiddenColumns.size();
       for (int i = 0; i < hSize; i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
           deletedHiddenColumns.add(region);
@@ -257,6 +260,7 @@ public class ColumnSelection
 
       if (temp >= start)
       {
+        // if this ever changes to List.set(), swap parameter order!!
         selected.setElementAt(new Integer(temp - change), i);
       }
     }
@@ -265,7 +269,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (region[0] >= start)
         {
           region[0] -= change;
@@ -302,13 +306,13 @@ public class ColumnSelection
   {
     if (shiftrecord != null)
     {
-      Vector shifts = shiftrecord.shifts;
+      final List<int[]> shifts = shiftrecord.getShifts();
       if (shifts != null && shifts.size() > 0)
       {
         int shifted = 0;
         for (int i = 0, j = shifts.size(); i < j; i++)
         {
-          int[] sh = (int[]) shifts.elementAt(i);
+          int[] sh = shifts.get(i);
           // compensateForEdit(shifted+sh[0], sh[1]);
           compensateForDelEdits(shifted + sh[0], sh[1]);
           shifted -= sh[1];
@@ -323,16 +327,17 @@ public class ColumnSelection
    * removes intersection of position,length ranges in deletions from the
    * start,end regions marked in intervals.
    * 
-   * @param deletions
+   * @param shifts
    * @param intervals
    * @return
    */
-  private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+  private boolean pruneIntervalVector(final List<int[]> shifts,
+          Vector<int[]> intervals)
   {
     boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
-    int hr[] = (int[]) intervals.elementAt(i);
-    int sr[] = (int[]) deletions.elementAt(s);
+    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+    int hr[] = intervals.elementAt(i);
+    int sr[] = shifts.get(s);
     while (i <= j && s <= t)
     {
       boolean trailinghn = hr[1] >= sr[0];
@@ -340,7 +345,7 @@ public class ColumnSelection
       {
         if (i < j)
         {
-          hr = (int[]) intervals.elementAt(++i);
+          hr = intervals.elementAt(++i);
         }
         else
         {
@@ -353,7 +358,7 @@ public class ColumnSelection
       { // leadinghc disjoint or not a deletion
         if (s < t)
         {
-          sr = (int[]) deletions.elementAt(++s);
+          sr = shifts.get(++s);
         }
         else
         {
@@ -373,7 +378,7 @@ public class ColumnSelection
           j--;
           if (i <= j)
           {
-            hr = (int[]) intervals.elementAt(i);
+            hr = intervals.elementAt(i);
           }
           continue;
         }
@@ -399,7 +404,7 @@ public class ColumnSelection
           // sr contained in hr
           if (s < t)
           {
-            sr = (int[]) deletions.elementAt(++s);
+            sr = shifts.get(++s);
           }
           else
           {
@@ -413,15 +418,16 @@ public class ColumnSelection
     // operations.
   }
 
-  private boolean pruneColumnList(Vector deletion, Vector list)
+  private boolean pruneColumnList(final List<int[]> shifts,
+          Vector<Integer> list)
   {
-    int s = 0, t = deletion.size();
-    int[] sr = (int[]) list.elementAt(s++);
+    int s = 0, t = shifts.size();
+    int[] sr = shifts.get(s++);
     boolean pruned = false;
     int i = 0, j = list.size();
     while (i < j && s <= t)
     {
-      int c = ((Integer) list.elementAt(i++)).intValue();
+      int c = list.elementAt(i++).intValue();
       if (sr[0] <= c)
       {
         if (sr[1] + sr[0] >= c)
@@ -433,7 +439,7 @@ public class ColumnSelection
         {
           if (s < t)
           {
-            sr = (int[]) deletion.elementAt(s);
+            sr = shifts.get(s);
           }
           s++;
         }
@@ -452,7 +458,7 @@ public class ColumnSelection
   {
     if (deletions != null)
     {
-      Vector shifts = deletions.shifts;
+      final List<int[]> shifts = deletions.getShifts();
       if (shifts != null && shifts.size() > 0)
       {
         // delete any intervals intersecting.
@@ -479,16 +485,14 @@ public class ColumnSelection
   }
 
   /**
-   * This Method is used to return all the HiddenColumn regions less than the
-   * given index.
+   * This Method is used to return all the HiddenColumn regions
    * 
-   * @param end
-   *          int
-   * @return Vector
+   * @return empty list or List of hidden column intervals
    */
-  public Vector getHiddenColumns()
+  public List<int[]> getHiddenColumns()
   {
-    return hiddenColumns;
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
   }
 
   /**
@@ -505,7 +509,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (result >= region[0])
         {
           result += region[1] - region[0] + 1;
@@ -533,7 +537,7 @@ public class ColumnSelection
       int[] region;
       do
       {
-        region = (int[]) hiddenColumns.elementAt(index++);
+        region = hiddenColumns.elementAt(index++);
         if (hiddenColumn > region[1])
         {
           result -= region[1] + 1 - region[0];
@@ -559,7 +563,7 @@ public class ColumnSelection
       int gaps = 0;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (hiddenRegion == 0)
         {
           return region[0];
@@ -590,7 +594,7 @@ public class ColumnSelection
       int index = 0;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (alPos < region[0])
         {
           return region[0];
@@ -618,7 +622,7 @@ public class ColumnSelection
       int index = hiddenColumns.size() - 1;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        int[] region = hiddenColumns.elementAt(index);
         if (alPos > region[1])
         {
           return region[1];
@@ -636,7 +640,7 @@ public class ColumnSelection
   {
     while (size() > 0)
     {
-      int column = ((Integer) getSelected().firstElement()).intValue();
+      int column = getSelected().firstElement().intValue();
       hideColumns(column);
     }
 
@@ -646,7 +650,7 @@ public class ColumnSelection
   {
     if (hiddenColumns == null)
     {
-      hiddenColumns = new Vector();
+      hiddenColumns = new Vector<int[]>();
     }
 
     boolean added = false;
@@ -654,7 +658,7 @@ public class ColumnSelection
 
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
+      int[] region = hiddenColumns.elementAt(i);
       if (start <= region[1] && end >= region[0])
       {
         hiddenColumns.removeElementAt(i);
@@ -663,8 +667,7 @@ public class ColumnSelection
       }
       else if (end < region[0] && start < region[0])
       {
-        hiddenColumns.insertElementAt(new int[]
-        { start, end }, i);
+        hiddenColumns.insertElementAt(new int[] { start, end }, i);
         added = true;
         break;
       }
@@ -676,8 +679,7 @@ public class ColumnSelection
     }
     else if (!added)
     {
-      hiddenColumns.addElement(new int[]
-      { start, end });
+      hiddenColumns.addElement(new int[] { start, end });
     }
 
   }
@@ -721,7 +723,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         for (int j = region[0]; j < region[1] + 1; j++)
         {
           addElement(j);
@@ -736,7 +738,7 @@ public class ColumnSelection
   {
     for (int i = 0; i < hiddenColumns.size(); i++)
     {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
+      int[] region = hiddenColumns.elementAt(i);
       if (res == region[0])
       {
         for (int j = region[0]; j < region[1] + 1; j++)
@@ -760,7 +762,7 @@ public class ColumnSelection
     {
       for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        int[] region = (int[]) hiddenColumns.elementAt(i);
+        int[] region = hiddenColumns.elementAt(i);
         if (column >= region[0] && column <= region[1])
         {
           return false;
@@ -782,7 +784,7 @@ public class ColumnSelection
     {
       if (copy.selected != null)
       {
-        selected = new Vector();
+        selected = new Vector<Integer>();
         for (int i = 0, j = copy.selected.size(); i < j; i++)
         {
           selected.addElement(copy.selected.elementAt(i));
@@ -790,11 +792,11 @@ public class ColumnSelection
       }
       if (copy.hiddenColumns != null)
       {
-        hiddenColumns = new Vector(copy.hiddenColumns.size());
+        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
         for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
         {
           int[] rh, cp;
-          rh = (int[]) copy.hiddenColumns.elementAt(i);
+          rh = copy.hiddenColumns.elementAt(i);
           if (rh != null)
           {
             cp = new int[rh.length];
@@ -823,7 +825,7 @@ public class ColumnSelection
       for (i = 0; i < iSize; i++)
       {
         StringBuffer visibleSeq = new StringBuffer();
-        Vector regions = getHiddenColumns();
+        List<int[]> regions = getHiddenColumns();
 
         int blockStart = start, blockEnd = end;
         int[] region;
@@ -831,7 +833,7 @@ public class ColumnSelection
 
         for (int j = 0; j < regions.size(); j++)
         {
-          region = (int[]) regions.elementAt(j);
+          region = regions.get(j);
           hideStart = region[0];
           hideEnd = region[1];
 
@@ -887,8 +889,8 @@ public class ColumnSelection
   {
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      Vector visiblecontigs = new Vector();
-      Vector regions = getHiddenColumns();
+      List<int[]> visiblecontigs = new ArrayList<int[]>();
+      List<int[]> regions = getHiddenColumns();
 
       int vstart = start;
       int[] region;
@@ -896,7 +898,7 @@ public class ColumnSelection
 
       for (int j = 0; vstart < end && j < regions.size(); j++)
       {
-        region = (int[]) regions.elementAt(j);
+        region = regions.get(j);
         hideStart = region[0];
         hideEnd = region[1];
 
@@ -906,32 +908,29 @@ public class ColumnSelection
         }
         if (hideStart > vstart)
         {
-          visiblecontigs.addElement(new int[]
-          { vstart, hideStart - 1 });
+          visiblecontigs.add(new int[] { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
 
       if (vstart < end)
       {
-        visiblecontigs.addElement(new int[]
-        { vstart, end - 1 });
+        visiblecontigs.add(new int[] { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
       {
-        int[] vc = (int[]) visiblecontigs.elementAt(i);
-        visiblecontigs.setElementAt(null, i);
+        int[] vc = visiblecontigs.get(i);
+        visiblecontigs.set(i, null);
         vcontigs[i * 2] = vc[0];
         vcontigs[i * 2 + 1] = vc[1];
       }
-      visiblecontigs.removeAllElements();
+      visiblecontigs.clear();
       return vcontigs;
     }
     else
     {
-      return new int[]
-      { start, end - 1 };
+      return new int[] { start, end - 1 };
     }
   }
 
@@ -972,16 +971,16 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       // then mangle the alignmentAnnotation annotation array
-      Vector annels = new Vector();
+      Vector<Annotation[]> annels = new Vector<Annotation[]>();
       Annotation[] els = null;
-      Vector regions = getHiddenColumns();
+      List<int[]> regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
       int[] region;
       int hideStart, hideEnd, w = 0;
 
       for (int j = 0; j < regions.size(); j++)
       {
-        region = (int[]) regions.elementAt(j);
+        region = regions.get(j);
         hideStart = region[0];
         hideEnd = region[1];
 
@@ -1028,12 +1027,12 @@ public class ColumnSelection
       {
         return;
       }
-      Enumeration e = annels.elements();
+
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;
-      while (e.hasMoreElements())
+
+      for (Annotation[] chnk : annels)
       {
-        Annotation[] chnk = (Annotation[]) e.nextElement();
         System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
                 chnk.length);
         w += chnk.length;
@@ -1081,15 +1080,13 @@ public class ColumnSelection
   {
     if (colsel != null && colsel.size() > 0)
     {
-      Enumeration e = colsel.getSelected().elements();
-      while (e.hasMoreElements())
+      for (Integer col : colsel.getSelected())
       {
-        Object eo = e.nextElement();
-        if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+        if (hiddenColumns != null && isVisible(col.intValue()))
         {
-          if (!selected.contains(eo))
+          if (!selected.contains(col))
           {
-            selected.addElement(eo);
+            selected.addElement(col);
           }
         }
       }
@@ -1104,22 +1101,20 @@ public class ColumnSelection
    */
   public void setElementsFrom(ColumnSelection colsel)
   {
-    selected = new Vector();
+    selected = new Vector<Integer>();
     if (colsel.selected != null && colsel.selected.size() > 0)
     {
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
         // only select visible columns in this columns selection
-        selected = new Vector();
         addElementsFrom(colsel);
       }
       else
       {
         // add everything regardless
-        Enumeration en = colsel.selected.elements();
-        while (en.hasMoreElements())
+        for (Integer col : colsel.getSelected())
         {
-          selected.addElement(en.nextElement());
+          addElement(col);
         }
       }
     }
@@ -1139,7 +1134,7 @@ public class ColumnSelection
    *         profileseq marked as hidden.
    */
   public static ColumnSelection propagateInsertions(SequenceI profileseq,
-          Alignment al, AlignmentView input)
+          AlignmentI al, AlignmentView input)
   {
     int profsqpos = 0;
 
@@ -1268,6 +1263,48 @@ 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;
+  }
+
+  /**
+   * 
+   * @return true if there are more than one set of columns hidden
+   */
+  public boolean hasManyHiddenColumns()
+  {
+    return hiddenColumns != null && hiddenColumns.size() > 1;
+  }
+
+  /**
+   * 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]);
+    }
+  }
+
   public boolean filterAnnotations(Annotation[] annotations,
           AnnotationFilterParameter filterParams)
   {