Merge branch 'develop' into feature_29/JAL-1372_referenceseq

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 93e03d1..6acca32 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -25,6 +25,7 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -37,7 +38,7 @@ public class ColumnSelection
   Vector selected = new Vector();
 
   // Vector of int [] {startCol, endCol}
-  Vector hiddenColumns;
+  Vector<int[]> hiddenColumns;
 
   /**
    * Add a column to the selection
@@ -210,7 +211,7 @@ 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);
@@ -265,7 +266,7 @@ 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;
@@ -479,16 +480,13 @@ public class ColumnSelection
   }
 
   /**
-   * This Method is used to return all the HiddenColumn regions less than the
-   * given index.
-   * 
-   * @param end
-   *          int
-   * @return Vector
+   * This Method is used to return all the HiddenColumn regions
+   * @return empty list or List of hidden column intervals
    */
-  public Vector getHiddenColumns()
+  public List<int[]> getHiddenColumns()
   {
-    return hiddenColumns;
+    return hiddenColumns == null ? Arrays.asList(new int[]
+    {}) : hiddenColumns;
   }
 
   /**
@@ -505,7 +503,7 @@ 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 +531,7 @@ 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 +557,7 @@ 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 +588,7 @@ 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 +616,7 @@ 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];
@@ -654,7 +652,7 @@ 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);
@@ -721,7 +719,7 @@ 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 +734,7 @@ 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 +758,7 @@ 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;
@@ -794,7 +792,7 @@ public class ColumnSelection
         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 +821,7 @@ 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 +829,7 @@ 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];
 
@@ -888,7 +886,7 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       Vector visiblecontigs = new Vector();
-      Vector regions = getHiddenColumns();
+      List<int[]> regions = getHiddenColumns();
 
       int vstart = start;
       int[] region;
@@ -896,7 +894,7 @@ 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];
 
@@ -974,14 +972,14 @@ public class ColumnSelection
       // then mangle the alignmentAnnotation annotation array
       Vector annels = new Vector();
       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];
 
@@ -1268,6 +1266,48 @@ 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)
   {