javadoc and operator for editing AlignmentAnnotation to remove hidden columns

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4904495..73b7899 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -108,11 +108,11 @@ public class ColumnSelection
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * Column number at position i in selection\r
    *\r
-   * @param i DOCUMENT ME!\r
+   * @param i index into selected columns\r
    *\r
-   * @return DOCUMENT ME!\r
+   * @return column number in alignment\r
    */\r
   public int columnAt(int i)\r
   {\r
@@ -130,9 +130,9 @@ public class ColumnSelection
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * rightmost selected column\r
    *\r
-   * @return DOCUMENT ME!\r
+   * @return rightmost column in alignment that is selected\r
    */\r
   public int getMax()\r
   {\r
@@ -150,9 +150,9 @@ public class ColumnSelection
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * Leftmost column in selection\r
    *\r
-   * @return DOCUMENT ME!\r
+   * @return column index of leftmost column in selection\r
    */\r
   public int getMin()\r
   {\r
@@ -900,4 +900,85 @@ public class ColumnSelection
           start, end - 1};\r
     }\r
   }\r
+\r
+  /**\r
+   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).\r
+   * @param alignmentAnnotation\r
+   */\r
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)\r
+  {\r
+    makeVisibleAnnotation(-1,-1,alignmentAnnotation);\r
+  }\r
+  /**\r
+   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).\r
+   * @param start remove any annotation to the right of this column\r
+   * @param end remove any annotation to the left of this column\r
+   * @param alignmentAnnotation the annotation to operate on\r
+   */\r
+  public void makeVisibleAnnotation(int start, int end, AlignmentAnnotation alignmentAnnotation)\r
+  {\r
+    if (alignmentAnnotation.annotations==null)\r
+    {\r
+      return;\r
+    }\r
+    if (start==end && end==-1)\r
+    {\r
+      start = 0;\r
+      end = alignmentAnnotation.annotations.length;\r
+    }\r
+    if (hiddenColumns != null && hiddenColumns.size() > 0)\r
+    {\r
+      // then mangle the alignmentAnnotation annotation array\r
+        Vector annels = new Vector();\r
+        Annotation[] els = null;\r
+        Vector regions = getHiddenColumns();\r
+        int blockStart = start, blockEnd = end;\r
+        int[] region;\r
+        int hideStart, hideEnd,w=0;\r
+\r
+        for (int j = 0; j < regions.size(); j++)\r
+        {\r
+          region = (int[]) regions.elementAt(j);\r
+          hideStart = region[0];\r
+          hideEnd = region[1];\r
+\r
+          if (hideStart < start)\r
+          {\r
+            continue;\r
+          }\r
+\r
+          blockStart = Math.min(blockStart, hideEnd + 1);\r
+          blockEnd = Math.min(blockEnd, hideStart);\r
+\r
+          if (blockStart > blockEnd)\r
+          {\r
+            break;\r
+          }\r
+\r
+          annels.addElement(els = new Annotation[blockEnd-blockStart]);\r
+          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);\r
+          w+=els.length;\r
+          blockStart = hideEnd + 1;\r
+          blockEnd = end;\r
+        }\r
+\r
+        if (end > blockStart)\r
+        {\r
+          annels.addElement(els = new Annotation[end-blockStart]);\r
+          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);\r
+          w+=els.length;\r
+        }\r
+        if (w==0)\r
+          return;\r
+        Enumeration e = annels.elements();\r
+        alignmentAnnotation.annotations = new Annotation[w];\r
+        w=0;\r
+        while (e.hasMoreElements())\r
+        {\r
+          Annotation[] chnk = (Annotation[]) e.nextElement();\r
+          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);\r
+          w+=chnk.length;\r
+        }\r
+    }\r
+  }\r
 }\r