refactored visible contig/gap map array intersection code to alignmentView

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index db95c71..76f7bd8 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
  * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
  * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.datamodel;\r
 \r
@@ -107,7 +106,7 @@ public class AlignmentView
    * regions\r
    * \r
    * @param gapCharacter\r
-   *                char\r
+   *          char\r
    * @return Object[] { SequenceI[], ColumnSelection}\r
    */\r
   public Object[] getAlignmentAndColumnSelection(char gapCharacter)\r
@@ -124,7 +123,7 @@ public class AlignmentView
    * getSequenceStrings\r
    * \r
    * @param c\r
-   *                char\r
+   *          char\r
    * @return String[]\r
    */\r
   public String[] getSequenceStrings(char c)\r
@@ -170,7 +169,7 @@ public class AlignmentView
    * get the contiguous subalignments in an alignment view.\r
    * \r
    * @param gapCharacter\r
-   *                char\r
+   *          char\r
    * @return SequenceI[][]\r
    */\r
   public SequenceI[][] getVisibleContigs(char gapCharacter)\r
@@ -193,7 +192,7 @@ public class AlignmentView
           njobs++;\r
         }\r
         fwidth += contigs[contig + 2]; // end up with full region width\r
-                                        // (including hidden regions)\r
+        // (including hidden regions)\r
         start = contigs[contig + 1] + contigs[contig + 2];\r
       }\r
       if (start < fwidth)\r
@@ -247,9 +246,9 @@ public class AlignmentView
    * sub alignments\r
    * \r
    * @param nvismsa\r
-   *                SequenceI[][]\r
+   *          SequenceI[][]\r
    * @param orders\r
-   *                AlignmentOrder[] corresponding to each SequenceI[] block.\r
+   *          AlignmentOrder[] corresponding to each SequenceI[] block.\r
    * @return Object[]\r
    */\r
   public Object[] getUpdatedView(SequenceI[][] nvismsa,\r
@@ -294,7 +293,7 @@ public class AlignmentView
                                 + sequences.length + ")");\r
               }\r
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded\r
-                                            // here.\r
+              // here.\r
               for (int s = 0; s < mseq.length; s++)\r
               {\r
                 if (alignment[s] == null)\r
@@ -495,7 +494,7 @@ public class AlignmentView
           nvis++;\r
         }\r
         fwidth += contigs[contig + 2]; // end up with full region width\r
-                                        // (including hidden regions)\r
+        // (including hidden regions)\r
         start = contigs[contig + 1] + contigs[contig + 2];\r
       }\r
       if (start < fwidth)\r
@@ -540,4 +539,42 @@ public class AlignmentView
     // TODO Auto-generated method stub\r
     return firstCol;\r
   }\r
+\r
+  /**\r
+   * compute a deletion map for the current view according to the given\r
+   * gap/match map\r
+   * \r
+   * @param gapMap (as returned from SequenceI.gapMap())\r
+   * @return int[] {intersection of visible regions with gapMap)\r
+   */\r
+  public int[] getVisibleContigMapFor(int[] gapMap)\r
+  {\r
+    int[] delMap = null;\r
+    int[] viscontigs = getVisibleContigs();\r
+    int spos = 0;\r
+    int i = 0;\r
+    if (viscontigs != null)\r
+    {\r
+      // viscontigs maps from a subset of the gapMap to the gapMap, so it will\r
+      // always be equal to or shorter than gapMap\r
+      delMap = new int[gapMap.length];\r
+      for (int contig = 0; contig < viscontigs.length; contig += 2)\r
+      {\r
+\r
+        while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])\r
+        {\r
+          spos++;\r
+        }\r
+        while (spos < gapMap.length\r
+                && gapMap[spos] <= viscontigs[contig + 1])\r
+        {\r
+          delMap[i++] = spos++;\r
+        }\r
+      }\r
+      int tmap[] = new int[i];\r
+      System.arraycopy(delMap, 0, tmap, 0, i);\r
+      delMap = tmap;\r
+    }\r
+    return delMap;\r
+  }\r
 }\r