X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=e3a8472059d3dabb7525ce8667f1c3a381695130;hb=d645ed1944459b6271dea2a8511a1e0f4f997530;hp=c23b77285db81afb5540345ce8d503acfbe59bf9;hpb=964c6de914dd7b2ef51feeb0d374cca23742f3ef;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index c23b772..e3a8472 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import jalview.util.Comparison;
 import jalview.util.ShiftList;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
@@ -207,6 +208,7 @@ public class ColumnSelection
   }
 
   IntList selected = new IntList();
+
   /*
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
@@ -741,8 +743,9 @@ public class ColumnSelection
 
   public void hideSelectedColumns()
   {
-    synchronized (selected) {
-      for (int[] selregions:selected.getRanges())
+    synchronized (selected)
+    {
+      for (int[] selregions : selected.getRanges())
       {
         hideColumns(selregions[0], selregions[1]);
       }
@@ -806,7 +809,7 @@ public class ColumnSelection
     /*
      * remaining case is that the new range follows everything else
      */
-      hiddenColumns.addElement(new int[] { start, end });
+    hiddenColumns.addElement(new int[] { start, end });
   }
 
   /**
@@ -1077,6 +1080,84 @@ public class ColumnSelection
   }
 
   /**
+   * Locate the first and last position visible for this sequence. if seq isn't
+   * visible then return the position of the left and right of the hidden
+   * boundary region, and the corresponding alignment column indices for the
+   * extent of the sequence
+   * 
+   * @param seq
+   * @return int[] { visible start, visible end, first seqpos, last seqpos,
+   *         alignment index for seq start, alignment index for seq end }
+   */
+  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+  {
+    int fpos=seq.getStart(),lpos= seq.getEnd();
+    int start = 0;
+    
+    if (hiddenColumns == null || hiddenColumns.size() == 0)
+    {
+      int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
+      return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+    }
+
+    // Simply walk along the sequence whilst watching for hidden column
+    // boundaries
+    List<int[]> regions = getHiddenColumns();
+    int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
+            .getLength(), hideEnd = -1;
+    int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+    boolean foundStart = false;
+    for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+            && p < pLen; p++)
+    {
+      if (!Comparison.isGap(seq.getCharAt(p)))
+      {
+        // keep track of first/last column
+        // containing sequence data regardless of visibility
+        if (firstP == -1)
+        {
+          firstP = p;
+        }
+        lastP = p;
+        // update hidden region start/end
+        while (hideEnd < p && rcount < regions.size())
+        {
+          int[] region = regions.get(rcount++);
+          visPrev = visNext;
+          visNext += region[0] - visPrev;
+          hideStart = region[0];
+          hideEnd = region[1];
+        }
+        if (hideEnd < p)
+        {
+          hideStart = seq.getLength();
+        }
+        // update visible boundary for sequence
+        if (p < hideStart)
+        {
+          if (!foundStart)
+          {
+            fpos = spos;
+            start = p;
+            foundStart = true;
+          }
+          lastvispos = p;
+          lpos = spos;
+        }
+        // look for next sequence position
+        spos++;
+      }
+    }
+    if (foundStart)
+    {
+      return new int[] { findColumnPosition(start),
+          findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+    }
+    // otherwise, sequence was completely hidden
+    return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+  }
+
+  /**
    * delete any columns in alignmentAnnotation that are hidden (including
    * sequence associated annotation).
    * 
@@ -1447,6 +1528,8 @@ public class ColumnSelection
   public boolean filterAnnotations(Annotation[] annotations,
           AnnotationFilterParameter filterParams)
   {
+    // JBPNote - this method needs to be refactored to become independent of
+    // viewmodel package
     this.revealAllHiddenColumns();
     this.clear();
     int count = 0;
@@ -1528,4 +1611,5 @@ public class ColumnSelection
     } while (count < annotations.length);
     return false;
   }
+
 }