X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=0098d760eabbcc12a13f43d8c7ab947a899ea2b8;hb=8c5cefb3ac80bd094a8dab7ce6735a11583b1772;hp=09facbffc22002c60200d9e87cb08e0c95e3075f;hpb=82b053436b1d354d5b09ab419cac65ca032aea94;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 09facbf..0098d76 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -24,6 +24,7 @@ import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -665,7 +666,7 @@ public class AlignmentAnnotation
     this.calcId = annotation.calcId;
     if (annotation.properties != null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
       for (Map.Entry<String, String> val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
@@ -701,7 +702,7 @@ public class AlignmentAnnotation
       if (annotation.sequenceMapping != null)
       {
         Integer p = null;
-        sequenceMapping = new HashMap<Integer, Annotation>();
+        sequenceMapping = new HashMap<>();
         Iterator<Integer> pos = annotation.sequenceMapping.keySet()
                 .iterator();
         while (pos.hasNext())
@@ -781,7 +782,7 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Map<Integer, Annotation> newmapping = new HashMap<>();
         Iterator<Integer> e = sequenceMapping.keySet().iterator();
         while (e.hasNext())
         {
@@ -908,7 +909,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new HashMap<Integer, Annotation>();
+    sequenceMapping = new HashMap<>();
 
     int seqPos;
 
@@ -1123,7 +1124,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    hidden.makeVisibleAnnotation(this);
+    makeVisibleAnnotation(hidden);
   }
 
   public void setPadGaps(boolean padgaps, char gapchar)
@@ -1189,7 +1190,7 @@ public class AlignmentAnnotation
   /**
    * properties associated with the calcId
    */
-  protected Map<String, String> properties = new HashMap<String, String>();
+  protected Map<String, String> properties = new HashMap<>();
 
   /**
    * base colour for line graphs. If null, will be set automatically by
@@ -1235,7 +1236,7 @@ public class AlignmentAnnotation
             : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+    Map<Integer, Annotation> mapForsq = new HashMap<>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1288,7 +1289,7 @@ public class AlignmentAnnotation
     if (mapping != null)
     {
       Map<Integer, Annotation> old = sequenceMapping;
-      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+      Map<Integer, Annotation> remap = new HashMap<>();
       int index = -1;
       for (int mp[] : mapping.values())
       {
@@ -1346,7 +1347,7 @@ public class AlignmentAnnotation
   {
     if (properties == null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
     }
     properties.put(property, value);
   }
@@ -1471,4 +1472,180 @@ public class AlignmentAnnotation
   {
     return graphMin < graphMax;
   }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+  {
+    if (annotations != null)
+    {
+      makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+    }
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  public void makeVisibleAnnotation(int start, int end,
+          HiddenColumns hiddenColumns)
+  {
+    if (annotations != null)
+    {
+      if (hiddenColumns.hasHiddenColumns())
+      {
+        removeHiddenAnnotation(start, end, hiddenColumns);
+      }
+      else
+      {
+        restrict(start, end);
+      }
+    }
+  }
+
+  /**
+   * The actual implementation of deleting hidden annotation columns
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  private void removeHiddenAnnotation(int start, int end,
+          HiddenColumns hiddenColumns)
+  {
+    // mangle the alignmentAnnotation annotation array
+    ArrayList<Annotation[]> annels = new ArrayList<>();
+    Annotation[] els = null;
+
+    int w = 0;
+
+    Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+            end + 1, false);
+
+    int copylength;
+    int annotationLength;
+    while (blocks.hasNext())
+    {
+      int[] block = blocks.next();
+      annotationLength = block[1] - block[0] + 1;
+
+      if (blocks.hasNext())
+      {
+        // copy just the visible segment of the annotation row
+        copylength = annotationLength;
+      }
+      else
+      {
+        if (annotationLength + block[0] <= annotations.length)
+        {
+          // copy just the visible segment of the annotation row
+          copylength = annotationLength;
+        }
+        else
+        {
+          // copy to the end of the annotation row
+          copylength = annotations.length - block[0];
+        }
+      }
+
+      els = new Annotation[annotationLength];
+      annels.add(els);
+      System.arraycopy(annotations, block[0], els, 0, copylength);
+      w += annotationLength;
+    }
+
+    if (w != 0)
+    {
+      annotations = new Annotation[w];
+
+      w = 0;
+      for (Annotation[] chnk : annels)
+      {
+        System.arraycopy(chnk, 0, annotations, w, chnk.length);
+        w += chnk.length;
+      }
+    }
+  }
+
+  public static Iterable<AlignmentAnnotation> findAnnotations(
+          Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
+          String label)
+  {
+
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+    for (AlignmentAnnotation ann : list)
+    {
+      if ((calcId == null || (ann.getCalcId() != null
+              && ann.getCalcId().equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null
+                      && ann.sequenceRef == seq))
+              && (label == null
+                      || (ann.label != null && ann.label.equals(label))))
+      {
+        aa.add(ann);
+      }
+    }
+    return aa;
+  }
+
+  /**
+   * Answer true if any annotation matches the calcId passed in (if not null).
+   * 
+   * @param list
+   *          annotation to search
+   * @param calcId
+   * @return
+   */
+  public static boolean hasAnnotation(List<AlignmentAnnotation> list,
+          String calcId)
+  {
+
+    if (calcId != null && !"".equals(calcId))
+    {
+      for (AlignmentAnnotation a : list)
+      {
+        if (a.getCalcId() == calcId)
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  public static Iterable<AlignmentAnnotation> findAnnotation(
+          List<AlignmentAnnotation> list, String calcId)
+  {
+
+    List<AlignmentAnnotation> aa = new ArrayList<>();
+    if (calcId == null)
+    {
+      return aa;
+    }
+    for (AlignmentAnnotation a : list)
+    {
+
+      if (a.getCalcId() == calcId || (a.getCalcId() != null
+              && calcId != null && a.getCalcId().equals(calcId)))
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
 }