JAL-1469 Added SVGOptions.java for lineart/text rendering rendering of svg

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 989d62a..c0d911e 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -22,14 +22,12 @@ package jalview.datamodel;
 
 import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
-
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
-
-import fr.orsay.lri.varna.models.rna.RNA;
+import java.util.Map.Entry;
 
 /**
  * DOCUMENT ME!
@@ -105,7 +103,7 @@ public class AlignmentAnnotation
     // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
   }
 
-  public java.util.Hashtable sequenceMapping;
+  public java.util.Hashtable<Integer, Annotation> sequenceMapping;
 
   /** DOCUMENT ME!! */
   public float graphMin;
@@ -259,6 +257,8 @@ public class AlignmentAnnotation
       // Check for RNA secondary structure
       {
         // System.out.println(annotations[i].secondaryStructure);
+        // TODO: 2.8.2 should this ss symbol validation check be a function in
+        // RNA/ResidueProperties ?
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
@@ -320,9 +320,7 @@ public class AlignmentAnnotation
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
                 && firstChar != '$'
-                && firstChar != '�' // JBPNote should explicitly express as
-                                    // unicode number to avoid source code
-                                    // translation problems
+                && firstChar != 0xCE
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -603,7 +601,9 @@ public class AlignmentAnnotation
   {
     this.label = new String(annotation.label);
     if (annotation.description != null)
+    {
       this.description = new String(annotation.description);
+    }
     this.graphMin = annotation.graphMin;
     this.graphMax = annotation.graphMax;
     this.graph = annotation.graph;
@@ -658,7 +658,7 @@ public class AlignmentAnnotation
           {
             // could optimise this!
             p = (Integer) pos.nextElement();
-            Annotation a = (Annotation) annotation.sequenceMapping.get(p);
+            Annotation a = annotation.sequenceMapping.get(p);
             if (a == null)
             {
               continue;
@@ -701,13 +701,21 @@ public class AlignmentAnnotation
       return;
     }
     if (startRes < 0)
+    {
       startRes = 0;
+    }
     if (startRes >= annotations.length)
+    {
       startRes = annotations.length - 1;
+    }
     if (endRes >= annotations.length)
+    {
       endRes = annotations.length - 1;
+    }
     if (annotations == null)
+    {
       return;
+    }
     Annotation[] temp = new Annotation[endRes - startRes + 1];
     if (startRes < annotations.length)
     {
@@ -869,7 +877,9 @@ public class AlignmentAnnotation
   public void adjustForAlignment()
   {
     if (sequenceRef == null)
+    {
       return;
+    }
 
     if (annotations == null)
     {
@@ -895,7 +905,7 @@ public class AlignmentAnnotation
       {
         position = sequenceRef.findIndex(a) - 1;
 
-        temp[position] = (Annotation) sequenceMapping.get(index);
+        temp[position] = sequenceMapping.get(index);
       }
     }
 
@@ -916,8 +926,10 @@ public class AlignmentAnnotation
       if (annotations[i] == null)
       {
         if (i + 1 < iSize)
+        {
           System.arraycopy(annotations, i + 1, annotations, i, iSize - i
                   - 1);
+        }
         iSize--;
       }
       else
@@ -948,10 +960,14 @@ public class AlignmentAnnotation
     {
       if (sequenceRef != null)
       {
+        boolean rIsDs=sequenceRef.getDatasetSequence()==null,tIsDs=sequenceI.getDatasetSequence()==null;
         if (sequenceRef != sequenceI
-                && !sequenceRef.equals(sequenceI)
-                && sequenceRef.getDatasetSequence() != sequenceI
+                && (rIsDs && !tIsDs && sequenceRef != sequenceI
+                        .getDatasetSequence())
+                && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI)
+                && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI
                         .getDatasetSequence())
+                && !sequenceRef.equals(sequenceI))
         {
           // if sequenceRef isn't intersecting with sequenceI
           // throw away old mapping and reconstruct.
@@ -1051,11 +1067,15 @@ public class AlignmentAnnotation
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] == null)
+        {
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
                   ' ', 0f, null);
+        }
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
+        {
           annotations[i].displayCharacter = String.valueOf(gapchar);
+        }
       }
     }
   }
@@ -1113,4 +1133,55 @@ public class AlignmentAnnotation
   {
     this.calcId = calcId;
   }
+
+  public boolean isRNA()
+  {
+    return isrna;
+  }
+
+  /**
+   * transfer annotation to the given sequence using the given mapping from the
+   * current positions or an existing sequence mapping
+   * 
+   * @param sq
+   * @param sp2sq
+   *          map involving sq as To or From
+   */
+  public void liftOver(SequenceI sq, Mapping sp2sq)
+  {
+    if (sp2sq.getMappedWidth() != sp2sq.getWidth())
+    {
+      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames
+      throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+    }
+    boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
+            .getTo() == sq.getDatasetSequence()) : false;
+
+    // TODO build a better annotation element map and get rid of annotations[]
+    Hashtable<Integer, Annotation> mapForsq = new Hashtable();
+    if (sequenceMapping != null)
+    {
+      if (sp2sq != null)
+      {
+        for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
+        {
+          Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
+                  .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
+                  .getKey()));
+          if (mpos >= sq.getStart() && mpos <= sq.getEnd())
+          {
+            mapForsq.put(mpos, ie.getValue());
+          }
+        }
+        sequenceMapping = mapForsq;
+        sequenceRef = sq;
+        adjustForAlignment();
+      }
+      else
+      {
+        // trim positions
+      }
+    }
+
+  }
 }