X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=40d2b7ee5056cebc8f8f5d12ffc2962c80ec988f;hb=30bc1314d4206cafea412dcd9decdea7e318481f;hp=f43529d310f93eb5c4f61e083107fb2b31ee99e4;hpb=ff37fec79b0304a4a9a67bbb512c7d2b120f6f34;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f43529d..40d2b7e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,7 +20,6 @@ package jalview.datamodel;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
-import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -55,6 +54,15 @@ public class AlignmentAnnotation
   /** DOCUMENT ME!! */
   public float graphMax;
 
+  /**
+   * Score associated with label and description.
+   */
+  public double score= Double.NaN;
+  /**
+   * flag indicating if annotation has a score.
+   */
+  public boolean hasScore=false;
+
   public GraphLine threshold;
 
   // Graphical hints and tips
@@ -80,12 +88,17 @@ public class AlignmentAnnotation
 
   public int graphHeight = 40;
 
+  public boolean padGaps = false;
+
   public static final int NO_GRAPH = 0;
 
   public static final int BAR_GRAPH = 1;
 
   public static final int LINE_GRAPH = 2;
 
+  public boolean belowAlignment = true;
+
+
   public static int getGraphValueFromString(String string)
   {
     if (string.equalsIgnoreCase("BAR_GRAPH"))
@@ -105,9 +118,9 @@ public class AlignmentAnnotation
   /**
    * Creates a new AlignmentAnnotation object.
    *
-   * @param label DOCUMENT ME!
-   * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
+   * @param label short label shown under sequence labels
+   * @param description text displayed on mouseover
+   * @param annotations set of positional annotation elements
    */
   public AlignmentAnnotation(String label, String description,
                              Annotation[] annotations)
@@ -118,35 +131,47 @@ public class AlignmentAnnotation
     this.description = description;
     this.annotations = annotations;
 
-    areLabelsSecondaryStructure();
+     validateRangeAndDisplay();
   }
 
   void areLabelsSecondaryStructure()
   {
     boolean nonSSLabel = false;
+    char firstChar=0;
     for (int i = 0; i < annotations.length; i++)
     {
       if (annotations[i] == null)
       {
         continue;
       }
-
       if (annotations[i].secondaryStructure == 'H' ||
           annotations[i].secondaryStructure == 'E')
       {
-        hasIcons = true;
+          hasIcons = true;
       }
 
-      if (annotations[i].displayCharacter.length() == 1
-          && !annotations[i].displayCharacter.equals("H")
-          && !annotations[i].displayCharacter.equals("E")
-          && !annotations[i].displayCharacter.equals("-")
-          && !annotations[i].displayCharacter.equals("."))
+      if(annotations[i].displayCharacter==null)
       {
-        if (jalview.schemes.ResidueProperties.aaIndex
-            [annotations[i].displayCharacter.charAt(0)] < 23)
+        continue;
+      }
+      if (annotations[i].displayCharacter.length() == 1)
+      {      
+        firstChar = annotations[i].displayCharacter.charAt(0);
+        // check to see if it looks like a sequence or is secondary structure labelling.
+        if (
+                // Uncomment to only catch case where displayCharacter==secondary Structure 
+              // to correctly redisplay SS annotation imported from Stockholm, exported to JalviewXML and read back in again.
+          // && annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+          firstChar!='H'
+          && firstChar!='E'
+          && firstChar!='-'
+          && firstChar!='-' && firstChar<jalview.schemes.ResidueProperties.aaIndex.length)
         {
-          nonSSLabel = true;
+          if (jalview.schemes.ResidueProperties.aaIndex
+                  [firstChar] < 23)
+          {
+            nonSSLabel = true;
+          }
         }
       }
 
@@ -169,7 +194,6 @@ public class AlignmentAnnotation
         }
 
       }
-
     }
 
     annotationId = this.hashCode() + "";
@@ -207,6 +231,13 @@ public class AlignmentAnnotation
    * if appropriate.
    */
   private void validateRangeAndDisplay() {
+
+    if (annotations==null)
+    {
+      visible=false; // try to prevent renderer from displaying.
+      return; // this is a non-annotation row annotation - ie a sequence score.
+    }
+
     int graphType = graph;
     float min = graphMin;
     float max = graphMax;
@@ -222,7 +253,9 @@ public class AlignmentAnnotation
           continue;
         }
 
-        if (drawValues && annotations[i].displayCharacter.length() > 1)
+        if (drawValues
+            && annotations[i].displayCharacter!=null
+            && annotations[i].displayCharacter.length() > 1)
         {
           drawValues = false;
         }
@@ -277,29 +310,44 @@ public class AlignmentAnnotation
     this.hasText = annotation.hasText;
     this.height = annotation.height;
     this.label = annotation.label;
+    this.padGaps = annotation.padGaps;
+    this.visible = annotation.visible;
+    if (this.hasScore = annotation.hasScore)
+    {
+      this.score = annotation.score;
+    }
     if (threshold!=null) {
       threshold = new GraphLine(annotation.threshold);
     }
     if (annotation.annotations!=null) {
-      Vector anvec = new Vector();
       Annotation[] ann = annotation.annotations;
       this.annotations = new Annotation[ann.length];
       for (int i=0; i<ann.length; i++) {
         annotations[i] = new Annotation(ann[i]);
-        anvec.addElement(ann[i]); // for lookup if sequenceMapping exists.
       };
       if (annotation.sequenceRef!=null) {
         this.sequenceRef = annotation.sequenceRef;
         if (annotation.sequenceMapping!=null)
         {
+          Integer p=null;
           sequenceMapping = new Hashtable();
           Enumeration pos=annotation.sequenceMapping.keys();
           while (pos.hasMoreElements()) {
-            Integer p = (Integer) pos.nextElement();
-            Annotation a = (Annotation) sequenceMapping.get(p);
-            sequenceMapping.put(p, annotations[anvec.indexOf(a)]);
+            // could optimise this!
+            p = (Integer) pos.nextElement();
+            Annotation a = (Annotation) annotation.sequenceMapping.get(p);
+            if (a==null)
+            {
+              continue;
+            }
+            for (int i=0; i<ann.length; i++)
+            {
+              if (ann[i]==a)
+              {
+                sequenceMapping.put(p, annotations[i]);
+              }
+            }
           }
-          anvec.removeAllElements();
         } else {
           this.sequenceMapping = null;
         }
@@ -309,6 +357,75 @@ public class AlignmentAnnotation
   }
 
   /**
+   * clip the annotation to the columns given by startRes and endRes (inclusive)
+   * and prune any existing sequenceMapping to just those columns.
+   * @param startRes
+   * @param endRes
+   */
+  public void restrict(int startRes, int endRes)
+  {
+    if (annotations==null)
+    {
+      // non-positional
+      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)
+    {
+      System.arraycopy(annotations, startRes, temp, 0, endRes-startRes+1);
+    }
+    if (sequenceRef!=null) {
+      // Clip the mapping, if it exists.
+      int spos = sequenceRef.findPosition(startRes);
+      int epos = sequenceRef.findPosition(endRes);
+      if (sequenceMapping!=null)
+      {
+        Hashtable newmapping = new Hashtable();
+        Enumeration e = sequenceMapping.keys();
+        while (e.hasMoreElements())
+        {
+          Integer pos = (Integer) e.nextElement();
+          if (pos.intValue()>=spos && pos.intValue()<=epos)
+          {
+            newmapping.put(pos, sequenceMapping.get(pos));
+          }
+        }
+        sequenceMapping.clear();
+        sequenceMapping = newmapping;
+      }
+    }
+    annotations=temp;
+  }
+  /**
+   * set the annotation row to be at least length Annotations
+   * @param length minimum number of columns required in the annotation row
+   * @return false if the annotation row is greater than length
+   */
+  public boolean padAnnotation(int length) {
+    if (annotations==null)
+    {
+      return true; // annotation row is correct - null == not visible and undefined length
+    }
+    if (annotations.length<length)
+    {
+      Annotation[] na = new Annotation[length];
+      System.arraycopy(annotations, 0, na, 0, annotations.length);
+      annotations = na;
+      return true;
+    }
+    return annotations.length>length;
+
+  }
+
+  /**
    * DOCUMENT ME!
    *
    * @return DOCUMENT ME!
@@ -381,10 +498,13 @@ public class AlignmentAnnotation
     {
       return;
     }
-
+    sequenceRef=seqRef;
+    if (annotations==null)
+    {
+      return;
+    }
     sequenceMapping = new java.util.Hashtable();
 
-    sequenceRef = seqRef;
     int seqPos;
 
     for (int i = 0; i < annotations.length; i++)
@@ -411,6 +531,11 @@ public class AlignmentAnnotation
     if (sequenceRef==null)
       return;
 
+    if (annotations==null)
+    {
+      return;
+    }
+
     int a = 0, aSize = sequenceRef.getLength();
 
     if (aSize == 0)
@@ -441,18 +566,23 @@ public class AlignmentAnnotation
    * number of non-null annotation elements.
    * @return
    */
-  private int compactAnnotationArray() {
-    int j=0;
-    for (int i=0;i<annotations.length; i++) {
-      if (annotations[i]!=null && j!=i) {
-        annotations[j++] = annotations[i];
+  public int compactAnnotationArray() {
+    int i=0,iSize=annotations.length;
+    while (i<iSize)
+    {
+      if (annotations[i]==null) {
+        if (i+1<iSize)
+          System.arraycopy(annotations, i+1, annotations, i, iSize-i-1);
+        iSize--;
+      } else {
+        i++;
       }
     }
     Annotation[] ann = annotations;
-    annotations = new Annotation[j];
-    System.arraycopy(ann, 0, annotations, 0, j);
+    annotations = new Annotation[i];
+    System.arraycopy(ann, 0, annotations, 0, i);
     ann = null;
-    return j;
+    return iSize;
   }
 
   /**
@@ -465,31 +595,108 @@ public class AlignmentAnnotation
    */
   public void setSequenceRef(SequenceI sequenceI)
   {
-    if (sequenceI!=null) {
-      if (sequenceRef!=null) {
-        if (sequenceRef!=sequenceI && !sequenceRef.equals(sequenceI)) {
+    if (sequenceI != null)
+    {
+      if (sequenceRef != null)
+      {
+        if (sequenceRef != sequenceI && !sequenceRef.equals(sequenceI) && sequenceRef.getDatasetSequence()!=sequenceI.getDatasetSequence())
+        {
+          // if sequenceRef isn't intersecting with sequenceI
           // throw away old mapping and reconstruct.
-          sequenceRef=null;
-          if (sequenceMapping!=null)
+          sequenceRef = null;
+          if (sequenceMapping != null)
           {
-            sequenceMapping=null;
+            sequenceMapping = null;
             // compactAnnotationArray();
           }
-          createSequenceMapping(sequenceI, 1,true);
+          createSequenceMapping(sequenceI, 1, true);
           adjustForAlignment();
-        } else {
+        }
+        else
+        {
           // Mapping carried over
           sequenceRef = sequenceI;
         }
-      } else {
+      }
+      else
+      {
         // No mapping exists
         createSequenceMapping(sequenceI, 1, true);
         adjustForAlignment();
       }
-    } else {
+    }
+    else
+    {
       // throw away the mapping without compacting.
-      sequenceMapping=null;
+      sequenceMapping = null;
       sequenceRef = null;
     }
   }
+
+  /**
+   * @return the score
+   */
+  public double getScore()
+  {
+    return score;
+  }
+
+  /**
+   * @param score the score to set
+   */
+  public void setScore(double score)
+  {
+    hasScore=true;
+    this.score = score;
+  }
+  /**
+   *
+   * @return true if annotation has an associated score
+   */
+  public boolean hasScore()
+  {
+    return hasScore || !Double.isNaN(score);
+  }
+  /**
+   * Score only annotation
+   * @param label
+   * @param description
+   * @param score
+   */
+  public AlignmentAnnotation(String label, String description, double score)
+  {
+    this(label, description, null);
+    setScore(score);
+  }
+  /**
+   * copy constructor with edit based on the hidden columns marked in colSel
+   * @param alignmentAnnotation
+   * @param colSel
+   */
+  public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+          ColumnSelection colSel)
+  {
+    this(alignmentAnnotation);
+    if (annotations==null)
+    {
+      return;
+    }
+    colSel.makeVisibleAnnotation(this);
+  }
+
+  public void setPadGaps(boolean padgaps, char gapchar)
+  {
+    this.padGaps = padgaps;
+    if(padgaps)
+    {
+      hasText = true;
+      for(int i=0; i<annotations.length; i++)
+      {
+        if(annotations[i]==null)
+          annotations[i] = new Annotation(String.valueOf(gapchar),null,' ',0f);
+        else if(annotations[i].displayCharacter==null ||annotations[i].displayCharacter.equals(" "))
+          annotations[i].displayCharacter=String.valueOf(gapchar);
+      }
+    }
+  }
 }