X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=381a05470cd0dfdbd398e150a1e51c3e2173c9ae;hb=12e7f97678ce85b0238f987d5f4eaf18512a0b94;hp=95af29ddc826611aa5ae455f838e8dc0874411d6;hpb=2a6873d5bfdd3c0f501545dbf4b07c184a7352b5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 95af29d..381a054 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -20,18 +20,19 @@ package jalview.datamodel;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
-import java.util.Vector;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class AlignmentAnnotation
 {
-  /** If true, this annotations is calculated every edit,
-   * eg consensus, quality or conservation graphs */
+  /**
+   * If true, this annotations is calculated every edit, eg consensus, quality
+   * or conservation graphs
+   */
   public boolean autoCalculated = false;
 
   public String annotationId;
@@ -55,6 +56,16 @@ 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
@@ -80,7 +91,7 @@ public class AlignmentAnnotation
 
   public int graphHeight = 40;
 
-  public boolean padGaps = true;
+  public boolean padGaps = false;
 
   public static final int NO_GRAPH = 0;
 
@@ -88,6 +99,8 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
+  public boolean belowAlignment = true;
+
   public static int getGraphValueFromString(String string)
   {
     if (string.equalsIgnoreCase("BAR_GRAPH"))
@@ -106,13 +119,16 @@ 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)
+          Annotation[] annotations)
   {
     // always editable?
     editable = true;
@@ -120,36 +136,51 @@ 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)
       {
-        padGaps = false;
         continue;
       }
-
-      if (annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E')
+      if (annotations[i].secondaryStructure == 'H'
+              || annotations[i].secondaryStructure == 'E')
       {
         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;
+          }
         }
       }
 
@@ -157,8 +188,6 @@ public class AlignmentAnnotation
       {
         hasText = true;
       }
-      else
-        padGaps = false;
     }
 
     if (nonSSLabel)
@@ -166,10 +195,11 @@ public class AlignmentAnnotation
       hasIcons = false;
       for (int j = 0; j < annotations.length; j++)
       {
-        if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
+        if (annotations[j] != null
+                && annotations[j].secondaryStructure != ' ')
         {
-          annotations[j].displayCharacter
-              = String.valueOf(annotations[j].secondaryStructure);
+          annotations[j].displayCharacter = String
+                  .valueOf(annotations[j].secondaryStructure);
           annotations[j].secondaryStructure = ' ';
         }
 
@@ -178,22 +208,28 @@ public class AlignmentAnnotation
 
     annotationId = this.hashCode() + "";
   }
+
   /**
    * Creates a new AlignmentAnnotation object.
-   *
-   * @param label DOCUMENT ME!
-   * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
-   * @param min DOCUMENT ME!
-   * @param max DOCUMENT ME!
-   * @param winLength DOCUMENT ME!
+   * 
+   * @param label
+   *                DOCUMENT ME!
+   * @param description
+   *                DOCUMENT ME!
+   * @param annotations
+   *                DOCUMENT ME!
+   * @param min
+   *                DOCUMENT ME!
+   * @param max
+   *                DOCUMENT ME!
+   * @param winLength
+   *                DOCUMENT ME!
    */
   public AlignmentAnnotation(String label, String description,
-                             Annotation[] annotations, float min, float max,
-                             int graphType)
+          Annotation[] annotations, float min, float max, int graphType)
   {
     // graphs are not editable
-    editable = graphType==0;
+    editable = graphType == 0;
 
     this.label = label;
     this.description = description;
@@ -203,14 +239,20 @@ public class AlignmentAnnotation
     graphMax = max;
     validateRangeAndDisplay();
   }
+
   /**
-   * checks graphMin and graphMax,
-   * secondary structure symbols,
-   * sets graphType appropriately,
-   * sets null labels to the empty string
-   * if appropriate.
+   * checks graphMin and graphMax, secondary structure symbols, sets graphType
+   * appropriately, sets null labels to the empty string if appropriate.
    */
-  private void validateRangeAndDisplay() {
+  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;
@@ -226,7 +268,8 @@ public class AlignmentAnnotation
           continue;
         }
 
-        if (drawValues && annotations[i].displayCharacter.length() > 1)
+        if (drawValues && annotations[i].displayCharacter != null
+                && annotations[i].displayCharacter.length() > 1)
         {
           drawValues = false;
         }
@@ -261,8 +304,9 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Copy constructor
-   * creates a new independent annotation row with the same associated sequenceRef
+   * Copy constructor creates a new independent annotation row with the same
+   * associated sequenceRef
+   * 
    * @param annotation
    */
   public AlignmentAnnotation(AlignmentAnnotation annotation)
@@ -281,30 +325,53 @@ public class AlignmentAnnotation
     this.hasText = annotation.hasText;
     this.height = annotation.height;
     this.label = annotation.label;
-    if (threshold!=null) {
+    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();
+    if (annotation.annotations != null)
+    {
       Annotation[] ann = annotation.annotations;
       this.annotations = new Annotation[ann.length];
-      for (int i=0; i<ann.length; i++) {
+      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) {
+      }
+      ;
+      if (annotation.sequenceRef != null)
+      {
         this.sequenceRef = annotation.sequenceRef;
-        if (annotation.sequenceMapping!=null)
+        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)]);
+          Enumeration pos = annotation.sequenceMapping.keys();
+          while (pos.hasMoreElements())
+          {
+            // 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 {
+        }
+        else
+        {
           this.sequenceMapping = null;
         }
       }
@@ -313,8 +380,85 @@ 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!
    */
   public String toString()
@@ -371,24 +515,29 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
+   * Attach the annotation to seqRef, starting from startRes position. If
+   * alreadyMapped is true then the indices of the annotation[] array are
+   * sequence positions rather than alignment column positions.
+   * 
    * @param seqRef
    * @param startRes
    * @param alreadyMapped
    */
-  public void createSequenceMapping(SequenceI seqRef,
-                                    int startRes,
-                                    boolean alreadyMapped)
+  public void createSequenceMapping(SequenceI seqRef, int startRes,
+          boolean alreadyMapped)
   {
 
     if (seqRef == null)
     {
       return;
     }
-
+    sequenceRef = seqRef;
+    if (annotations == null)
+    {
+      return;
+    }
     sequenceMapping = new java.util.Hashtable();
 
-    sequenceRef = seqRef;
     int seqPos;
 
     for (int i = 0; i < annotations.length; i++)
@@ -412,14 +561,19 @@ public class AlignmentAnnotation
 
   public void adjustForAlignment()
   {
-    if (sequenceRef==null)
+    if (sequenceRef == null)
       return;
 
+    if (annotations == null)
+    {
+      return;
+    }
+
     int a = 0, aSize = sequenceRef.getLength();
 
     if (aSize == 0)
     {
-      //Its been deleted
+      // Its been deleted
       return;
     }
 
@@ -440,60 +594,178 @@ public class AlignmentAnnotation
 
     annotations = temp;
   }
+
   /**
-   * remove any null entries in annotation row and return the
-   * number of non-null annotation elements.
+   * remove any null entries in annotation row and return the 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;
   }
 
   /**
    * Associate this annotion with the aligned residues of a particular sequence.
-   * sequenceMapping will be updated in the following way:
-   *   null sequenceI - existing mapping will be discarded but annotations left in mapped positions.
-   *   valid sequenceI not equal to current sequenceRef: mapping is discarded and rebuilt assuming 1:1 correspondence
-   *   TODO: overload with parameter to specify correspondence between current and new sequenceRef
+   * sequenceMapping will be updated in the following way: null sequenceI -
+   * existing mapping will be discarded but annotations left in mapped
+   * positions. valid sequenceI not equal to current sequenceRef: mapping is
+   * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+   * parameter to specify correspondence between current and new sequenceRef
+   * 
    * @param sequenceI
    */
   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);
+      }
+    }
+  }
+
+  /**
+   * format description string for display
+   * 
+   * @param seqname
+   * @return Get the annotation description string optionally prefixed by
+   *         associated sequence name (if any)
+   */
+  public String getDescription(boolean seqname)
+  {
+    if (seqname && this.sequenceRef != null)
+    {
+      return sequenceRef.getName() + " : " + description;
+    }
+    return description;
+  }
 }