X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=c675a759bb71fe620a4fd7e5c2bf4f939b9f9e22;hb=ef3acde250d7d83304fb328a428b4d834fe3ac05;hp=8326c3a4374bd385bd1bd643c527d1d1e1da6219;hpb=c1231e2f4fd7d48b1a7ad915e4450bbba7a2b939;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8326c3a..c675a75 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,84 +1,365 @@
-package jalview.datamodel;
-
-public class AlignmentAnnotation
-{
-  public String label;
-  public String description;
-  public Annotation  [] annotations;
-  public boolean isGraph = false;
-  public float graphMin, graphMax;
-  public int windowLength;
-
-  // Graphical hints and tips
-  public boolean editable = false;
-  public boolean hasIcons; //
-  public boolean hasText;
-  public boolean visible = true;
-  public int height=0;
-
-  public AlignmentAnnotation(String label, String description, Annotation [] annotations)
-  {
-    // always editable?
-    editable = true;
-    this.label = label;
-    this.description = description;
-    this.annotations = annotations;
-    for(int i=0; i<annotations.length; i++)
-    {
-      if (annotations[i]!=null &&(
-          annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E'))
-        hasIcons = true;
-
-      if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)
-        hasText = true;
-    }
-  }
-
-  public AlignmentAnnotation(String label, String description, Annotation [] annotations, float min, float max, int winLength)
-  {
-    // graphs are not editable
-    this.label = label;
-    this.description = description;
-    this.annotations = annotations;
-    isGraph = true;
-    if(min==max)
-    {
-      for(int i=0; i<annotations.length; i++)
-      {
-        if(annotations[i]==null)
-          continue;
-        if(annotations[i].value>max)
-          max = annotations[i].value;
-        if(annotations[i].value<min)
-          min = annotations[i].value;
-      }
-    }
-
-    graphMin = min;
-    graphMax = max;
-    windowLength = winLength;
-    for(int i=0; i<annotations.length; i++)
-    {
-      if (annotations[i]!=null &&(
-          annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E'))
-        hasIcons = true;
-
-      if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)
-        hasText = true;
-    }
-  }
-
-  public String toString()
-  {
-    StringBuffer buffer = new StringBuffer();
-    for(int i=0; i<annotations.length; i++)
-   {
-     buffer.append( annotations[i].value );
-     buffer.append(", ");
-   }
-   return buffer.toString();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ */
+package jalview.datamodel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentAnnotation
+{
+  /** If true, this annotations is calculated every edit,
+   * eg consensus, quality or conservation graphs */
+  public boolean autoCalculated = false;
+
+  public String annotationId;
+
+  public SequenceI sequenceRef;
+
+  /** DOCUMENT ME!! */
+  public String label;
+
+  /** DOCUMENT ME!! */
+  public String description;
+
+  /** DOCUMENT ME!! */
+  public Annotation[] annotations;
+
+  public java.util.Hashtable sequenceMapping;
+
+  /** DOCUMENT ME!! */
+  public float graphMin;
+
+  /** DOCUMENT ME!! */
+  public float graphMax;
+
+  public GraphLine threshold;
+
+  // Graphical hints and tips
+
+  /** DOCUMENT ME!! */
+  public boolean editable = false;
+
+  /** DOCUMENT ME!! */
+  public boolean hasIcons; //
+
+  /** DOCUMENT ME!! */
+  public boolean hasText;
+
+  /** DOCUMENT ME!! */
+  public boolean visible = true;
+
+  public int graphGroup = -1;
+
+  /** DOCUMENT ME!! */
+  public int height = 0;
+
+  public int graph = 0;
+
+  public int graphHeight = 40;
+
+  public static final int NO_GRAPH = 0;
+
+  public static final int BAR_GRAPH = 1;
+
+  public static final int LINE_GRAPH = 2;
+
+  public static int getGraphValueFromString(String string)
+  {
+    if (string.equalsIgnoreCase("BAR_GRAPH"))
+    {
+      return BAR_GRAPH;
+    }
+    else if (string.equalsIgnoreCase("LINE_GRAPH"))
+    {
+      return LINE_GRAPH;
+    }
+    else
+    {
+      return NO_GRAPH;
+    }
+  }
+
+  /**
+   * Creates a new AlignmentAnnotation object.
+   *
+   * @param label DOCUMENT ME!
+   * @param description DOCUMENT ME!
+   * @param annotations DOCUMENT ME!
+   */
+  public AlignmentAnnotation(String label, String description,
+                             Annotation[] annotations)
+  {
+    // always editable?
+    editable = true;
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+
+    areLabelsSecondaryStructure();
+  }
+
+  void areLabelsSecondaryStructure()
+  {
+    boolean nonSSLabel = false;
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] == null)
+      {
+        continue;
+      }
+
+      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 (jalview.schemes.ResidueProperties.aaIndex
+            [annotations[i].displayCharacter.charAt(0)] < 23)
+        {
+          nonSSLabel = true;
+        }
+      }
+
+      if (annotations[i].displayCharacter.length() > 0)
+      {
+        hasText = true;
+      }
+    }
+
+    if (nonSSLabel)
+    {
+      hasIcons = false;
+      for (int j = 0; j < annotations.length; j++)
+      {
+        if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
+        {
+          annotations[j].displayCharacter
+              = String.valueOf(annotations[j].secondaryStructure);
+          annotations[j].secondaryStructure = ' ';
+        }
+
+      }
+
+    }
+
+    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!
+   */
+  public AlignmentAnnotation(String label, String description,
+                             Annotation[] annotations, float min, float max,
+                             int graphType)
+  {
+    // graphs are not editable
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+    graph = graphType;
+
+    boolean drawValues = true;
+
+    if (min == max)
+    {
+      min = 999999999;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] == null)
+        {
+          continue;
+        }
+
+        if (drawValues && annotations[i].displayCharacter.length() > 1)
+        {
+          drawValues = false;
+        }
+
+        if (annotations[i].value > max)
+        {
+          max = annotations[i].value;
+        }
+
+        if (annotations[i].value < min)
+        {
+          min = annotations[i].value;
+        }
+      }
+    }
+
+    graphMin = min;
+    graphMax = max;
+
+    areLabelsSecondaryStructure();
+
+    if (!drawValues && graphType != NO_GRAPH)
+    {
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
+        {
+          annotations[i].displayCharacter = "";
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String toString()
+  {
+    StringBuffer buffer = new StringBuffer();
+
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] != null)
+      {
+        if (graph != 0)
+        {
+          buffer.append(annotations[i].value);
+        }
+        else if (hasIcons)
+        {
+          buffer.append(annotations[i].secondaryStructure);
+        }
+        else
+        {
+          buffer.append(annotations[i].displayCharacter);
+        }
+      }
+
+      buffer.append(", ");
+    }
+
+    if (label.equals("Consensus"))
+    {
+      buffer.append("\n");
+
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
+        {
+          buffer.append(annotations[i].description);
+        }
+
+        buffer.append(", ");
+      }
+    }
+
+    return buffer.toString();
+  }
+
+  public void setThreshold(GraphLine line)
+  {
+    threshold = line;
+  }
+
+  public GraphLine getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * 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)
+  {
+
+    if (seqRef == null)
+    {
+      return;
+    }
+
+    sequenceMapping = new java.util.Hashtable();
+
+    sequenceRef = seqRef;
+    int seqPos;
+
+    for (int i = 0; i < annotations.length; i++)
+    {
+      if (annotations[i] != null)
+      {
+        if (alreadyMapped)
+        {
+          seqPos = seqRef.findPosition(i);
+        }
+        else
+        {
+          seqPos = i + startRes;
+        }
+
+        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+      }
+    }
+
+  }
+
+  public void adjustForAlignment()
+  {
+    int a = 0, aSize = sequenceRef.getLength();
+
+    if (aSize == 0)
+    {
+      //Its been deleted
+      return;
+    }
+
+    int position;
+    Annotation[] temp = new Annotation[aSize];
+    Integer index;
+
+    for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    {
+      index = new Integer(a);
+      if (sequenceMapping.containsKey(index))
+      {
+        position = sequenceRef.findIndex(a) - 1;
+
+        temp[position] = (Annotation) sequenceMapping.get(index);
+      }
+    }
+
+    annotations = temp;
+  }
+}