X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=a97ca7fa5103aec4e8b774344a766cc2fb55d411;hb=0c355acb1b5ddab95961d703ca6bc383a4464def;hp=337d8797a398d125178535ac8f74f01f1dab3673;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 337d879..a97ca7f 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,122 +1,343 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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;
-
-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++)
-   {
-     if(annotations[i]!=null)
-     {
-       if(isGraph)
-         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();
-  }
-
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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
+{
+    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("-"))
+        {
+          if(jalview.schemes.ResidueProperties.aaIndex
+             [annotations[i].displayCharacter.charAt(0)]>0)
+          {
+            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 = ' ';
+          }
+
+        }
+
+      }
+
+    }
+
+    /**
+     * 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]);
+            }
+         }
+
+        adjustForAlignment();
+      }
+
+      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;
+      }
+}
+
+