From 80f46a9ba6bea3531ff6e59cf68f9f870e5af4da Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 20 Aug 2006 12:00:35 +0000
Subject: [PATCH] javadoc

---
 src/jalview/datamodel/AlignmentAnnotation.java |  660 ++++++++++++------------
 1 file changed, 331 insertions(+), 329 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 5a2c46e..04689cd 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,329 +1,331 @@
-/*
-* 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;
-
-
-/**
- * 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;
-
-        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;
-            }
-        }
-    }
-
-    /**
-     * 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;
-
-        for (int i = 0; i < annotations.length; i++)
-        {
-            if (!hasIcons
-                && annotations[i] != null
-                && ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E')))
-            {
-                hasIcons = true;
-            }
-
-            if (!hasText
-                && annotations[i]!=null
-                && annotations[i].displayCharacter.length() > 0)
-            {
-                hasText = true;
-            }
-        }
-
-        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;
-      }
-
-      /**
-       * This
-       */
-      public void createSequenceMapping(SequenceI seqRef, int startRes)
-      {
-        if(seqRef == null)
-          return;
-
-        sequenceMapping = new java.util.Hashtable();
-
-        sequenceRef = seqRef;
-
-        if(startRes < sequenceRef.getStart())
-          startRes = sequenceRef.getStart();
-
-        int seqPos;
-
-        int fileOffset = 0;
-        if(startRes > sequenceRef.getStart())
-        {
-          fileOffset = startRes - sequenceRef.getStart();
-        }
-
-        for(int i = 0; i < annotations.length; i++)
-        {
-            seqPos = sequenceRef.findPosition(i + fileOffset);
-            if(seqPos<annotations.length)
-            {
-              if (annotations[i] != null)
-              {
-                  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;
-      }
-}
-
-
+/*
+* 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;
+
+
+/**
+ * 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;
+
+        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;
+            }
+        }
+    }
+
+    /**
+     * 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;
+
+        for (int i = 0; i < annotations.length; i++)
+        {
+            if (!hasIcons
+                && annotations[i] != null
+                && ((annotations[i].secondaryStructure == 'H') ||
+                    (annotations[i].secondaryStructure == 'E')))
+            {
+                hasIcons = true;
+            }
+
+            if (!hasText
+                && annotations[i]!=null
+                && annotations[i].displayCharacter.length() > 0)
+            {
+                hasText = true;
+            }
+        }
+
+        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.
+       * @param seqRef
+       * @param startRes
+       */
+      public void createSequenceMapping(SequenceI seqRef, int startRes)
+      {
+        if(seqRef == null)
+          return;
+
+        sequenceMapping = new java.util.Hashtable();
+
+        sequenceRef = seqRef;
+
+        if(startRes < sequenceRef.getStart())
+          startRes = sequenceRef.getStart();
+
+        int seqPos;
+
+        int fileOffset = 0;
+        if(startRes > sequenceRef.getStart())
+        {
+          fileOffset = startRes - sequenceRef.getStart();
+        }
+
+        for(int i = 0; i < annotations.length; i++)
+        {
+            seqPos = sequenceRef.findPosition(i + fileOffset);
+            if(seqPos<annotations.length)
+            {
+              if (annotations[i] != null)
+              {
+                  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;
+      }
+}
+
+
-- 
1.7.10.2