add partial button fix to annotation and statistics output

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 334d380..cce4e67 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -87,7 +87,9 @@ import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ResidueProperties;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
@@ -123,7 +125,9 @@ import java.awt.event.MouseEvent;
 import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
+import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.PrintWriter;
 import java.net.URL;
@@ -131,8 +135,11 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
+import java.util.Scanner;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -154,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
+  Map<String, Float> distribution = new HashMap<>(); // temporary
+
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -181,6 +190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   String fileName = null;
 
+
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -920,6 +930,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
     showSequenceLogo.setSelected(av.isShowSequenceLogo());
     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+    showInformationHistogram.setSelected(av.isShowInformationHistogram());
+    showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+    normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 
     ColourMenuHelper.setColourSelected(colourMenu,
             av.getGlobalColourScheme());
@@ -4666,6 +4679,144 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             getViewport().getAlignment().addAnnotation(annotation);
             annotation.setHMM(hmm);
             isAnnotation = true;
+
+            BufferedReader input = new BufferedReader(new FileReader(
+                    "H:/Desktop/Distributions/BadAlignment-8.csv"));
+            String line = input.readLine();
+
+            while (!("".equals(line)) && line != null)
+            {
+              Scanner scanner = new Scanner(line);
+              if (scanner.hasNext())
+              {
+                scanner.useDelimiter(",");
+                String value = scanner.next();
+
+                distribution.put(value, scanner.nextFloat());
+                line = input.readLine();
+              }
+            }
+
+
+            AlignmentI alignment = getViewport().getAlignment();
+            Integer alpha = 0;
+            final int AMINO = 0;
+            final int DNA = 1;
+            if ("amino".equals(hmm.getAlphabetType()))
+            {
+              alpha = AMINO;
+            }
+            else if ("DNA".equals(hmm.getAlphabetType()))
+            {
+              alpha = DNA;
+            }
+            
+
+            int size = 0;
+
+            for (int l = 1; l < hmm.getLength() + 1; l++)
+            {
+              for (int n = 0; n < alignment.getHeight(); n++)
+              {
+
+                char character = alignment.getSequenceAt(n)
+                        .getCharAt(hmm.getNodeAlignmentColumn(l));
+                character = Character.toUpperCase(character);
+
+                boolean containedN;
+                boolean containedA;
+
+                containedN = ResidueProperties.nucleotideBackgroundFrequencies
+                        .containsKey(character);
+                containedA = ResidueProperties.aminoBackgroundFrequencies
+                        .containsKey(character);
+
+                if (!Comparison.isGap(character)
+                        && ((alpha == DNA && containedN)
+                                || (alpha == AMINO && containedA)))
+                {
+                  size++;
+                }
+
+              }
+            }
+            
+            for (int l = 1; l < hmm.getLength() + 1; l++)
+            {
+              for (int n = 0; n < alignment.getHeight(); n++)
+              {
+                Double prob;
+                char character;
+                character = alignment.getSequenceAt(n)
+                        .getCharAt(hmm.getNodeAlignmentColumn(l));
+                character = Character.toUpperCase(character);
+                boolean containedN;
+                boolean containedA;
+
+                containedN = ResidueProperties.nucleotideBackgroundFrequencies
+                        .containsKey(character);
+                containedA = ResidueProperties.aminoBackgroundFrequencies
+                        .containsKey(character);
+
+                if (!Comparison.isGap(character)
+                        && ((alpha == DNA && containedN)
+                                || (alpha == AMINO && containedA)))
+                {
+                  prob = hmm.getMatchEmissionProbability(
+                          hmm.getNodeAlignmentColumn(l), character);
+                  if (prob == 0d)
+                  {
+                    System.out.println("?");
+                  }
+
+                  double freq = 0;
+                  if (alpha == AMINO)
+                  {
+                    freq = ResidueProperties.aminoBackgroundFrequencies
+                            .get(character);
+                  }
+                  if (alpha == DNA)
+                  {
+                    freq = ResidueProperties.nucleotideBackgroundFrequencies
+                            .get(character);
+                  }
+                    Double doubleValue = Math.log(prob / freq);
+
+                      String value = String.format("%.1f", doubleValue);
+                      if ("-0.0".equals(value))
+                      {
+                        value = "0.0";
+                      }
+                        if (distribution.containsKey(value))
+                        {
+                        float prev = distribution.get(value);
+                        prev = prev + (10000f / size);
+                          distribution.put(value, prev);
+                        }
+                        else
+                        {
+                    distribution.put(value, 10000f / size);
+                        }
+
+
+                }
+            
+              }
+            }
+            
+            PrintWriter writer = new PrintWriter(
+                    new File(
+                            "H:/Desktop/Distributions/BadAlignment-8.csv"));
+            for (Map.Entry<String, Float> entry : distribution
+                    .entrySet())
+            {
+              writer.println(entry.getKey() + "," + entry.getValue());
+            
+            }
+            
+            writer.close();
+
+
           }
           else if (FileFormat.Jnet.equals(format))
           {
@@ -5285,6 +5436,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  protected void showInformationHistogram_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowInformationHistogram(
+            showInformationHistogram.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  @Override
+  protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  @Override
+  protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    showHMMSequenceLogo.setState(true);
+    viewport.setShowHMMSequenceLogo(true);
+    viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  @Override
   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
   {
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());