From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Thu, 20 Jul 2017 11:42:48 +0000 (+0100)
Subject: JAL-2616 remove statistical analysis from AlignFrame
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6aba8db32fcc88b6263b4dd8cd305a0bb3fa1ae5;p=jalview.git

JAL-2616 remove statistical analysis from AlignFrame
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 44d96ca..74e7652 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -87,9 +87,7 @@ 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;
@@ -125,9 +123,7 @@ 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;
@@ -139,7 +135,6 @@ 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;
@@ -4680,159 +4675,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             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;
-            final int RNA = 2;
-            if ("amino".equals(hmm.getAlphabetType()))
-            {
-              alpha = AMINO;
-            }
-            else if ("DNA".equals(hmm.getAlphabetType()))
-            {
-              alpha = DNA;
-            }
-            else if ("RNA".equals(hmm.getAlphabetType()))
-            {
-              alpha = RNA;
-            }
-            
-
-            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 containedD;
-                boolean containedR;
-                boolean containedA;
-
-                containedD = ResidueProperties.dnaBackgroundFrequencies
-                        .containsKey(character);
-                containedA = ResidueProperties.aminoBackgroundFrequencies
-                        .containsKey(character);
-                containedR = ResidueProperties.rnaBackgroundFrequencies
-                        .containsKey(character);
-
-                if (!Comparison.isGap(character)
-                        && ((alpha == DNA && containedD)
-                                || (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;
-                boolean containedR;
-
-                containedN = ResidueProperties.dnaBackgroundFrequencies
-                        .containsKey(character);
-                containedA = ResidueProperties.aminoBackgroundFrequencies
-                        .containsKey(character);
-                containedR = ResidueProperties.rnaBackgroundFrequencies
-                        .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.dnaBackgroundFrequencies
-                            .get(character);
-                  }
-                  if (alpha == RNA)
-                  {
-                    freq = ResidueProperties.rnaBackgroundFrequencies
-                            .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))
           {