From 56f696a86aea0c3fd8111870a6184d459a852ace Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Tue, 20 Jun 2017 17:58:30 +0100
Subject: [PATCH] create method to test HMM model as string

---
 test/jalview/io/HMMFileTest.java |   61 ++++++++++++++++++++++++++++++--------
 1 file changed, 48 insertions(+), 13 deletions(-)

diff --git a/test/jalview/io/HMMFileTest.java b/test/jalview/io/HMMFileTest.java
index 9beaab0..55e3721 100644
--- a/test/jalview/io/HMMFileTest.java
+++ b/test/jalview/io/HMMFileTest.java
@@ -7,7 +7,6 @@ import jalview.datamodel.HMMNode;
 import jalview.datamodel.HiddenMarkovModel;
 
 import java.io.BufferedReader;
-import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -137,6 +136,7 @@ public class HMMFileTest {
     FileReader fr = new FileReader(fn3.getDataObject());
     BufferedReader br = new BufferedReader(fr);
     fn3.parseFileProperties(br);
+    fn3.parseModel(br); // this is for a later test
     HiddenMarkovModel testHMM = new HiddenMarkovModel();
     testHMM = fn3.getHmm();
     br.close();
@@ -231,6 +231,7 @@ public class HMMFileTest {
     assertEquals(testHMM.getMSV(), "-8.5786  0.71858");
     assertEquals(testHMM.getForward(), "-3.4823  0.71858");
 
+
   }
 
   @Test
@@ -367,17 +368,10 @@ public class HMMFileTest {
     scanner2.close();
   }
 
-  @Test(priority = 2)
+  @Test(priority = 3)
   public void testExportFile() throws IOException
   {
-    File file = new File(fn3.getDataObject());
-    FileReader fr = new FileReader(file);
-    BufferedReader br = new BufferedReader(fr);
-    for (int i = 0; i < 23; i++)
-    {
-      br.readLine();
-    }
-    fn3.parseModel(br);
+
     fn3.exportFile("H:/WriteFileTest.hmm");
   }
 
@@ -406,11 +400,52 @@ public class HMMFileTest {
     testScanner.close();
   }
 
-  public moveAheadBy(Scanner scanner, int nodeChange, int indexChange)
+  @Test(priority = 2)
+  public void testAppendModel()
+  {
+    StringBuilder testBuilder = new StringBuilder();
+    fn3.appendModel(testBuilder);
+    String string = testBuilder.toString();
+    assertEquals(findValue(2, 2, 2, string), "4.42225");
+    assertEquals(findValue(12, 14, 1, string), "2.79307");
+  }
+
+  public String findValue(int symbolIndex, int nodeIndex, int line,
+          String model)
   {
-    for (int y = 0; y < nodeChange; y++)
+
+    String value = "";
+    Scanner scanner = new Scanner(model);
+    scanner.nextLine();
+    scanner.nextLine();
+
+    for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
+    {
+      scanner.nextLine();
+    }
+    for (int node = 0; node < nodeIndex; node++)
     {
-      
+      scanner.nextLine();
+      scanner.nextLine();
+      scanner.nextLine();
     }
+
+    for (int symbol = 0; symbol < symbolIndex; symbol++)
+    {
+      value = scanner.next();
+      if ("COMPO".equals(value))
+      {
+        scanner.next();
+      }
+      else if (value.length() < 7)
+      {
+        scanner.next();
+      }
+
+    }
+    return value;
+
   }
+
 }
+
-- 
1.7.10.2