X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;fp=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=1b2578ec951ce3993d929cecaa37a66e9d1c5391;hb=4687e1243f51bd09334792b8a7ce518a5aa07de7;hp=34a21e690670b0d49197a1e523607a38dc5974b3;hpb=7e441a4a9594821ec56539b29cb3b8a13bfa3c65;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 34a21e6..1b2578e 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -36,6 +36,7 @@ import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.Graphics;
+import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -49,6 +50,14 @@ import java.util.StringTokenizer;
  */
 public class AlignSeq
 {
+  private static final int MAX_NAME_LENGTH = 30;
+
+  private static final int GAP_OPEN_COST = 120;
+
+  private static final int GAP_EXTEND_COST = 20;
+
+  private static final int GAP_INDEX = -1;
+
   public static final String PEP = "pep";
 
   public static final String DNA = "dna";
@@ -61,7 +70,7 @@ public class AlignSeq
 
   float[][] F;
 
-  int[][] traceback;
+  int[][] traceback; // todo is this actually used?
 
   int[] seq1;
 
@@ -96,30 +105,20 @@ public class AlignSeq
   /** DOCUMENT ME!! */
   public int seq2start;
 
-  /** DOCUMENT ME!! */
   public int seq2end;
 
   int count;
 
-  /** DOCUMENT ME!! */
   public float maxscore;
 
-  float pid;
-
   int prev = 0;
 
-  int gapOpen = 120;
-
-  int gapExtend = 20;
-
   StringBuffer output = new StringBuffer();
 
   String type; // AlignSeq.PEP or AlignSeq.DNA
 
   private ScoreMatrix scoreMatrix;
 
-  private static final int GAP_INDEX = -1;
-
   /**
    * Creates a new AlignSeq object.
    * 
@@ -378,11 +377,10 @@ public class AlignSeq
       }
     }
 
-    // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
     int i = maxi;
     int j = maxj;
     int trace;
-    maxscore = score[i][j] / 10;
+    maxscore = score[i][j] / 10f;
 
     seq1end = maxi + 1;
     seq2end = maxj + 1;
@@ -451,49 +449,48 @@ public class AlignSeq
   /**
    * DOCUMENT ME!
    */
-  public void printAlignment(java.io.PrintStream os)
+  public void printAlignment(PrintStream os)
   {
     // TODO: Use original sequence characters rather than re-translated
     // characters in output
     // Find the biggest id length for formatting purposes
-    String s1id = s1.getName(), s2id = s2.getName();
-    int maxid = s1.getName().length();
-    if (s2.getName().length() > maxid)
-    {
-      maxid = s2.getName().length();
-    }
-    if (maxid > 30)
+    String s1id = getAlignedSeq1().getDisplayId(true);
+    String s2id = getAlignedSeq2().getDisplayId(true);
+    int nameLength = Math.max(s1id.length(), s2id.length());
+    if (nameLength > MAX_NAME_LENGTH)
     {
-      maxid = 30;
+      int truncateBy = nameLength - MAX_NAME_LENGTH;
+      nameLength = MAX_NAME_LENGTH;
       // JAL-527 - truncate the sequence ids
-      if (s1.getName().length() > maxid)
+      if (s1id.length() > nameLength)
       {
-        s1id = s1.getName().substring(0, 30);
+        int slashPos = s1id.lastIndexOf('/');
+        s1id = s1id.substring(0, slashPos - truncateBy)
+                + s1id.substring(slashPos);
       }
-      if (s2.getName().length() > maxid)
+      if (s2id.length() > nameLength)
       {
-        s2id = s2.getName().substring(0, 30);
+        int slashPos = s2id.lastIndexOf('/');
+        s2id = s2id.substring(0, slashPos - truncateBy)
+                + s2id.substring(slashPos);
       }
     }
-    int len = 72 - maxid - 1;
+    int len = 72 - nameLength - 1;
     int nochunks = ((aseq1.length - count) / len)
             + ((aseq1.length - count) % len > 0 ? 1 : 0);
-    pid = 0;
+    float pid = 0f;
 
     output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
     output.append("Length of alignment = ")
             .append(String.valueOf(aseq1.length - count)).append(NEWLINE);
     output.append("Sequence ");
-    output.append(new Format("%" + maxid + "s").form(s1.getName()));
-    output.append(" :  ").append(String.valueOf(s1.getStart()))
-            .append(" - ").append(String.valueOf(s1.getEnd()));
+    Format nameFormat = new Format("%" + nameLength + "s");
+    output.append(nameFormat.form(s1id));
     output.append(" (Sequence length = ")
             .append(String.valueOf(s1str.length())).append(")")
             .append(NEWLINE);
     output.append("Sequence ");
-    output.append(new Format("%" + maxid + "s").form(s2.getName()));
-    output.append(" :  ").append(String.valueOf(s2.getStart()))
-            .append(" - ").append(String.valueOf(s2.getEnd()));
+    output.append(nameFormat.form(s2id));
     output.append(" (Sequence length = ")
             .append(String.valueOf(s2str.length())).append(")")
             .append(NEWLINE).append(NEWLINE);
@@ -503,7 +500,7 @@ public class AlignSeq
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(s1id)).append(" ");
+      output.append(nameFormat.form(s1id)).append(" ");
 
       for (int i = 0; i < len; i++)
       {
@@ -514,7 +511,7 @@ public class AlignSeq
       }
 
       output.append(NEWLINE);
-      output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
+      output.append(nameFormat.form(" ")).append(" ");
 
       /*
        * Print out the match symbols:
@@ -534,7 +531,7 @@ public class AlignSeq
             pid++;
             output.append("|");
           }
-          else if (type.equals("pep"))
+          else if (PEP.equals(type))
           {
             if (pam250.getPairwiseScore(c1, c2) > 0)
             {
@@ -554,8 +551,7 @@ public class AlignSeq
 
       // Now print the second aligned sequence
       output = output.append(NEWLINE);
-      output = output.append(new Format("%" + (maxid) + "s").form(s2id))
-              .append(" ");
+      output = output.append(nameFormat.form(s2id)).append(" ");
 
       for (int i = 0; i < len; i++)
       {
@@ -569,7 +565,8 @@ public class AlignSeq
     }
 
     pid = pid / (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
+    output.append(new Format("Percentage ID = %3.2f\n").form(pid));
+    output.append(NEWLINE);
     try
     {
       os.print(output.toString());
@@ -591,7 +588,6 @@ public class AlignSeq
   public int findTrace(int i, int j)
   {
     int t = 0;
-    // float pairwiseScore = lookup[seq1[i]][seq2[j]];
     float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
             s2str.charAt(j));
     float max = score[i - 1][j - 1] + (pairwiseScore * 10);
@@ -640,19 +636,19 @@ public class AlignSeq
     // top left hand element
     score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
             s2str.charAt(0)) * 10;
-    E[0][0] = -gapExtend;
+    E[0][0] = -GAP_EXTEND_COST;
     F[0][0] = 0;
 
     // Calculate the top row first
     for (int j = 1; j < m; j++)
     {
       // What should these values be? 0 maybe
-      E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
-      F[0][j] = -gapExtend;
+      E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST, E[0][j - 1] - GAP_EXTEND_COST);
+      F[0][j] = -GAP_EXTEND_COST;
 
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
               s2str.charAt(j));
-      score[0][j] = max(pairwiseScore * 10, -gapOpen, -gapExtend);
+      score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST, -GAP_EXTEND_COST);
 
       traceback[0][j] = 1;
     }
@@ -660,8 +656,8 @@ public class AlignSeq
     // Now do the left hand column
     for (int i = 1; i < n; i++)
     {
-      E[i][0] = -gapOpen;
-      F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
+      E[i][0] = -GAP_OPEN_COST;
+      F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST, F[i - 1][0] - GAP_EXTEND_COST);
 
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
               s2str.charAt(0));
@@ -674,8 +670,8 @@ public class AlignSeq
     {
       for (int j = 1; j < m; j++)
       {
-        E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - gapExtend);
-        F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - gapExtend);
+        E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST, E[i][j - 1] - GAP_EXTEND_COST);
+        F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST, F[i - 1][j] - GAP_EXTEND_COST);
 
         float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
                 s2str.charAt(j));