From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:11:34 +0000 (+0000)
Subject: isGap method added to utils
X-Git-Tag: Release_2_0~820
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git

isGap method added to utils
---

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index f99661e..eed6d0a 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -119,17 +119,19 @@ public class Conservation {
     }
   }
 
-  public int countGaps(int j) {
+  public int countGaps(int j)
+  {
     int count = 0;
 
-    for (int i = 0; i < sequences.size();i++) {
+    for (int i = 0; i < sequences.size();i++)
+    {
       if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())
       {  count++; continue;}
 
-      String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);
-      if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {
+      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
+      if (jalview.util.Comparison.isGap((c)))
         count++;
-      }
+
     }
     return count;
   }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cc5d760..d35cbe8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -144,19 +144,18 @@ public class Sequence implements SequenceI
 
     while (i< sequence.length() && j <= end && j <= pos) {
 
-      String s = sequence.substring(i,i+1);
+      char c = sequence.charAt(i);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         j++;
-      }
+
       i++;
     }
-    if (j == end && j < pos) {
+    if (j == end && j < pos)
       return end+1;
-    } else {
-
+    else
       return i;
-    }
+
   }
 
   public int findPosition(int i) {
@@ -164,12 +163,13 @@ public class Sequence implements SequenceI
     int j   = 0;
     int pos = start;
 
-    while (j < i) {
-      String s = sequence.substring(j,j+1);
+    while (j < i)
+    {
+      char c = sequence.charAt(j);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         pos++;
-      }
+
       j++;
     }
     return pos;
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2512978..cba91df 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -161,12 +161,12 @@ public class SequenceFeature {
       }
 
       for (int i = fstart; i <= fend; i++) {
-        String s = sequence.sequence.substring(i,i+1);
-        if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+        char c = sequence.sequence.charAt(i);
+        if (!jalview.util.Comparison.isGap((c)))
           g.fillRect(x1+(i-fstart)*width,y1,width,height);
-        } else {
+        else
           g.drawString("-",x1+(i-fstart)*width,y1+height);
-        }
+
       }
 
     }
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 72fb1d1..d8e599b 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -16,27 +16,22 @@ public class Comparison {
      int ilen = end-start+1;
      int jlen = end-start+1;
 
-     if ( si.substring(start + ilen).equals("-") ||
-          si.substring(start + ilen).equals(".") ||
-          si.substring(start + ilen).equals(" ")) {
-
+     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
+      {
        ilen--;
 
-       while (si.substring(start + ilen,start + ilen+1).equals("-")  ||
-              si.substring(start + ilen,start + ilen+1).equals(".")  ||
-              si.substring(start + ilen,start + ilen+1).equals(" ")) {
+       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))
+       {
          ilen--;
        }
      }
 
-     if ( sj.substring(start + jlen).equals("-")  ||
-          sj.substring(start + jlen).equals(".")  ||
-          sj.substring(start + jlen).equals(" ")) {
+     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )
+     {
        jlen--;
 
-       while (sj.substring(start + jlen,start + jlen+1).equals("-")  ||
-              sj.substring(start + jlen,start + jlen+1).equals(".")  ||
-              sj.substring(start + jlen,start + jlen+1).equals(" ")) {
+       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))
+       {
          jlen--;
        }
      }
@@ -68,47 +63,47 @@ public class Comparison {
   }
 
   /**    */
-  public static float PID(Sequence s1 , Sequence s2) {
-    int res = 0;
+  public static float PID(Sequence s1 , Sequence s2)
+  {
     int len;
 
-    if (s1.getSequence().length() > s2.getSequence().length()) {
+    if (s1.getSequence().length() > s2.getSequence().length())
       len = s1.getSequence().length();
-    } else {
+    else
       len = s2.getSequence().length();
-    }
+
 
     int bad = 0;
 
-    for (int i = 0; i < len; i++) {
-      String str1 = "";
-      String str2 = "";
+    for (int i = 0; i < len; i++)
+    {
+      char chr1;
+      char chr2;
 
-      if (i < s1.getSequence().length()) {
-        str1 = s1.getSequence().substring(i,i+1);
-      } else {
-        str1 = ".";
-      }
+      if (i < s1.getSequence().length())
+        chr1 = s1.getSequence().charAt(i);
+      else
+        chr1 = '.';
 
-      if (i < s2.getSequence().length()) {
-        str2 = s2.getSequence().substring(i,i+1);
-      } else {
-        str2 = ".";
-      }
 
-      if (!(str1.equals(".") ||
-            str1.equals("-") ||
-            str1.equals(" "))   &&
-          !(str2.equals(".") ||
-            str2.equals("-") ||
-            str2.equals(" "))) {
+      if (i < s2.getSequence().length())
+        chr2 = s2.getSequence().charAt(i);
+      else
+        chr2 = '.';
+
 
-        if (!str1.equals(str2)) {
+      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
+      {
+        if (chr1!=chr2)
           bad++;
-        }
       }
     }
 
     return (float)100*(len-bad)/len;
   }
+
+  public static boolean isGap(char c)
+  {
+    return  (c != '.' && c != '-' && c != ' ') ? false : true;
+  }
 }